Fungi and algae co-occur in snow: an issue of shared habitat or algal facilitation of heterotrophs?

Citation: Brown, S. P., Olson, B., & Jumpponen, A. (2015). Fungi and algae co-occur in snow: an issue of shared habitat or algal facilitation of heterotrophs? Arctic Antarctic and Alpine Research, 47(4), 729-749. doi:10.1657/aaar0014-071Late season alpine snows are often colonized by psychrophilic snow algae that may provide a source of nutrients for microbes. Such late season snows are a harsh environment, but support a diverse and complex fungal community. We used culture independent methods (Illumina MiSeq) to test if the presence of snow algae influences fungal communities. We compared algae-colonized snows to adjacent (3 m distant) noncolonized snows in a paired experimental design. Our data indicate that several fungi are locally enriched in algae colonized snows. Although many such fungi were basidiomycetous yeasts, our analyses identified a large number of snow-borne members of phylum Chytridiomycota. While the ecology and function of these Chytridiomycetes remain unclear, we hypothesize that their enrichment in the algal patches suggests that they depend on algae for nutrition. We propose that these chytrids are important components in snow ecosystems, highlighting the underestimation of their diversity and importance. Taken together, our data strongly indicate that fungal communities are heterogeneous in snow even among adjacent samples. Further, fungal and algal communities may be influenced by similar environmental drivers resulting in their co-occurrence in snow

A community of clones: Snow algae are diverse communities of spatially structured clones

Citation: Brown, S. P., Ungerer, M. C., & Jumpponen, A. (2016). A community of clones: Snow algae are diverse communities of spatially structured clones. International Journal of Plant Sciences, 177(5), 432-439. doi:10.1086/686019Premise of research. Snow algae are cosmopolitan and often colonize late-season snowpacks. These snow algae do not occur in isolation; rather, visible algal blooms consist of multispecies communities. Although several of these common snow algae have been characterized taxonomically, their inter- and intraspecific diversity remains unknown. Further, the phylogeographic and biogeographic structuring of snow algal species is poorly understood. Methodology. Algal communities were censused by sequencing the variable internal transcribed spacer 2 locus using Illumina MiSeq. We further analyzed two of the most common and abundant algal operational taxonomic units (OTUs) for biogeographic haplotype diversity. Pivotal results. Our data show that the communities are diverse and taxonomically broad (orders: Chlamydomonadales [74% of OTUs], Microthamniales [20% OTUs], and Chlorellales [6% OTUs]). We demonstrate that the two most common species (best nucleotide basic local alignment search tool match to Coenochloris sp. and Chlamydomonas sp.) have distinct haplotype distributions locally and regionally. Each sampled algal colony was dominated by one and only one haplotype, with negligible intraspecific haplotype diversity. Conclusions. Our results suggest that snow algae are communities of clones within a discrete patch yet are heterogeneous across the landscape. Thus, these communities are likely structured via strong priority effects, intense kin competition, and dispersal limitations. © 2016 by The University of Chicago. All rights reserved

Rules and patterns of microbial community assembly

Doctor of PhilosophyDivision of BiologyAri M. JumpponenMicroorganisms are critically important for establishing and maintaining ecosystem properties and processes that fuel and sustain higher-trophic levels. Despite the universal importance of microbes, we know relatively little about the rules and processes that dictate how microbial communities establish and assemble. Largely, we rely on assumptions that microbial community establishment follow similar trajectories as plants, but on a smaller scale. However, these assumptions have been rarely validated and when validation has been attempted, the plant-based theoretical models apply poorly to microbial communities. Here, I utilized genomics-inspired tools to interrogate microbial communities at levels near community saturation to elucidate the rules and patterns of microbial community assembly. I relied on a community filtering model as a framework: potential members of the microbial community are filtered through environmental and/or biotic filters that control which taxa can establish, persist, and coexist. Additionally, I addressed whether two different microbial groups (fungi and bacteria) share similar assembly patterns. Similar dispersal capabilities and mechanisms are thought to result in similar community assembly rules for fungi and bacteria. I queried fungal and bacterial communities along a deglaciated primary successional chronosequence to determine microbial successional dynamics and to determine if fungal and bacterial assemblies are similar or follow trajectories similar to plants. These experiments demonstrate that not only do microbial community assembly dynamics not follow plant-based models of succession, but also that fungal and bacterial community assembly dynamics are distinct. We can no longer assume that because fungi and bacteria share small propagule sizes they follow similar trends. Further, additional studies targeting biotic filters (here, snow algae) suggest strong controls during community assembly, possibly because of fungal predation of the algae or because of fungal utilization of algal exudates. Finally, I examined various technical aspects of sequence-based ecological investigations. These studies aimed to improve microbial community data reliability and analyses

Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem

Prescribed burning is a common management tool to control fuel loads, ground vegetation, and facilitate desirable game species. We evaluated soil fungal community responses to long-term prescribed fire treatments in a loblolly pine forest on the Piedmont of Georgia and utilized deep Internal Transcribed Spacer Region 1 (ITS1) amplicon sequencing afforded by the recent Ion Torrent Personal Genome Machine (PGM). These deep sequence data (19,000+ reads per sample after subsampling) indicate that frequent fires (3 year fire interval) shift soil fungus communities whereas infrequent fires (6 year fire interval) permit system resetting to a state similar to that without prescribed fire. Furthermore, in nonmetric multidimensional scaling analyses, primarily ectomycorrhizal taxa were correlated with axes associated with long fire intervals whereas soil saprobes tended to be correlated with the frequent fire recurrence. We conclude that 1) multiplexed Ion Torrent PGM analyses allow deep cost effective sequencing of fungal communities, but may suffer from short read lengths and inconsistent sequence quality adjacent to the sequencing adaptor; 2) frequent prescribed fires elicit a shift in soil fungal communities; and, 3) such shifts do not occur when fire intervals are longer. Our results emphasize the general responsiveness of these forests to management, and the importance of fire return intervals in meeting management objectives

The distribution of ammonia on Jupiter from a preliminary inversion of Juno Microwave Radiometer data

The Juno microwave radiometer measured the thermal emission from Jupiter's atmosphere from the cloud tops at about 1 bar to as deep as a hundred bars of pressure during its first flyby over Jupiter (PJ1). The nadir brightness temperatures show that the Equatorial Zone is likely to be an ideal adiabat, which allows a determination of the deep ammonia abundance in the range 362^(+33)_(-33) ppm. The combination of Markov chain Monte Carlo method and Tikhonov regularization is studied to invert Jupiter's global ammonia distribution assuming a prescribed temperature profile. The result shows (1) that ammonia is depleted globally down to 50–60 bars except within a few degrees of the equator, (2) the North Equatorial Belt is more depleted in ammonia than elsewhere, and (3) the ammonia concentration shows a slight inversion starting from about 7 bars to 2 bars. These results are robust regardless of the choice of water abundance

Lessons Learned During the Implementation of a Cold Gas Propulsion System for the SunRISE Mission

The SunRISE mission utilizes a two-phase cold gas propulsion system, which provides several advantages over other cold gas systems but experienced challenges during assembly and testing. Since 2020, Georgia Tech Research Corporation (GTRC), Utah State University Space Dynamics Laboratory (SDL), and the Jet Propulsion Laboratory (FPL) have implemented several improvements to the SunRISE propulsion system. The SunRISE propulsion system leverages an additively manufactured monolithic structure, commercial off-the-shelf (COTS) valves and transducers, and the benign working fluid R-236fa to provide a suitable propulsion system for the SunRise mission. While the GTRC propulsion system had been developed for other missions, the multi-organizational team found and corrected several previously undetected design issues, including filters with highly variable flow performance, solenoid valve drive circuit issues, and inconsistencies in the tank additive manufacturing process that impacted manufacturing yield, thrust consistency, and quality of seals. Leaks in metallic fittings were also identified, and process improvements were put in place to mitigate them. Solenoid valve stiction was the last issue which was mitigated through valve screening and drive circuit adjustments. In this paper, we present lessons learned from the SunRISE propulsion system effort to aid future teams in identifying and addressing similar issues

