ALBERT

Description: The introduction of alien plants can influence biodiversity and ecosystems. However, its consequences for soil microbial communities remain poorly understood. We addressed the impact of alien ectomycorrhizal (EcM) pines on local arbuscular mycorrhizal (AM) fungal communities in two regions with contrasting biogeographic histories: in South Africa, where no native EcM plant species are present; and in Argentina, where EcM trees occur naturally. The effect of alien pines on AM fungal communities differed between these regions. In South Africa, plantations of alien EcM pines exhibited lower AM fungal richness and significantly altered community composition, compared with native fynbos. In Argentina, the richness and composition of local AM fungal communities were similar in plantations of alien EcM pines and native forest. However, the presence of alien pines resulted in slight changes to the phylogenetic structure of root AM fungal communities in both regions. In pine clearcut areas in South Africa, the richness and composition of AM fungal communities were intermediate between the native fynbos and the alien pine plantation, which is consistent with natural regeneration of former AM fungal communities following pine removal. We conclude that the response of local AM fungal communities to alien EcM pines differs between biogeographic regions with different histories of species coexistence.

Description: Infections of Asian elephants (Elephas maximus) with elephant endotheliotropic herpesvirus (EEHV) can cause a rapid, highly lethal, hemorrhagic disease, which primarily affects juvenile animals up to the age of four years. So far, the majority of deaths have been attributed to infections with genotype EEHV1 or, more rarely, EEHV3 and EEHV4. Here, we report the pathological characteristics of the first fatality linked to EEHV5 infection, and describe the complete viral DNA sequence. Gross post-mortem and histological findings were indistinguishable from lethal cases previously attributed to other EEHV genotypes, and the presence of characteristic herpesviral inclusions in capillary endothelial cells at several sites was consistent with the diagnosis of acute EEHV infection. Molecular analysis confirmed the presence of EEHV5 DNA and was followed by sequencing of the viral genome directly from post-mortem material. The genome is 180,800 bp in size and contains 120 predicted protein-coding genes, five of which are fragmented and presumably nonfunctional. The seven families of paralogous genes recognized in EEHV1 are also represented in EEHV5. The overall degree of divergence (37%) between the EEHV5 and EEHV1 genomes, and phylogenetic analysis of eight conserved genes, support the proposed classification of EEHV5 into a new species (Elephantid herpesvirus 5). Scientific Reports 4 doi: 10.1038/srep06299

