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      Endolithic Fungal Species Markers for Harshest Conditions in the McMurdo Dry Valleys, Antarctica

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          Abstract

          The microbial communities that inhabit lithic niches inside sandstone in the Antarctic McMurdo Dry Valleys of life’s limits on Earth. The cryptoendolithic communities survive in these ice-free areas that have the lowest temperatures on Earth coupled with strong thermal fluctuations, extreme aridity, oligotrophy and high levels of solar and UV radiation. In this study, based on DNA metabarcoding, targeting the fungal Internal Transcribed Spacer region 1 (ITS1) and multivariate statistical analyses, we supply the first comprehensive overview onto the fungal diversity and composition of these communities sampled over a broad geographic area of the Antarctic hyper-arid cold desert. Six locations with surfaces that experience variable sun exposure were sampled to compare communities from a common area across a gradient of environmental pressure. The Operational Taxonomic Units (OTUs) identified were primarily members of the Ascomycota phylum, comprised mostly of the Lecanoromycetes and Dothideomycetes classes. The fungal species Friedmanniomyces endolithicus, endemic to Antarctica, was found to be a marker species to the harshest conditions occurring in the shady, south exposed rock surfaces. Analysis of community composition showed that sun exposure was an environmental property that explained community diversity and structured endolithic colonization.

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          Beyond the Venn diagram: the hunt for a core microbiome.

          Discovering a core microbiome is important for understanding the stable, consistent components across complex microbial assemblages. A core is typically defined as the suite of members shared among microbial consortia from similar habitats, and is represented by the overlapping areas of circles in Venn diagrams, in which each circle contains the membership of the sample or habitats being compared. Ecological insight into core microbiomes can be enriched by 'omics approaches that assess gene expression, thereby extending the concept of the core beyond taxonomically defined membership to community function and behaviour. Parameters defined by traditional ecology theory, such as composition, phylogeny, persistence and connectivity, will also create a more complex portrait of the core microbiome and advance understanding of the role of key microorganisms and functions within and across ecosystems. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.
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            Warming of the Antarctic ice-sheet surface since the 1957 International Geophysical Year.

            Assessments of Antarctic temperature change have emphasized the contrast between strong warming of the Antarctic Peninsula and slight cooling of the Antarctic continental interior in recent decades. This pattern of temperature change has been attributed to the increased strength of the circumpolar westerlies, largely in response to changes in stratospheric ozone. This picture, however, is substantially incomplete owing to the sparseness and short duration of the observations. Here we show that significant warming extends well beyond the Antarctic Peninsula to cover most of West Antarctica, an area of warming much larger than previously reported. West Antarctic warming exceeds 0.1 degrees C per decade over the past 50 years, and is strongest in winter and spring. Although this is partly offset by autumn cooling in East Antarctica, the continent-wide average near-surface temperature trend is positive. Simulations using a general circulation model reproduce the essential features of the spatial pattern and the long-term trend, and we suggest that neither can be attributed directly to increases in the strength of the westerlies. Instead, regional changes in atmospheric circulation and associated changes in sea surface temperature and sea ice are required to explain the enhanced warming in West Antarctica.
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              Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

              Recent advances in molecular approaches and DNA sequencing have greatly progressed the field of ecology and allowed for the study of complex communities in unprecedented detail. Next generation sequencing (NGS) can reveal powerful insights into the diversity, composition, and dynamics of cryptic organisms, but results may be sensitive to a number of technical factors, including molecular practices used to generate amplicons, sequencing technology, and data processing. Despite the popularity of some techniques over others, explicit tests of the relative benefits they convey in molecular ecology studies remain scarce. Here we tested the effects of PCR replication, sequencing depth, and sequencing platform on ecological inference drawn from environmental samples of soil fungi. We sequenced replicates of three soil samples taken from pine biomes in North America represented by pools of either one, two, four, eight, or sixteen PCR replicates with both 454 pyrosequencing and Illumina MiSeq. Increasing the number of pooled PCR replicates had no detectable effect on measures of α- and β-diversity. Pseudo-β-diversity – which we define as dissimilarity between re-sequenced replicates of the same sample – decreased markedly with increasing sampling depth. The total richness recovered with Illumina was significantly higher than with 454, but measures of α- and β-diversity between a larger set of fungal samples sequenced on both platforms were highly correlated. Our results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs. This study also demonstrates the potential for continuous integration of older datasets with newer technology.
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                Author and article information

                Journal
                Life (Basel)
                Life (Basel)
                life
                Life
                MDPI
                2075-1729
                06 February 2020
                February 2020
                : 10
                : 2
                : 13
                Affiliations
                [1 ]Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; coleine@ 123456unitus.it (C.C.); zucconi@ 123456unitus.it (L.Z.); onofri@ 123456unitus.it (S.O.)
                [2 ]Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; npomb001@ 123456ucr.edu
                [3 ]Italian National Antarctic Museum (MNA), Mycological Section, 16166 Genoa, Italy
                Author notes
                [* ]Correspondence: jason.stajich@ 123456ucr.edu (J.E.S.); selbmann@ 123456unitus.it (L.S.); Tel.: +1-951-827-2363 (J.E.S.); +39-0761-35738 (L.S.)
                Author information
                https://orcid.org/0000-0001-9793-2303
                https://orcid.org/0000-0002-7591-0020
                Article
                life-10-00013
                10.3390/life10020013
                7175349
                32041249
                72cb69dc-4253-407a-8107-55ab0efcdf74
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 30 December 2019
                : 04 February 2020
                Categories
                Article

                antarctica,cryptoendolithic communities,mcmurdo dry valleys,its metabarcoding,fungi,marker species

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