Beringian Paleoecology Inferred from Permafrost-Preserved Fungal DNA

ABSTRACT The diversity of fungi in permanently frozen soil from northeastern Siberia was studied by culture-independent PCR amplification of diverse environmental 18S rRNA genes. Elaborate protocols to avoid contamination during drilling, sampling, and amplification were used. A broad diversity of eukaryotic DNA sequences that were 510 bp long, including sequences of various fungi, plants, and invertebrates, could be obtained reproducibly from samples that were up to 300,000 to 400,000 years old. The sequences revealed that ancient fungal communities included a diversity of cold-adapted yeasts, dark-pigmented fungi, plant-parasitic fungi, and lichen mycobionts. DNA traces of tree-associated macrofungi in a modern tundra sample indicated that there was a shift in fungal diversity following the last ice age and supported recent results showing that there was a severe change in the plant composition in northeastern Siberia during this period. Interestingly, DNA sequences with high homology to sequences of coprophilic and keratinophilic fungi indicated that feces, hair, skin, and nails could have been sources of ancient megafauna DNA recently reported to be present in small amounts of Siberian permafrost sediments.

[1]  E. Willerslev,et al.  Isolation of nucleic acids and cultures from fossil ice and permafrost. , 2004, Trends in ecology & evolution.

[2]  C. Wiuf,et al.  Long-term persistence of bacterial DNA , 2004, Current Biology.

[3]  S. Baldauf,et al.  The Deep Roots of Eukaryotes , 2003, Science.

[4]  Carsten Wiuf,et al.  Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments , 2003, Science.

[5]  H. Gregory McDonald,et al.  Phylogeny, diet, and habitat of an extinct ground sloth from Cuchillo Curá, Neuquén Province, southwest Argentina , 2003, Quaternary Research.

[6]  I. Marota,et al.  Ötzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[7]  J. McInerney,et al.  Bacteria and Archaea: Molecular techniques reveal astonishing diversity , 2002 .

[8]  N. Tyler,et al.  Nutritive Value of Terricolous Lichens for Reindeer in Winter , 2002, The Lichenologist.

[9]  B. Shapiro,et al.  Dynamics of Pleistocene Population Extinctions in Beringian Brown Bears , 2002, Science.

[10]  C. Millar,et al.  Rates of Evolution in Ancient DNA from Adélie Penguins , 2002, Science.

[11]  C. Robinson Cold adaptation in Arctic and Antarctic fungi , 2001 .

[12]  N. Ivanova,et al.  Sequences of psychrophilic fungi amplified from glacier-preserved ascolichens , 2000 .

[13]  S. Pääbo,et al.  Nuclear DNA sequences from late Pleistocene megafauna. , 1999, Molecular biology and evolution.

[14]  P. Arctander,et al.  Diversity of Holocene life forms in fossil glacier ice. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[15]  M. Girlanda,et al.  Psychrooligotrophic fungi from Arctic soils of Franz Joseph Land , 1999, Polar Biology.

[16]  G. Weiller Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. , 1998, Molecular biology and evolution.

[17]  K. Egger,et al.  Towards a subordinal classification of the Pezizales (Ascomycota): phylogenetic analyses of SSU rDNA sequences. , 1997 .

[18]  T. Vishnivetskaya,et al.  The deep cold biosphere: facts and hypothesis , 1997 .

[19]  H. Vishniac Biodiversity of yeasts and filamentous microfungi in terrestrial Antarctic ecosystems , 1996, Biodiversity & Conservation.

[20]  S. Pääbo,et al.  DNA damage and DNA sequence retrieval from ancient tissues. , 1996, Nucleic acids research.

[21]  D. Gilichinsky,et al.  Preservation of cell structures in permafrost: a model for exobiology. , 1995, Advances in space research : the official journal of the Committee on Space Research.

[22]  S. Pääbo,et al.  Ancient DNA: Methodological challenges , 1994, Experientia.

[23]  S. Pääbo,et al.  Ancient DNA and the polymerase chain reaction. The emerging field of molecular archaeology. , 1989, The Journal of biological chemistry.

[24]  D. Gilichinsky,et al.  Long-term preservation of microbial ecosystems in permafrost. , 1992, Advances in space research : the official journal of the Committee on Space Research.

[25]  T. White Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics , 1990 .

[26]  Thomas J. White,et al.  PCR protocols: a guide to methods and applications. , 1990 .