Distinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae.

Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.

Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes.

Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of long terminal repeat-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice- and wheat-infecting M. oryzae lineages and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.

Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen.

Background: Fungi use the accessory segments of their pan-genomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping these accessory gene reservoirs, whether these events happen in specific genomic contexts remains unclear. Additionally, since pan-genome studies often group together all members of the same species, it is uncertain whether genomic or epigenomic features shaping pan-genome evolution are consistent across populations within the same species. Fungal plant pathogens are useful models for answering these questions because members of the same species often infect distinct hosts, and they frequently rely on gene PAV to adapt to these hosts. Results: We analyzed gene PAV in the rice and wheat blast fungus, Magnaporthe oryzae, and found that PAV of disease-causing effectors, antibiotic production, and non-self-recognition genes may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features and data from available datasets for patterns that might help explain these PAV events. We observed that proximity to transposable elements (TEs), gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between PAV genes and conserved genes, among other features. We used these features to construct a random forest classifier that was able to predict whether a gene is likely to experience PAV with high precision (86.06%) and recall (92.88%) in rice-infecting M. oryzae. Finally, we found that PAV in wheat- and rice-infecting pathotypes of M. oryzae differed in their number and their genomic context. Conclusions: Our results suggest that genomic and epigenomic features of gene PAV can be used to better understand and even predict fungal pan-genome evolution. We also show that substantial intra-species variation can exist in these features.

The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors.

BACKGROUND: One of the ways genomes respond to stress is by producing extrachromosomal circular DNAs (eccDNAs). EccDNAs can contain genes and dramatically increase their copy number. They can also reinsert into the genome, generating structural variation. They have been shown to provide a source of phenotypic and genotypic plasticity in several species. However, whole circularome studies have so far been limited to a few model organisms. Fungal plant pathogens are a serious threat to global food security in part because of their rapid adaptation to disease prevention strategies. Understanding the mechanisms fungal pathogens use to escape disease control is paramount to curbing their threat. RESULTS: We present a whole circularome sequencing study of the rice blast pathogen, Magnaporthe oryzae. We find that M. oryzae has a highly diverse circularome that contains many genes and shows evidence of large LTR retrotransposon activity. We find that genes enriched on eccDNAs in M. oryzae occur in genomic regions prone to presence-absence variation and that disease-associated genes are frequently on eccDNAs. Finally, we find that a subset of genes is never present on eccDNAs in our data, which indicates that the presence of these genes on eccDNAs is selected against. CONCLUSIONS: Our study paves the way to understanding how eccDNAs contribute to adaptation in M. oryzae. Our analysis also reveals how M. oryzae eccDNAs differ from those of other species and highlights the need for further comparative characterization of eccDNAs across species to gain a better understanding of these molecules.

Community mental health literacy in Tshwane region 1: A quantitative study.

Background: Although mental health literacy is a major determining factor of mental health outcomes and functional capacity of individuals, there is dearth of research on the issue in South Africa. Aim: To assess the literacy of three mental disorders, namely major depressive disorder (MDD), schizophrenia and generalised anxiety disorder (GAD) and to compare the resultant assumed literacy level between urban and townships participants. Setting: Five clinics of region 1 in Tshwane, South Africa. Method: A cross-sectional descriptive study was performed between November 2019 and January 2020. A total of 385 questionnaires were distributed equally in all five clinics. By means of questions about three fictive cases with clinical pictures indicative of MDD, schizophrenia and GAD the following were assessed: recognising a mental disorder, identifying the cause and knowledge about what would help best. Results: The majority of participants (67.3%) recognised the clinical picture indicative of schizophrenia as a mental disorder, almost half of the participants (49.9%) recognised the clinical picture indicative of MDD as a mental disorder, whilst just more than one third (36.3%) of participants recognised the clinical picture GAD as a mental disorder. Concerning the causes for the clinical pictures, most participants indicated that stress was the cause for MDD and GAD (77.4% and 68.1%, respectively), whilst indicating that biological or psychological (59.5%) causes are relevant to the clinical picture indicative of schizophrenia symptoms. Fewer participants indicated supernatural causes for any of the clinical case (MDD: 2.6%; schizophrenia 15.3%; GAD 4.2%). Most participants chose professional help as the best option for all three cases (MDD 81.3%, schizophrenia 82.2%, GAD 66.1%). The indicators for health literacy in this study show that urban participants had better knowledge than township participants across all questions about the cases. Conclusion: Overall, the study indicated a variable knowledge regarding the three mental disorders in region 1 of Tshwane and variable literacy levels in townships compared with urban settings. The results indicate that awareness campaigns should focus on the deficient areas.

Influence of first- and second-generation antipsychotics on anthropometric parameters of male psychiatric patients.

