Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve Bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50–100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys

Habitat and Host Indicate Lineage Identity in Colletotrichum gloeosporioides s.l. from Wild and Agricultural Landscapes in North America

Understanding the factors that drive the evolution of pathogenic fungi is central to revealing the mechanisms of virulence and host preference, as well as developing effective disease control measures. Prerequisite to these pursuits is the accurate delimitation of species boundaries. Colletotrichum gloeosporioides s.l. is a species complex of plant pathogens and endophytic fungi for which reliable species recognition has only recently become possible through a multi-locus phylogenetic approach. By adopting an intensive regional sampling strategy encompassing multiple hosts within and beyond agricultural zones associated with cranberry (Vaccinium macrocarpon Aiton), we have integrated North America strains of Colletotrichum gloeosporioides s.l. from these habitats into a broader phylogenetic framework. We delimit species on the basis of genealogical concordance phylogenetic species recognition (GCPSR) and quantitatively assess the monophyly of delimited species at each of four nuclear loci and in the combined data set with the genealogical sorting index (gsi). Our analysis resolved two principal lineages within the species complex. Strains isolated from cranberry and sympatric host plants are distributed across both of these lineages and belong to seven distinct species or terminal clades. Strains isolated from V. macrocarpon in commercial cranberry beds belong to four species, three of which are described here as new. Another species, C. rhexiae Ellis & Everh., is epitypified. Intensive regional sampling has revealed a combination of factors, including the host species from which a strain has been isolated, the host organ of origin, and the habitat of the host species, as useful indicators of species identity in the sampled regions. We have identified three broadly distributed temperate species, C. fructivorum, C. rhexiae, and C. nupharicola, that could be useful for understanding the microevolutionary forces that may lead to species divergence in this important complex of endophytes and plant pathogens

An Exploration of Posttraumatic Growth, Loneliness, Depression, Resilience, and Social Capital Among Survivors of Hurricane Katrina and the Deepwater Horizon Oil Spill

The aim of this study was to examine the relationships among posttraumatic growth (PTG), loneliness, depression, psychological resilience, and social capital among survivors of Hurricane Katrina in 2005 and the Deepwater Horizon oil spill in 2010. The survey was administered to a spatially stratified, random sample of households in the three coastal counties of Mississippi. A total of 216 participants were included in this study who lived in close proximity to the Gulf of Mexico coastline during both disasters. Results from structural equation modeling analyses indicated that there was a significant and inverse relationship between PTG and loneliness. Conversely, a direct relationship was not found between PTG and depressive symptoms; instead, the results revealed an indirect relationship between PTG and depressive symptoms through loneliness. Social capital was related to loneliness only indirectly through PTG, while psychological resilience was related to loneliness both directly and indirectly through PTG. Understanding the relationships among these factors, particularly the importance of PTG, can provide insight into the long‐term adaptation among those who have survived multiple disasters. Further, these findings may lead to nuanced methods for behavioral health practitioners in assessing and treating individuals with symptoms of depression in disaster‐prone communities

Adapting to Life after Hurricane Katrina and the Deepwater Horizon Oil Spill: An Examination of Psychological Resilience and Depression on the Mississippi Gulf Coast

The purpose of this study was to examine relationships among depression, psychological resilience, and other sociodemographic factors of individuals who were highly exposed to Hurricane Katrina in 2005 and the Deepwater Horizon Oil Spill in 2010. A spatially stratified random sample of 294 Mississippi Gulf Coast residents living in close proximity to the Gulf of Mexico were surveyed. Findings indicated that low education attainment, financial hardship, and disaster-related damages increased the likelihood of depression, whereas psychological resilience and having health insurance reduced the odds of depression. Implications for enhancing psychological resilience and increasing access to health insurance are discussed

Community Resilience, Psychological Resilience, and Depressive Symptoms: An Examination of the Mississippi Gulf Coast 10 Years After Hurricane Katrina and 5 Years After the Deepwater Horizon Spill

Objective: This study examined the role of community resilience and psychological resilience on depressive symptoms in areas on the Mississippi Gulf Coast that have experienced multiple disasters. Methods: Survey administration took place in the spring of 2015 to a spatially stratified, random sample of households. This analysis included a total of 294 subjects who lived in 1 of the 3 counties of the Mississippi Gulf Coast at the time of both Hurricane Katrina in 2005 and the Deepwater Horizon oil spill in 2010. The survey included the Communities Advancing Resilience Toolkit (CART) scale, the Connor-Davidson Resilience Scale (CD-RISC 10), and the Center for Epidemiologic Studies Depression Scale (CES-D). Results: There was a significant inverse relationship between psychological resilience and depressive symptoms and a significant positive relationship between community resilience and psychological resilience. The results also revealed that community resilience was indirectly related to depressive symptoms through the mediating variable of psychological resilience. Conclusions: These findings highlight the importance of psychological resilience in long-term disaster recovery and imply that long-term recovery efforts should address factors associated with both psychological and community resilience to improve mental health outcomes. (Disaster Med Public Health Preparedness. 2018;12:241–248