Coccidioidomycosis: a reemerging infectious disease.

Coccidioides immitis, the primary pathogenic fungus that causes coccidioidomycosis, is most commonly found in the deserts of the southwestern United States and Central and South America. During the early 1990s, the incidence of coccidioidomycosis in California increased dramatically. Even though most infections are subclinical or self-limited, the outbreak is estimated to have cost more than $66 million in direct medical expenses and time lost from work in Kern County, California, alone. In addition to the financial loss, this pathogen causes serious and life-threatening disseminated infections, especially among the immunosuppressed, including AIDS patients. This article discusses factors that may be responsible for the increased incidence of coccidioidomycosis (e.g., climatic and demographic changes and the clinical problems of coccidioidomycosis in the immunocompromised) and new approaches to therapy and prevention

A rapid change in virulence gene expression during the transition from the intestinal lumen into tissue promotes systemic dissemination of Salmonella.

Bacterial pathogens causing systemic disease commonly evolve from organisms associated with localized infections but differ from their close relatives in their ability to overcome mucosal barriers by mechanisms that remain incompletely understood. Here we investigated whether acquisition of a regulatory gene, tviA, contributed to the ability of Salmonella enterica serotype Typhi to disseminate from the intestine to systemic sites of infection during typhoid fever. To study the consequences of acquiring a new regulator by horizontal gene transfer, tviA was introduced into the chromosome of S. enterica serotype Typhimurium, a closely related pathogen causing a localized gastrointestinal infection in immunocompetent individuals. TviA repressed expression of flagellin, a pathogen associated molecular pattern (PAMP), when bacteria were grown at osmotic conditions encountered in tissue, but not at higher osmolarity present in the intestinal lumen. TviA-mediated flagellin repression enabled bacteria to evade sentinel functions of human model epithelia and resulted in increased bacterial dissemination to the spleen in a chicken model. Collectively, our data point to PAMP repression as a novel pathogenic mechanism to overcome the mucosal barrier through innate immune evasion

Soil bacterial and fungal communities across a pH gradient in an arable soil

Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth. The ISME Journal (2010) 4, 1340-1351; doi: 10.1038/ismej.2010.58; published online 6 May 2010&nbsp

SitePainter: a tool for exploring biogeographical patterns

As microbial ecologists take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic spatial patterns and structures of these populations is crucial. Here we present SitePainter, an interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses data and display both diversity and taxonomy results in a spatial context. Features of SitePainter include: visualizing α -diversity, using taxonomic summaries; visualizing β -diversity, using results from multidimensional scaling methods; and animating relationships among microbial taxa or pathways overtime. SitePainter thus increases the visual power and ability to explore spatially explicit studies

Contrasting environmental preferences of photosynthetic and non‐photosynthetic soil cyanobacteria across the globe

Aim: Cyanobacteria have shaped the history of life on Earth and continue to play important roles as carbon and nitrogen fixers in terrestrial ecosystems. However, their global distribution and ecological preferences remain poorly understood, particularly for two recently discovered non‐photosynthetic cyanobacterial classes (Sericytochromatia and Melainabacteria). Location: Two hundred and thirty‐seven locations across six continents encompassing multiple climates (arid, temperate, tropical, continental and polar) and vegetation types (forests, grasslands and shrublands). Time period: Sampling was carried out between 2003 and 2015. Major taxa studied: Photosynthetic and non‐photosynthetic cyanobacterial taxa. Methods: We conducted a field survey and used co‐occurrence network analysis and structural equation modelling to evaluate the distribution and environmental preferences of soil cyanobacteria across the globe. These ecological preferences were used to create a global atlas (predictive distribution maps) of soil cyanobacteria. Results: Network analyses identified three major groups of cyanobacterial taxa, which resembled the three main cyanobacterial classes: the photosynthetic Oxyphotobacteria‐dominated cluster, which were prevalent in arid and semi‐arid areas, and the non‐photosynthetic Sericytochromatia‐ and Melainabacteria‐dominated clusters, which preferred hyper‐arid oligotrophic and acidic/humid environments, respectively. Main conclusions: This study provides new insights into the environmental preferences of non‐photosynthetic cyanobacteria in soils globally. Our findings highlight the contrasting environmental preferences among the three clusters of cyanobacteria and suggest that alterations in environmental conditions linked to climate change might result in important changes in the ecology and biogeography of these functionally important microorganisms.M.D.-B. is supported by a Ramón y Cajal grant from the Spanish Ministry of Science and Innovation (RYC2018-025483-I), and by the BES grant agreement No LRB17\1019 (MUSGONET). The work of C.C.-D. and F.T.M. and the global drylands database were supported by the European Research Council [ERC Grant Agreements 242658 (BIOCOM) and 647038 (BIODESERT)] and by the Spanish Ministry of Economy and Competitiveness (BIOMOD project, ref. CGL2013-44661-R). F.T.M. acknowledges support from Generalitat Valenciana (BIOMORES project, ref. CIDEGENT/2018/041). Research on biodiversity by B.K.S. is supported by the Australian Research Council (DP170104634). R.D.B. was supported by the U.K. Department of Environment, Food and Rural Affairs (DEFRA) project no. BD5003 and a Biotechnology and Biological Sciences Research Council (BBSRC) International Exchange Grant (BB/L026406/1)

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (\u3ci\u3eSus scrofa\u3c/i\u3e)

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free-ranging exotic ungulate in the United States. Large and ever-increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/ year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing-based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations

Microbes Should Be Central to Ecological Education and Outreach.

Our planet is changing rapidly, and responding to the ensuing environmental challenges will require an informed citizenry that can understand the inherent complexity of ecological systems. However, microorganisms are usually neglected in the narratives that we use to understand nature. Here, we advocate for the inclusion of microbial ecology across education levels and delineate the often neglected benefits of incorporating microbes into ecology curricula. We provide examples across education levels, from secondary school (by considering one's self as a microbial ecosystem), to higher education (by incorporating our knowledge of the global ecological role and medical application of microbes), to the general public (by engagement through citizen-science projects). The greater inclusion of microbes in ecological education and outreach will not only help us appreciate the natural world we are part of, but will ultimately aid in building a citizenry better prepared to make informed decisions on health and environmental policies

Exploring the boundaries of microbial habitability in soil

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dragone, N. B., Diaz, M. A., Hogg, I., Lyons, W. B., Jackson, W. A., Wall, D. H., Adams, B. J., & Fierer, N. Exploring the boundaries of microbial habitability in soil. Journal of Geophysical Research: Biogeosciences, 126(6), (2021): e2020JG006052, https://doi.org/10.1029/2020JG006052.Microbes are widely assumed to be capable of colonizing even the most challenging terrestrial surface environments on Earth given enough time. We would not expect to find surface soils uninhabited by microbes as soils typically harbor diverse microbial communities and viable microbes have been detected in soils exposed to even the most inhospitable conditions. However, if uninhabited soils do exist, we might expect to find them in Antarctica. We analyzed 204 ice-free soils collected from across a remote valley in the Transantarctic Mountains (84–85°S, 174–177°W) and were able to identify a potential limit of microbial habitability. While most of the soils we tested contained diverse microbial communities, with fungi being particularly ubiquitous, microbes could not be detected in many of the driest, higher elevation soils—results that were confirmed using cultivation-dependent, cultivation-independent, and metabolic assays. While we cannot confirm that this subset of soils is completely sterile and devoid of microbial life, our results suggest that microbial life is severely restricted in the coldest, driest, and saltiest Antarctic soils. Constant exposure to these conditions for thousands of years has limited microbial communities so that their presence and activity is below detectable limits using a variety of standard methods. Such soils are unlikely to be unique to the studied region with this work supporting previous hypotheses that microbial habitability is constrained by near-continuous exposure to cold, dry, and salty conditions, establishing the environmental conditions that limit microbial life in terrestrial surface soils.This work was supported by grants from the U.S. National Science Foundation (ANT 1341629 to B. J. Adams, N. Fierer, W. Berry Lyons, and D. H. Wall and OPP 1637708 to B. J. Adams) with additional support provided to N. B. Dragone from University Colorado Department of Ecology and Evolutionary Biology

Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (&sim;5&ndash;10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars. &nbsp;</p