8 Search Results

Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derivedmore » carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.« less

Fungi are increasingly recognized as key players in various extreme environments. Here we present an analysis of publicly-sourced metagenomes from global extreme environments, focusing on fungal taxonomy and function. The majority of 855 selected metagenomes contained scaffolds assigned to fungi. Relative abundance of fungi was as high as 10% of protein-coding genes with taxonomic annotation, with up to 289 fungal genera per sample. Despite taxonomic clustering by environment, fungal communities were more dissimilar than archaeal and bacterial communities, both for within- and between-environment comparisons. Relatively abundant fungal classes in extreme environments included Dothideomycetes, Eurotiomycetes, Leotiomycetes, Pezizomycetes, Saccharomycetes, and Sordariomycetes. Broadmore » generalists and prolific aerial spore formers were the most relatively abundant fungal genera detected in most of the extreme environments, bringing up the question of whether they are actively growing in those environments or just surviving as spores. More specialized fungi were common in some environments, such as zoosporic taxa in cryosphere water and hot springs. Relative abundances of genes involved in adaptation to general, thermal, oxidative, and osmotic stress were greatest in soda lake, acid mine drainage, and cryosphere water samples.« less

U-splines are a novel approach to the construction of a spline basis for representing smooth objects in Computer-Aided Design (CAD) and Computer-Aided Engineering (CAE). A spline is a piecewise-defined function that satisfies continuity constraints between adjacent cells in a mesh. U-splines differ from existing spline constructions, such as Non-Uniform Rational B-splines (NURBS), subdivision surfaces, T-splines, and hierarchical B-splines, in that they can accommodate local variation in cell size, polynomial degree, and smoothness simultaneously over more varied mesh configurations. Mixed cell types (e.g., triangle and quadrilateral cells in the same mesh) and T-junctions are also supported, although the continuity of interfacesmore » with triangle and tetrahedral cells is limited in the present work. The U-spline algorithm introduces a new technique for using local null space solutions to construct basis functions for the global spline null space problem. The U-spline construction is presented for curves, surfaces, and volumes with higher dimensional generalizations possible. Lastly, a set of requirements are given to ensure that the U-spline basis is positive, forms a partition of unity, is complete, and is locally linearly independent.« less

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments,more » thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.« less

Cyanobacteria are integral to soil development in the earliest stages of primary succession by fixing carbon (C) and nitrogen (N) essential for organismal growth. Here, we examined soil cyanobacterial communities at the earliest stage of succession (<5 years) at two disparate glacial forefields to reveal cyanobacterial patterns central to ecosystem development. Despite vast differences in climate and the relative dominance of heterotrophic versus autotrophic bacteria in these forefields, we found common patterns in cyanobacterial community composition in early soils. This work adds to limited research suggesting the importance of non-heterocytous filamentous cyanobacteria in initial soil colonization and development of primarymore » succession of glacier forefields. Further, a phosphorus (P) addition experiment suggests P-limitation as a mechanism underlying the restricted presence of ecologically important, putatively N-fixing, Nostocales in these emerging landscapes.« less

While it is well established that microbial composition and diversity shift along environmental gradients, how interactions among microbes change is poorly understood. Here, we tested how community structure and species interactions among diverse groups of soil microbes (bacteria, fungi, non-fungal eukaryotes) change across a fundamental ecological gradient, succession. Our study system is a high-elevation alpine ecosystem that exhibits variability in successional stage due to topography and harsh environmental conditions. We used hierarchical Bayesian joint distribution modeling to remove the influence of environmental covariates on species distributions and generated interaction networks using the residual species-to-species variance-covariance matrix. We hypothesized that asmore » ecological succession proceeds, diversity will increase, species composition will change, and soil microbial networks will become more complex. As expected, we found that diversity of most taxonomic groups increased over succession, and species composition changed considerably. Interestingly, and contrary to our hypothesis, interaction networks became less complex over succession (fewer interactions per taxon). Interactions between photosynthetic microbes and any other organism became less frequent over the gradient, whereas interactions between plants or soil microfauna and any other organism were more abundant in late succession. Results demonstrate that patterns in diversity and composition do not necessarily relate to patterns in network complexity and suggest that network analyses provide new insight into the ecology of highly diverse, microscopic communities.« less

In post-disturbance landscapes nutrient availability has proven a major control on ecological succession. In this study, we examined variation in connections between soil nutrient availability and decomposition extracellular enzyme activity (EEA) across post fire secondary succession in forest soils as well as after a secondary flood disturbance. We also examined possible linkages between edaphic properties and bacterial communities based on 16S rRNA gene analysis. We found that with advancing succession in a post-fire landscape, the relationship between soil nutrients and EEA became stronger over time. In general, late successional soils showed stronger connections between EEA and soil nutrient status, whilemore » early successional soils were marked by a complete decoupling of nutrients and EEA. We also found that soil moisture and bacterial communities of post-fire disturbance soils were susceptible to change following the secondary flood disturbance, while undisturbed, reference forest soils were not. Our results demonstrate that nutrient pools correlating with EEA change over time. While past work has largely focused on ecosystem succession on decadal timescales, our work suggests that nutrients shift in their relative importance as a control of decomposition EEA in the earliest stages of secondary succession. Furthermore, this work emphasizes the relevance of successional stage, even on short timescales, in predicting rates of carbon and nitrogen cycling, especially as disturbances become more frequent in a rapidly changing world.« less