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

Metabarcoding data generated using next-generation sequencing (NGS) technologies are overwhelmed with rare taxa and skewed in Operational Taxonomic Unit (OTU) frequencies comprised of few dominant taxa. Low frequency OTUs comprise a rare biosphere of singleton and doubleton OTUs, which may include many artifacts. We present an in-depth analysis of global singletons across sixteen NGS libraries representing different ribosomal RNA gene regions, NGS technologies and chemistries. Our data indicate that many singletons (average of 38 % across gene regions) are likely artifacts or potential artifacts, but a large fraction can be assigned to lower taxonomic levels with very high bootstrap support (~32 % of sequences to genus with ≥90 % bootstrap cutoff). Further, many singletons clustered into rare OTUs from other datasets highlighting their overlap across datasets or the poor performance of clustering algorithms. These data emphasize a need for caution when discarding rare sequence data en masse: such practices may result in throwing the baby out with the bathwater, and underestimating the biodiversity. Yet, the rare sequences are unlikely to greatly affect ecological metrics. As a result, it may be prudent to err on the side of caution and omit rare OTUs prior to downstream analyses

Regulation of pH by Carbonic Anhydrase 9 Mediates Survival of Pancreatic Cancer Cells With Activated KRAS in Response to Hypoxia.

Background & Aims Most pancreatic ductal adenocarcinomas (PDACs) express an activated form of KRAS, become hypoxic and dysplastic, and are refractory to chemo and radiation therapies. To survive in the hypoxic environment, PDAC cells upregulate enzymes and transporters involved in pH regulation, including the extracellular facing carbonic anhydrase 9 (CA9). We evaluated the effect of blocking CA9, in combination with administration of gemcitabine, in mouse models of pancreatic cancer. Methods We knocked down expression of KRAS in human (PK-8 and PK-1) PDAC cells with small hairpin RNAs. Human and mouse (KrasG12D/Pdx1-Cre/Tp53/RosaYFP) PDAC cells were incubated with inhibitors of MEK (trametinib) or extracellular signal-regulated kinase (ERK), and some cells were cultured under hypoxic conditions. We measured levels and stability of the hypoxia-inducible factor 1 subunit alpha (HIF1A), endothelial PAS domain 1 protein (EPAS1, also called HIF2A), CA9, solute carrier family 16 member 4 (SLC16A4, also called MCT4), and SLC2A1 (also called GLUT1) by immunoblot analyses. We analyzed intracellular pH (pHi) and extracellular metabolic flux. We knocked down expression of CA9 in PDAC cells, or inhibited CA9 with SLC-0111, incubated them with gemcitabine, and assessed pHi, metabolic flux, and cytotoxicity under normoxic and hypoxic conditions. Cells were also injected into either immune-compromised or immune-competent mice and growth of xenograft tumors was assessed. Tumor fragments derived from patients with PDAC were surgically ligated to the pancreas of mice and the growth of tumors was assessed. We performed tissue microarray analyses of 205 human PDAC samples to measure levels of CA9 and associated expression of genes that regulate hypoxia with outcomes of patients using the Cancer Genome Atlas database. Results Under hypoxic conditions, PDAC cells had increased levels of HIF1A and HIF2A, upregulated expression of CA9, and activated glycolysis. Knockdown of KRAS in PDAC cells, or incubation with trametinib, reduced the posttranscriptional stabilization of HIF1A and HIF2A, upregulation of CA9, pHi, and glycolysis in response to hypoxia. CA9 was expressed by 66% of PDAC samples analyzed; high expression of genes associated with metabolic adaptation to hypoxia, including CA9, correlated with significantly reduced survival times of patients. Knockdown or pharmacologic inhibition of CA9 in PDAC cells significantly reduced pHi in cells under hypoxic conditions, decreased gemcitabine-induced glycolysis, and increased their sensitivity to gemcitabine. PDAC cells with knockdown of CA9 formed smaller xenograft tumors in mice, and injection of gemcitabine inhibited tumor growth and significantly increased survival times of mice. In mice with xenograft tumors grown from human PDAC cells, oral administration of SLC-0111 and injection of gemcitabine increased intratumor acidosis and increased cell death. These tumors, and tumors grown from PDAC patient-derived tumor fragments, grew more slowly than xenograft tumors in mice given control agents, resulting in longer survival times. In KrasG12D/Pdx1-Cre/Tp53/RosaYFP genetically modified mice, oral administration of SLC-0111 and injection of gemcitabine reduced numbers of B cells in tumors. Conclusions In response to hypoxia, PDAC cells that express activated KRAS increase expression of CA9, via stabilization of HIF1A and HIF2A, to regulate pH and glycolysis. Disruption of this pathway slows growth of PDAC xenograft tumors in mice and might be developed for treatment of pancreatic cancer

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie