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Beneficial microbial associations enhance the fitness of most living organisms, and wood-feeding insects offer some of the most striking examples of this. Odontotaenius disjunctus is a wood-feeding beetle that possesses a digestive tract with four main compartments, each of which contains well-differentiated microbial populations, suggesting that anatomical properties and separation of these compartments may enhance energy extraction from woody biomass. Here, using integrated chemical analyses, we demonstrate that lignocellulose deconstruction and fermentation occur sequentially across compartments, and that selection for microbial groups and their metabolic pathways is facilitated by gut anatomical features. Metaproteogenomics showed that higher oxygen concentration in the midgut drives lignocellulose depolymerization, while a thicker gut wall in the anterior hindgut reduces oxygen diffusion and favours hydrogen accumulation, facilitating fermentation, homoacetogenesis and nitrogen fixation. We demonstrate that depolymerization continues in the posterior hindgut, and that the beetle excretes an energy- and nutrient-rich product on which its offspring subsist and develop. Our results show that the establishment of beneficial microbial partners within a host requires both the acquisition of the microorganisms and the formation of specific habitats within the host to promote key microbial metabolic functions. Together, gut anatomical properties and microbial functional assembly enable lignocellulose deconstruction and colony subsistence on an extremely nutrient-poor diet.

Phylogenetic taxon definitions (PTDs) are explicit, phylogeny-based statements that specify clades. PTDs are central to the system of rank-free classification that is governed by the PhyloCode, but they can also be used to clarify the meanings of ranked names. We present PTDs for four major groups: Fungi, Dikarya, Ascomycota, and Basidiomycota.

The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

Yeasts are important for industrial and biotechnological processes and show remarkable metabolic and phylogenetic diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. Phylogenetic analysis of these and previously published yeast genomes helped resolve the placement of species including Saitoella complicata, Babjeviella inositovora, Hyphopichia burtonii, and Metschnikowia bicuspidata. Moreover, we find that alternative nuclear codon usage, where CUG encodes serine instead of leucine, are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes, and a tendency towards more introns in early-diverging species. Analysis of enzyme phylogeny gives insights into the evolution of metabolic capabilities such as methanol utilization and assimilation of alternative carbon sources.

Yeasts are important for many industrial and biotechnological processes and show remarkable diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. A comparison of these with several other previously published yeast genomes have added increased confidence to the phylogenetic positions of previously poorly placed species including Saitoella complicata, Babjeviella inositovora and Metschnikowia bicuspidata.Phylogenetic analysis also showed that yeasts with alternative nuclear codon usage where CUG encodes serine instead of leucine are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes with Lipomyces starkeyi and the previously published Pneumocystis jirovecii being notable exceptions. Intron analysis suggests that early diverging species have more introns. We also observed a large number of unclassified lineage specific non-simple repeats in these genomes.

Coarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, we have characterized the gut microbiome and physiology of Odontotaenius disjunctus, a wood-feeding beetle native to the eastern United States. We hypothesized that morphological and physiological differences among gut regions would correspond to distinct microbial populations and activities. In fact, significantly different communities were found in the foregut (FG), midgut (MG)/posterior hindgut (PHG) and anterior hindgut (AHG), with Actinobacteria and Rhizobiales being more abundant toward the FG and PHG. Conversely, fermentative bacteria such as Bacteroidetes and Clostridia were more abundant in the AHG, and also the sole region where methanogenic Archaea were detected. Although each gut region possessed an anaerobic core, micron-scale profiling identified radial gradients in oxygen concentration in all regions. Nitrogen fixation was confirmed by (15)N2 incorporation, and nitrogenase gene (nifH) expression was greatest in the AHG. Phylogenetic analysis of nifH identified the most abundant transcript as related to Ni-Fe nitrogenase of a Bacteroidetes species, Paludibacter propionicigenes. Overall, we demonstrate not only a compartmentalized microbiome in this beetle digestive tract but also sharp oxygen gradients that may permit aerobic and anaerobic metabolism to occur within the same regions in close proximity. We provide evidence for the microbial fixation of N2 that is important for this beetle to subsist on woody biomass.

Objective: Precision medicine is an area with great potential for mental health, but has made limited gains prognostically in predicting effective treatments. For refugees exposed to violence, culture may be a crucial factor in predicting treatment outcomes. Method: For this study, 290 participants from three regions (Afghanistan, the Great Lakes region of Africa, and Iraq and Syria) participated in a randomized controlled trial of an advocacy-based intervention. Emotional distress symptoms were measured prior to intervention, midintervention (3 months), postintervention (6 months), and follow-up (6 months after the end of intervention). Number of traumatic events, resource access, social support, and English proficiency were tested for potential predictive effects on intervention outcome. Results: Multilevel generalized linear models revealed that Afghans' (B = −0.259, SE = 0.108, p =.013), and Great Lakes Africans' (B = −0.116, SE = 0.057, p =.042) emotional distress symptoms improved as a function of the intervention, while Iraqis and Syrians showed no intervention effects. For Afghans, English proficiency (B = −0.453, SE = 0.157, p <.01) and social support (B = −0.179, SE = 0.086, p =.037) were most strongly correlated to emotional distress, while for Africans, resource access (B = −0.483, SE = 0.082, p <.001) and social support (B = −0.100, SE = 0.048, p =.040) were the strongest predictors of emotional distress. Conclusions: Response to advocacy-based interventions and active ingredients may be influenced by culture; findings have implications for refugees and precision medicine. What is the public health significance of this article?: An advocacy-based intervention reduced symptoms of distress for Afghan and Great Lakes African refugees, but not Iraqi and Syrian refugees, highlighting varying mental health needs. Further, different predictors of mental health outcomes were important to each group, suggesting a heterogeneous path to symptom remission. These findings may be used to help expand precision medicine to diverse populations. [ABSTRACT FROM AUTHOR]

