Background: The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in soil stability, plant biomass decomposition, and endophytic interactions with plants. They may also form symbiotic associations with biocrust components or be latent saprotrophs or pathogens that live on plant tissues. However, their functional potential in arid soils, where organic matter, nutrients and water are very low or only periodically available, is poorly characterized.Results: Five Ascomycota fungi were isolated from different soil crust microhabitats and rhizosphere soils around the native bunchgrassPleuraphis jamesiiin an arid grassland near Moab, UT, USA. Putative genera wereConiochaeta, isolated from lichen biocrust,Embellisiafrom cyanobacteria biocrust, Chaetomiumfrom below lichen biocrust,Phomafrom a moss microhabitat, andAspergillusfrom the soil. The fungi were grown in replicate cultures on different carbon sources (chitin, native bunchgrass or pine wood) relevant to plant biomass and soil carbon sources. Secretomes produced by the fungi on each substrate were characterized. Results demonstrate that these fungi likely interact with primary producers (biocrust or plants) by secreting a wide range of proteins that facilitate symbiotic associations. Each of the fungal isolates secreted enzymes that degrade plant biomass, small secreted effector proteins, and proteins involved in either beneficial plant interactions or virulence.AspergillusandPhomaexpressed more plant biomass degrading enzymes when grown in grass- and pine-containing cultures than in chitin.ConiochaetaandEmbellisiaexpressed similar numbers of these enzymes under all conditions, whileChaetomiumsecreted more of these enzymes in grass-containing cultures.Conclusions: This study of Ascomycota genomes and secretomes provides important insights about the lifestyles and the roles that Ascomycota fungi likely play in arid grassland, ecosystems. However, the exact nature of those interactions, whether any or all of the isolates are true endophytes, latent saprotrophs or opportunistic phytopathogens, will be the topic of future studies.

The Francisella genus includes several recognized species, additional potential species, and other representatives that inhabit a range of incredibly diverse ecological niches, but are not closely related to the named species. Francisella species have been obtained from a wide variety of clinical and environmental sources; documented species include highly virulent human and animal pathogens, fish pathogens, opportunistic human pathogens, tick endosymbionts, and free-living isolates inhabiting brackish water. While more than 120 Francisella genomes have been sequenced to date, only a few contain plasmids, and most of these appear to be cryptic, with unknown benefit to the host cell. We have identified several putative cryptic plasmids in the sequenced genomes of three Francisella novicida and F. novicida-like strains (TX07-6608, AZ06-7470, DPG_3A-IS) and two new Francisella species (F. frigiditurris CA97-1460 and F. opportunistica MA06-7296). These plasmids were compared to each other and to previously identified plasmids from other Francisella species. Some of the plasmids encoded functions potentially involved in replication, conjugal transfer and partitioning, environmental survival (transcriptional regulation, signaling, metabolism), and hypothetical proteins with no assignable functions. Genomic and phylogenetic comparisons of these new plasmids to the other known Francisella plasmids revealed some similarities that add to our understanding of the evolutionary relationships among the diverse Francisella species.

A large circular plasmid detected in Francisella novicida-like strain PA10-7858, designated pFNPA10, was sequenced completely and analyzed. This 41 013-bp plasmid showed no homology to any of the previously sequenced Francisella plasmids and was 8–10 times larger in size than them. A total of 57 ORFs were identified within pFNPA10 and at least 9 of them encoded putative proteins with homology to different conjugal transfer proteins. The presence of iteron-like direct repeats and an ORF encoding a putative replication protein within pFNPA10 suggested that it replicated by the theta mode. Phylogenetic analyses indicated that pFNPA10 had no near neighbors in the databases and that it may have originated within an environmental Francisella lineage. Based on its features, pFNPA10 appears to be a novel extra-chromosomal genetic element within the genus Francisella. The suitability of pFNPA10 as a vector for transformation of species of Francisella by conjugation remains to be explored.

The intracellular pathogen Burkholderia pseudomallei, which is endemic to parts of southeast Asia and northern Australia, causes the disease melioidosis. Although acute infections can be treated with antibiotics, melioidosis is difficult to cure, and some patients develop chronic infections or a recrudescence of the disease months or years after treatment of the initial infection. B. pseudomallei strains have a high level of natural resistance to a variety of antibiotics, and with limited options for new antibiotics on the horizon, new alternatives are needed. The aim of the present study was to characterize the metabolic capabilities of B. pseudomallei , identify metabolites crucial for pathogen survival, understand the metabolic interactions that occur between pathogen and host cells, and determine if metabolic enzymes produced by the pathogen might be potential antibacterial targets. This aim was accomplished through genome scale metabolic modeling under different external conditions: 1) including all nutrients that could be consumed by the model, and 2) providing only the nutrients available in culture media. Using this approach, candidate chokepoint enzymes were identified, then knocked out in silico under the different nutrient conditions. The effect of each knockout on the metabolic network was examined. When five of the candidate chokepoints were knocked out in silico , the flux through the B. pseudomallei network was decreased, depending on the nutrient conditions. These results demonstrate the utility of genome-scale metabolic modeling methods for drug target identification in B. pseudomallei.

The fetal period is a critical time for brain development, characterized by neurogenesis, neural migration, and synaptogenesis ^1-3 . Microglia, the tissue resident macrophages of the brain, are observed as early as the fourth week of gestation ⁴ and are thought to engage in a variety of processes essential for brain development and homeostasis ^5-11 . Conversely, microglia phenotypes are highly regulated by the brain environment ^12-14 . Mechanisms by which human brain development influences the maturation of microglia and microglia potential contribution to neurodevelopmental disorders remain poorly understood. Here, we performed transcriptomic analysis of human fetal and postnatal microglia and corresponding cortical tissue to define age-specific brain environmental factors that may drive microglia phenotypes. Comparative analysis of open chromatin profiles using bulk and single-cell methods in conjunction with a new computational approach that integrates epigenomic and single-cell RNA-seq data allowed decoding of cellular heterogeneity with inference of subtype- and development stage-specific transcriptional regulators. Interrogation of in vivo and in vitro iPSC-derived microglia models provides evidence for roles of putative instructive signals and downstream gene regulatory networks which establish human-specific fetal and postnatal microglia gene expression programs and potentially contribute to neurodevelopmental disorders.