Background: The use of antipsychotic medication, particularly second generation antipsychotics (SGAs) is a major risk factor for cardiovascular disease in people with severe mental illness (SMI). Few studies have compared body measures of people with SMI taking first generation antipsychotics (FGAs) to those taking SGAs. Aim: We compare body measures between long-term male inpatients using either FGAs or SGAs. Setting: The study was conducted at Weskoppies Psychiatric Hospital, in Pretoria, Gauteng. Methods: A total of 30 patients were selected from a list of male inpatients and were included in our study. Each participant had the following anthropometric measures done and these were compared between the two groups: Waist circumference (WC), body mass index (BMI), waist to hip ratio (WHR), waist to height ratio (WHtR) and hip circumference (HC). Hospital records were used to record demographic variables, diagnosis, comorbid disease and psychotropic medication for each participant. Results: Participants in the FGA and SGA groups had similar body measures, resulting in similar BMI, WHR and WHtR. Participants had a mean HC of 100.5 cm, 95% confidence interval (CI) (97.68, 103.22). BMI ranged from 21.87 kg/m² to 37.65 kg/m², with an overall mean of 28.5 kg/m², 95% CI (26.69, 30.22). Participants had a mean WHtR of 0.59, 95% CI (0.56, 0.61). Participants had a mean WC of 100.6 cm and 95% CI (96.26, 104.87), and the mean WHR of both groups was 1.0. Conclusion: Participants using FGAs and SGAs had similar body measures, and these indicated that this sample of male inpatients with SMI is at high risk for CVD.

Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms.

The plant microbiome can be used to bolster plant defense against abiotic and biotic stresses. Some strains of endophytes, the microorganisms within plants, can directly inhibit the growth of plant fungal pathogens. A previously isolated endophyte from wild Populus (poplar), WPB of the species Burkholderia vietnamiensis, had robust in vitro antifungal activity against pathogen strains that are highly virulent and of concern to Pacific Northwest agriculture: Rhizoctonia solani AG-8, Fusarium culmorum 70110023, and Gaemannomyces graminis var. tritici (Ggt) ARS-A1, as well as activity against the oomycete, Pythium ultimum 217. A direct screening method was developed for isolation of additional anti-fungal endophytes from wild poplar extracts. By challenging pathogens directly with dilute extracts, eleven isolates were found to be inhibitory to at least two plant pathogen strains and were therefore chosen for further characterization. Genomic analysis was conducted to determine if these endophyte strains harbored genes known to be involved in antimicrobial activities. The newly isolated Bacillus strains had gene clusters for production of bacillomycin, fengicyn, and bacillibactin, while the gene cluster for the synthesis of sessilin, viscosin and tolaasin were found in the Pseudomonas strains. The biosynthesis gene cluster for occidiofungin (ocf) was present in the Burkholderia vietnamiensis WPB genome, and an ocf deletion mutant lost inhibitory activity against 3 of the 4 pathogens. The new isolates lacked the gene cluster for occidiofungin implying they employ different modes of action. Other symbiotic traits including nitrogen fixation, phosphate solubilization, and the production of auxins and siderophores were investigated. Although it will be necessary to conduct in vivo tests of the candidates with pathogen-infected agricultural crops, the wild poplar tree microbiome may be a rich source of beneficial endophyte strains with potential for biocontrol applications against a variety of pathogens and utilizing varying modes of action.

Population and comparative genetics of thermotolerance divergence between yeast species.

Many familiar traits in the natural world-from lions' manes to the longevity of bristlecone pine trees-arose in the distant past, and have long since fixed in their respective species. A key challenge in evolutionary genetics is to figure out how and why species-defining traits have come to be. We used the thermotolerance growth advantage of the yeast Saccharomyces cerevisiae over its sister species Saccharomyces paradoxus as a model for addressing these questions. Analyzing loci at which the S. cerevisiae allele promotes thermotolerance, we detected robust evidence for positive selection, including amino acid divergence between the species and conservation within S. cerevisiae populations. Because such signatures were particularly strong at the chromosome segregation gene ESP1, we used this locus as a case study for focused mechanistic follow-up. Experiments revealed that, in culture at high temperature, the S. paradoxus ESP1 allele conferred a qualitative defect in biomass accumulation and cell division relative to the S. cerevisiae allele. Only genetic divergence in the ESP1 coding region mattered phenotypically, with no functional impact detectable from the promoter. Our data support a model in which an ancient ancestor of S. cerevisiae, under selection to boost viability at high temperature, acquired amino acid variants at ESP1 and many other loci, which have been constrained since then. Complex adaptations of this type hold promise as a paradigm for interspecies genetics, especially in deeply diverged traits that may have taken millions of years to evolve.

Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection.

There is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across 5 plant genotypes for 4 45-d passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (internal transcribed spacer region amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment, suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted within the experimental setting. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond. In light of the consistent response of the microbiome to selection in the absence of reciprocal host evolution (coevolution) described here, future studies should address how such adaptation influences host health.

Patients' opinions about referral from a tertiary specialist psychiatric hospital to primary healthcare.

