Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments

Comparative Genomic Analysis of Pathogenic and Probiotic Enterococcus faecalis Isolates, and Their Transcriptional Responses to Growth in Human Urine

Urinary tract infection (UTI) is the most common infection caused by enterococci, and Enterococcus faecalis accounts for the majority of enterococcal infections. Although a number of virulence related traits have been established, no comprehensive genomic or transcriptomic studies have been conducted to investigate how to distinguish pathogenic from non-pathogenic E. faecalis in their ability to cause UTI. In order to identify potential genetic traits or gene regulatory features that distinguish pathogenic from non-pathogenic E. faecalis with respect to UTI, we have performed comparative genomic analysis, and investigated growth capacity and transcriptome profiling in human urine in vitro. Six strains of different origins were cultivated and all grew readily in human urine. The three strains chosen for transcriptional analysis showed an overall similar response with respect to energy and nitrogen metabolism, stress mechanism, cell envelope modifications, and trace metal acquisition. Our results suggest that citrate and aspartate are significant for growth of E. faecalis in human urine, and manganese appear to be a limiting factor. The majority of virulence factors were either not differentially regulated or down-regulated. Notably, a significant up-regulation of genes involved in biofilm formation was observed. Strains from different origins have similar capacity to grow in human urine. The overall similar transcriptional responses between the two pathogenic and the probiotic strain suggest that the pathogenic potential of a certain E. faecalis strain may to a great extent be determined by presence of fitness and virulence factors, rather than the level of expression of such traits

The terrestrial and freshwater invertebrate biodiversity of the archipelagoes of the Barents Sea; Svalbard, Franz Josef Land and Novaya Zemlya

Arctic terrestrial ecosystems are generally considered to be species poor, fragile and often isolated. Nonetheless, their intricate complexity, especially that of the invertebrate component, is beginning to emerge. Attention has become focused on the Arctic both due to the importance of this rapidly changing region for the Earth and also the inherent interest of an extreme and unique environment. The three archipelagoes considered here, Svalbard, Franz Josef Land and Novaya Zemlya, delineate the Barents Sea to the west, north and east. This is a region of convergence for Palearctic and Nearctic faunas re-colonising the Arctic following the retreat of the ice after the Last Glacial Maximum (LGM). Despite the harsh Arctic environment and the short period since deglaciation, the archipelagoes of the Barents Sea are inhabited by diverse invertebrate communities. But there is an obvious imbalance in our knowledge of many taxa of each archipelago, and in our knowledge of many taxa. Research effort in Svalbard is increasing rapidly while there are still few reports, particularly in the western literature, from Franz Josef Land and Novaya Zemlya. Nevertheless, there appears to be a surprising degree of dissimilarity between the invertebrate faunas, possibly reflecting colonization history. We provide a baseline synthesis of the terrestrial and freshwater invertebrate fauna of the Barents Sea archipelagoes, highlight the taxa present, the characteristic elements of fauna and the complexity of their biogeography. In doing so, we provide a background from which to assess responses to environmental change for a region under increasing international attention from scientific, industrial and political communities as well as non-governmental organizations and the general public

The arthropod community of Scots pine (Pinus sylvestris L.) canopies in Norway

We summarise the findings of arthropods collected by fogging the canopy of 24 pine trees in two sites in Eastern and Western Norway. From the samples, taken in 1998 and in 1999, almost 30,000 specimens were determined to 512 species, with Diptera being most species rich (210 species), followed by Coleoptera (76 species) and Araneae (49 species). Of the 96 new species records, nine were new to science (5 Diptera and 4 Oribatida), two were new to the European, three to the Scandinavian and 82 to the Norwegian faunas. The paper demonstrates the need for detailed faunistical inventories of European forests