Description: Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25-15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Willerslev, Eske -- Davison, John -- Moora, Mari -- Zobel, Martin -- Coissac, Eric -- Edwards, Mary E -- Lorenzen, Eline D -- Vestergard, Mette -- Gussarova, Galina -- Haile, James -- Craine, Joseph -- Gielly, Ludovic -- Boessenkool, Sanne -- Epp, Laura S -- Pearman, Peter B -- Cheddadi, Rachid -- Murray, David -- Brathen, Kari Anne -- Yoccoz, Nigel -- Binney, Heather -- Cruaud, Corinne -- Wincker, Patrick -- Goslar, Tomasz -- Alsos, Inger Greve -- Bellemain, Eva -- Brysting, Anne Krag -- Elven, Reidar -- Sonstebo, Jorn Henrik -- Murton, Julian -- Sher, Andrei -- Rasmussen, Morten -- Ronn, Regin -- Mourier, Tobias -- Cooper, Alan -- Austin, Jeremy -- Moller, Per -- Froese, Duane -- Zazula, Grant -- Pompanon, Francois -- Rioux, Delphine -- Niderkorn, Vincent -- Tikhonov, Alexei -- Savvinov, Grigoriy -- Roberts, Richard G -- MacPhee, Ross D E -- Gilbert, M Thomas P -- Kjaer, Kurt H -- Orlando, Ludovic -- Brochmann, Christian -- Taberlet, Pierre -- England -- Nature. 2014 Feb 6;506(7486):47-51. doi: 10.1038/nature12921.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark [2]. ; 1] Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia [2]. ; 1] Laboratoire d'Ecologie Alpine (LECA) CNRS UMR 5553, University Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France [2]. ; 1] Geography and Environment, University of Southampton, Southampton SO17 1BJ, UK [2]. ; 1] Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark [2] Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, 94720 California, USA [3]. ; 1] National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway [2] Department of Botany, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia [3]. ; 1] Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark [2] Ancient DNA Laboratory, Veterinary and Life Sciences School, Murdoch University, 90 South Street, Perth, 6150 Western Australia, Australia [3]. ; Division of Biology, Kansas State University, Manhattan, 66506-4901 Kansas, USA. ; Laboratoire d'Ecologie Alpine (LECA) CNRS UMR 5553, University Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France. ; 1] National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway [2] Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, NO-0318 Oslo, Norway (S.B.); Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Research Unit Potsdam, Telegrafenberg A 43, 14473 Potsdam, Germany (L.S.E.); SpyGen, Savoie Technolac, 17 allee du lac Saint Andre, BP 274, 73375 Le Bourget-du-Lac Cedex, France (E.B.). ; Landscape Dynamics Unit, Swiss Federal Research Institute WSL, Zurcherstrasse 111, CH-8903 Birmensdorf, Switzerland. ; Institut des Sciences de l'Evolution de Montpellier, UMR 5554 Universite Montpellier 2, Bat.22, CC061, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France. ; University of Alaska Museum of the North, Fairbanks, 99775-6960 Alaska, USA. ; Department of Arctic and Marine Biology, UiT, The Arctic University of Norway, NO-9037 Tromso, Norway. ; Geography and Environment, University of Southampton, Southampton SO17 1BJ, UK. ; Genoscope, Institut de Genomique du Commissariat a l'Energie Atomique (CEA), 91000 Evry, France. ; 1] Adam Mickiewicz University, Faculty of Physics, Umultowska 85, 61-614 Poznan, Poland [2] Poznan Radiocarbon Laboratory, Poznan Science and Technology Park, Rubiez 46, 61-612 Poznan, Poland. ; Tromso University Museum, NO-9037 Tromso, Norway. ; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway. ; National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway. ; Permafrost Laboratory, Department of Geography, University of Sussex, Brighton BN1 9QJ, UK. ; 1] Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prospect, 119071 Moscow, Russia [2]. ; Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark. ; Department of Biology, Terrestrial Ecology, Universitetsparken 15, DK- 2100 Copenhagen O, Denmark. ; Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, University of Adelaide, Adelaide, 5005 South Australia, Australia. ; Department of Geology/Quaternary Sciences, Lund University Solvegatan 12, SE-223 62 Lund, Sweden. ; Department of Earth and Atmospheric Sciences, University of Alberta, T6G 2E3 Edmonton, Alberta, Canada. ; Government of Yukon, Department of Tourism and Culture, Yukon Palaeontology Program, PO Box 2703 L2A, Y1A 2C6 Whitehorse, Yukon Territory, Canada. ; INRA, UMR1213 Herbivores, F-63122 Saint-Genes-Champanelle, France. ; Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint-Petersburg, Russia. ; Institute of Applied Ecology of the North of North-Eastern Federal University, Belinskogo Street 58, 677000 Yakutsk, Republic of Sakha (Yakutia), Russia. ; Centre for Archaeological Science, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, 2522 New South Wales, Australia. ; Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, 10024 New York, USA. ; 1] National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24499916" target="_blank"〉PubMed〈/a〉

Description: The global biogeography of microorganisms remains largely unknown, in contrast to the well-studied diversity patterns of macroorganisms. We used arbuscular mycorrhizal (AM) fungus DNA from 1014 plant-root samples collected worldwide to determine the global distribution of these plant symbionts. We found that AM fungal communities reflected local environmental conditions and the spatial distance between sites. However, despite AM fungi apparently possessing limited dispersal ability, we found 93% of taxa on multiple continents and 34% on all six continents surveyed. This contrasts with the high spatial turnover of other fungal taxa and with the endemism displayed by plants at the global scale. We suggest that the biogeography of AM fungi is driven by unexpectedly efficient dispersal, probably via both abiotic and biotic vectors, including humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davison, J -- Moora, M -- Opik, M -- Adholeya, A -- Ainsaar, L -- Ba, A -- Burla, S -- Diedhiou, A G -- Hiiesalu, I -- Jairus, T -- Johnson, N C -- Kane, A -- Koorem, K -- Kochar, M -- Ndiaye, C -- Partel, M -- Reier, U -- Saks, U -- Singh, R -- Vasar, M -- Zobel, M -- New York, N.Y. -- Science. 2015 Aug 28;349(6251):970-3. doi: 10.1126/science.aab1161.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu 51005, Estonia. ; Centre for Mycorrhizal Research, The Energy and Resources Institute (TERI), India Habitat Centre, Lodhi Road, New Delhi 110 003, India. ; Laboratoire des Symbioses Tropicales et Mediterraneennes, Unite Mixte de Recherche 113, Laboratoire de Biologie et Physiologie Vegetales, Faculte des Sciences Exactes et Naturelles, Universite des Antilles, BP 592, 97159, Pointe-a-Pitre, Guadeloupe (French West Indies). ; Laboratoire Commun de Microbiologie de l'Institut de Recherche pour le Developpement-Institut Senegalais de Recherches Agricoles-Universite Cheikh Anta Diop (UCAD), Departement de Biologie Vegetale, UCAD, BP 5005 Dakar, Senegal. ; Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu 51005, Estonia. Institute of Botany, Czech Academy of Sciences, Dukelska 135, 379 01 Trebon, Czech Republic. ; School of Earth Sciences and Environmental Sustainability, Northern Arizona University, Flagstaff, AZ 86011-5694, USA. ; Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu 51005, Estonia. Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands. ; TERI-Deakin Nano Biotechnology Centre, Biotechnology and Management of Bioresources Division, TERI, India Habitat Centre, Lodhi Road, New Delhi 110 003, India.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26315436" target="_blank"〉PubMed〈/a〉