BACKGROUND: Referral of patients from tertiary specialist psychiatric hospitals to primary healthcare settings is a worldwide goal. This is of particular importance in South Africa with its considerable burden of mental disorders and limited resources. However, patients are often reluctant to be referred and studies have shown that patients may prefer a dedicated psychiatric service over an integrated primary healthcare service. AIM: This study explored the opinions of patients receiving care at a tertiary psychiatric hospital's outpatient department (OPD) about referral to a primary healthcare clinic (PHCC). SETTING: The study was conducted at Weskoppies Psychiatric Hospital OPD. METHODS: This was a qualitative study based on grounded theory. Participants were recruited through purposive-theoretical sampling. Data were collected by means of individual interviews and mini-essays. RESULTS: From the 80 participants, 18 had individual interviews and 62 wrote mini-essays. Thirty-nine participants had previously attended a PHCC, while 41 had not. Perceived advantages of referral to PHCCs included: close proximity to participants' homes, resulting in saving on travelling time and transport costs, as well as the convenience of receiving psychiatric and other medical treatment at the same healthcare facility. Perceived disadvantages of PHCCs included: unavailability of treatment; lack of doctor-based care; lack of specialised care; loss of established relationships with hospital healthcare workers; mistreatment by PHCC nursing staff; longer waiting times; more stigmatisation. CONCLUSION: The perceived disadvantages of referral from a tertiary psychiatric hospital to a PHCC outweighed the perceived advantages. Nonetheless, participants expressed willingness for such a referral if their concerns were addressed.

Patients' opinions about referral from a tertiary specialist psychiatric hospital to primary healthcare

Background: Referral of patients from tertiary specialist psychiatric hospitals to primary healthcare settings is a worldwide goal. This is of particular importance in South Africa with its considerable burden of mental disorders and limited resources. However, patients are often reluctant to be referred and studies have shown that patients may prefer a dedicated psychiatric service over an integrated primary healthcare service. Aim: This study explored the opinions of patients receiving care at a tertiary psychiatric hospital's outpatient department (OPD) about referral to a primary healthcare clinic (PHCC). Setting: The study was conducted at Weskoppies Psychiatric Hospital OPD. Methods: This was a qualitative study based on grounded theory. Participants were recruited through purposive-theoretical sampling. Data were collected by means of individual interviews and mini-essays. Results: From the 80 participants, 18 had individual interviews and 62 wrote mini-essays. Thirty-nine participants had previously attended a PHCC, while 41 had not. Perceived advantages of referral to PHCCs included: close proximity to participants' homes, resulting in saving on travelling time and transport costs, as well as the convenience of receiving psychiatric and other medical treatment at the same healthcare facility. Perceived disadvantages of PHCCs included: unavailability of treatment; lack of doctor-based care; lack of specialised care; loss of established relationships with hospital healthcare workers; mistreatment by PHCC nursing staff; longer waiting times; more stigmatisation. Conclusion: The perceived disadvantages of referral from a tertiary psychiatric hospital to a PHCC outweighed the perceived advantages. Nonetheless, participants expressed willingness for such a referral if their concerns were addressed

Corrigendum: An In vitro Study of Bio-Control and Plant Growth Promotion Potential of Salicaceae Endophytes.

[This corrects the article DOI: 10.3389/fmicb.2017.00386.].

An In vitro Study of Bio-Control and Plant Growth Promotion Potential of Salicaceae Endophytes.

Microbial communities in the endosphere of Salicaceae plants, poplar (Populus trichocarpa) and willow (Salix sitchensis), have been demonstrated to be important for plant growth promotion, protection from biotic and abiotic stresses, and degradation of toxic compounds. Our study aimed to investigate bio-control activities of Salicaceae endophytes against various soil borne plant pathogens including Rhizoctonia solani AG-8, Fusarium culmorum, Gaeumannomyces graminis var. tritici, and Pythium ultimum. Additionally, different plant growth promoting traits such as biological nitrogen fixation (BNF), indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, and siderophore production were assessed in all bio-control positive strains. Burkholderia, Rahnella, Pseudomonas, and Curtobacterium were major endophyte genera that showed bio-control activities in the in-vitro assays. The bio-control activities of Burkholderia strains were stronger across all tested plant pathogens as compared to other stains. Genomes of sequenced Burkholderia strains WP40 and WP42 were surveyed to identify the putative genes involved in the bio-control activities. The ocf and hcnABC gene clusters responsible for biosynthesis of the anti-fungal metabolites, occidiofungin and hydrogen cyanide, are present in the genomes of WP40 and WP42. Nearly all endophyte strains showing the bio-control activities produced IAA, solubilized tricalcium phosphate, and synthesized siderophores in the culture medium. Moreover, some strains reduced acetylene into ethylene in the acetylene reduction assay, a common assay used for BNF. Salicaceae endophytes could be useful for bio-control of various plant pathogens, and plant growth promotion possibly through the mechanisms of BNF, IAA production, and nutrient acquisition.