Two hundred forty-seven (N = 247) undergraduate women at a medium-sized, Southwestern university provided written descriptions of a hypothetical sexual assault (SA). Women with a prior history of SA also described their actual SA experiences; women without a SA history provided a written description of a prior bad date or hookup. The contextual features of SA scripts were compared to those of actual SA experiences. Several characteristics of a stereotypical or "blitz rape" (e.g., physical force by a stranger) were more likely to be included in SA scripts relative to women's actual SA experiences. Victimized women were also more likely to include verbal coercion, a hangout/hookup context, and previous consensual kissing in their SA experiences, in comparison to their SA scripts. The contextual features of SA experiences were also compared to the contextual features of bad dates or bad hookups. SA experiences, relative to bad dates, were more likely to include alcohol use, physical and verbal coercion by the perpetrator, and passive resistance. SA experiences, relative to bad hookups, were more likely to include physical and verbal coercion by the perpetrator, and knowing the man for less than 1 week. Victimized participants SA experiences were also found to be less likely to include previous consensual kissing and consensual intercourse in comparison to bad hookup experiences of nonvictimized women. Overall, there was considerable overlap between the contextual features present across all experiences. The lack of differentiation among these events may explain why women experience difficulty acknowledging whether they have experienced SA. [ABSTRACT FROM AUTHOR]

Stress associated with resource deprivation is an active social determinant of mental health. However, mixed findings around the strength of this association and its persistence over time obscure optimal interventions to improve mental health in forcibly displaced populations. A reciprocal model was analyzed between resource access and measures of depression, anxiety and posttraumatic stress (PTSD) symptoms at three different assessments conducted 6 months apart (Time [T] 1, T2, and T3). Participants included resettled refugees (N = 290) from three geocultural regions (i.e., Afghanistan, the Great Lakes Region of Africa, and Iraq/Syria). The results showed that although limited resource access at T1 was related to depressive and anxiety symptoms, B = 0.26, SE = 0.16, p =.023, r2 = 0.55; posttraumatic stress disorder (PTSD) symptoms, B = 0.20, SE = 0.10, p <.001, r2 =.56; and culturally specific depression and anxiety at T2, B = 0.22, SE = 0.16, p <.001, r2 = 0.65, these were not reciprocally related to resource access at T3. The results help clarify the strength and direction of effects between resource deprivation and depression, anxiety , and PTSD sympotms over time. Although resource deprivation is predictive of depression, anxiety, and PTSD symptoms among recently resettled refugees, the effect may not persist in the long term. These findings have critical implications, including the urgency of ensuring initial access to resources for resettled refugees to stave off the development of depression, anxiety and PTSD symptoms, as delaying immediate resource access may result in the development of chronic, hard‐to‐treat mental health disorders. [ABSTRACT FROM AUTHOR]

Floral microbes, including bacteria and fungi, alter nectar quality, thus changing pollinator visitation. Conversely, pollinator visitation can change the floral microbial community.Most studies on dispersal of floral microbes have focused on bees, ants or hummingbirds, yet Lepidoptera are important pollinators.We asked (a) where are microbes present on the butterfly body, (b) do butterflies transfer microbes while foraging, and (c) how does butterfly foraging affect microbial abundance on different floret structures.The tarsi and proboscis had significantly more microbes than the thorax in wild‐caught Glaucopsyche lygdamus (Lepidoptera: Lycaenidae) and Speyeria mormonia (Lepidoptera: Nymphalidae). Glaucopsyche lygdamus, a smaller‐bodied species, had fewer microbes than S. mormonia.As a marker for microbes, we used a bacterium (Rhodococcus fascians, near NCBI Y11196) isolated from a S. mormonia that was foraging for nectar, and examined its dispersal by G. lygdamus and S. mormonia visiting florets of Pyrrocoma crocea (Asteraceae). Microbial dispersal among florets correlated positively with bacterial abundance in the donor floret. Dispersal also depended on butterfly species, age, and bacterial load carried by the butterfly.Recipient florets had less bacteria than donor florets. The nectaries had more bacteria than the anthers or the stigmas, while anthers and stigmas did not differ from each other. There was no differential transmission among floral organs.Lepidoptera thus act as vectors of floral microbes. Including Lepidoptera is thus crucial to an understanding of plant–pollinator–microbe interactions. Future studies should consider the role of vectored microbes in lepidopteran ecology and fitness. [ABSTRACT FROM AUTHOR]