Description: Bruns and Taylor argue that our finding of widespread distribution among Glomeromycota "virtual taxa" is undermined by the species definition applied. Although identifying appropriate species concepts and accessing taxonomically informative traits are challenges for microorganism biogeography, the virtual taxa represent a pragmatic classification that corresponds approximately to the species rank of classical Glomeromycota taxonomy, yet is applicable to environmental DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Opik, Maarja -- Davison, John -- Moora, Mari -- Partel, Meelis -- Zobel, Martin -- New York, N.Y. -- Science. 2016 Feb 19;351(6275):826. doi: 10.1126/science.aad5495.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia. maarja.opik@ut.ee. ; Department of Botany, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26912890" target="_blank"〉PubMed〈/a〉

Description: Nature Reviews Microbiology 15, 161 (2017). doi:10.1038/nrmicro.2016.177 Authors: Peter Simmonds, Mike J. Adams, Mária Benkő, Mya Breitbart, J. Rodney Brister, Eric B. Carstens, Andrew J. Davison, Eric Delwart, Alexander E. Gorbalenya, Balázs Harrach, Roger Hull, Andrew M.Q. King, Eugene V. Koonin, Mart Krupovic, Jens H. Kuhn, Elliot J. Lefkowitz, Max L. Nibert, Richard Orton, Marilyn J. Roossinck, Sead Sabanadzovic, Matthew B. Sullivan, Curtis A. Suttle, Robert B. Tesh, René A. van der Vlugt, Arvind Varsani & F. Murilo Zerbini The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data

Description: Mammalian body condition is an important individual fitness metric as it affects both survival and reproductive success. The ability to accurately measure condition has key implications for predicting individual and population health, and therefore monitoring the population-level effects of changing environments. No consensus currently exists on the best measure to quantitatively estimate body condition in many species, including cetaceans. Here, two measures of body condition were investigated in the harbor porpoise ( Phocoena phocoena ). First, the most informative morphometric body condition index was identified. The mass/length 2 ratio was the most appropriate morphometric index of 10 indices tested, explaining 50% of the variation in condition in stranded, male porpoises with different causes of death and across age classes ( n  = 291). Mass/length 2 was then used to evaluate a second measure, blubber cortisol concentration, as a metabolic condition marker. Cortisol is the main glucocorticoid hormone involved in the regulation of lipolysis and overall energy balance in mammals, and concentrations could provide information on physiological state. Blubber cortisol concentrations did not significantly vary around the girth ( n  = 20), but there was significant vertical stratification through the blubber depth with highest concentrations in the innermost layer. Concentrations in the dorsal, outermost layer were representative of concentrations through the full blubber depth, showed variation by sex and age class, and were negatively correlated with mass/length 2 . Using this species as a model for live cetaceans from which standard morphometric measurements cannot be taken, but from which blubber biopsy samples are routinely collected, cortisol concentrations in the dorsal, outermost blubber layer could potentially be used as a biomarker of condition in free-ranging animals. There is currently no consensus on the most appropriate body condition index for many species, including cetaceans. Here, mass/length 2 was identified as a robust body condition index for harbor porpoises and used to evaluate blubber cortisol concentration as a novel, physiological marker of condition applicable to free-ranging cetaceans. The ability to measure the condition of free-ranging individuals has important implications for studying both individual and population level health.