Microbial communities and processes in Arctic permafrost environments

In polar regions, huge layers of frozen ground, termed permafrost, are formed. Permafrost covers more than 25 % of the land surface and significant parts of the coastal sea shelfs. Its habitats are controlled by extreme climate and terrain conditions. Particularly, the seasonal freezing and thawing in the upper active layer of permafrost leads to distinct gradients in temperature and geochemistry. Microorganisms in permafrost environments have to survive extremely cold temperatures, freeze-thaw cycles, desiccation and starvation under long-lasting background radiation over geological time scales. Although the biology of permafrost microorganisms remains relatively unexplored, recent findings show that microbial communities in this extreme environment are composed by members of all three domains of life (Archaea, Bacteria, Eukarya), with a total biomass comparable to temperate soil ecosystems. This chapter describes the environmental conditions of permafrost and reviews recent studies on microbial processes and diversity in permafrost-affected soils as well as the role and significance of microbial communities with respect to global biogeochemical cycles

Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium

The genera Exiguobacterium and Psychrobacter have been frequently detected in and isolated from polar permafrost and ice. These two genera have members that can grow at temperatures as low as -5 and -10 degrees C, respectively. We used quantitative PCR (Q-PCR) to quantify members of these genera in 54 soil or sediment samples from polar, temperate and tropical environments to determine to what extent they are selected by cold environments. These results were further analyzed by multiple linear regression to identify the most relevant environmental factors corresponding to their distribution. Exiguobacterium was detected in all three climatic zones at similar densities, but was patchier in the temperate and tropical samples. Psychrobacter was present in almost all polar samples, was at highest densities in Antarctica sediment samples, but was in very low densities and infrequently detected in temperate and tropical soils. Clone libraries, specific for the 16S rRNA gene for each genus, were constructed from a sample from each climatic region. The clone libraries were analyzed for alpha and beta diversities, as well as for variation in population structure by using analysis of molecular variance. Results confirm that both genera were found in all three climatic zones; however, Psychrobacter populations seemed to be much more diverse than Exiguobacterium in all three climatic zones. Furthermore, Psychrobacter populations from Antarctica are different from those in Michigan and Puerto Rico, which are similar to each other. The ISME Journal (2009) 3, 658-665; doi: 10.1038/ismej.2009.25; published online 26 March 2009NASA[NCC2-1274]NASANSFNSFCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Molecular Identification of Bacteria by Total Sequence Screening: Determining the Cause of Death in Ancient Human Subjects

Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17th to the 19th century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity $95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17th century to the early 18th century