How Our Health Depends on Biodiversity

The eminent Harvard biology Professor Edward O.Wilson once said about ants, “We need them to survive, but they don’t need us at all.” The same, in fact, could be said about countless other insects, bacteria, fungi, plankton, plants, and other organisms. This fundamental truth, however, is largely lost to many of us. Rather, we humans often act as if we are totally independent of Nature, as if our driving thousands of other species to extinction and disrupting the life-giving services they provide will have no effect on us whatsoever. This summary, using concrete examples from our award-winning Oxford University Press book, Sustaining Life: How Human Health Depends on Biodiversity, co-sponsored by the U.N. (CBD Secretariat, UNEP, and UNDP) and the International Union for the Conservation of Nature (IUCN), has been prepared to demonstrate that human beings are an integral, inseparable part of the natural world, and that our health depends ultimately on the health of its species and on the natural functioning of its ecosystems

Climate change and extreme weather events - Implications for food production, plant diseases, and pests

Current and future energy use from burning of fossil fuels and clearing of forests for cultivation can have profound effects on the global environment, agriculture, and the availability of low-cost, high-quality food for humans. Individual farmers and consumers are expected to be affected by changes in global and regional climate. The agricultural sector in both developing and developed areas needs to understand what is at stake and to prepare for the potential for change wisely. Despite tremendous improvements in technology and crop yield potential, food production remains highly dependent on climate, because solar radiation, temperature, and precipitation are the main drivers of crop growth. Plant diseases and pest infestations, as well as the supply of and demand for irrigation water are influenced by climate. For example, in recent decades, the persistent drought in the Sahelian region of Africa has caused continuing deterioration of food production; the 1988 Midwest drought led to a 30% reduction in U.S. corn production and cost taxpayers $3 billion in direct relief payments to farmers and, weather anomalies associated with the 1997-98 El Niño affected agriculture adversely in Nordeste, Brazil and Indonesia. Earlier in the century, the 1930s U.S. Southern Great Plains drought caused some 200,000 farm bankruptcies in the Dust Bowl; yields of wheat and corn were reduced by as much as 50%

Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem

We have constructed a conceptual model of biogeochemical cycles and metabolic and microbial community shifts within a hot spring ecosystem via coordinated analysis of the “Bison Pool” (BP) Environmental Genome and a complementary contextual geochemical dataset of ∼75 geochemical parameters. 2,321 16S rRNA clones and 470 megabases of environmental sequence data were produced from biofilms at five sites along the outflow of BP, an alkaline hot spring in Sentinel Meadow (Lower Geyser Basin) of Yellowstone National Park. This channel acts as a >22 m gradient of decreasing temperature, increasing dissolved oxygen, and changing availability of biologically important chemical species, such as those containing nitrogen and sulfur. Microbial life at BP transitions from a 92°C chemotrophic streamer biofilm community in the BP source pool to a 56°C phototrophic mat community. We improved automated annotation of the BP environmental genomes using BLAST-based Markov clustering. We have also assigned environmental genome sequences to individual microbial community members by complementing traditional homology-based assignment with nucleotide word-usage algorithms, allowing more than 70% of all reads to be assigned to source organisms. This assignment yields high genome coverage in dominant community members, facilitating reconstruction of nearly complete metabolic profiles and in-depth analysis of the relation between geochemical and metabolic changes along the outflow. We show that changes in environmental conditions and energy availability are associated with dramatic shifts in microbial communities and metabolic function. We have also identified an organism constituting a novel phylum in a metabolic “transition” community, located physically between the chemotroph- and phototroph-dominated sites. The complementary analysis of biogeochemical and environmental genomic data from BP has allowed us to build ecosystem-based conceptual models for this hot spring, reconstructing whole metabolic networks in order to illuminate community roles in shaping and responding to geochemical variability

Sustaining life : how human health depends on biodiversity/ Edit.: Eric Chivian M.D.

xxiii, 542 hal.: ill.; 28 cm

MicrobesOnline: an integrated portal for comparative and functional genomics

Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html

The complete genome of the uncultivated bacterium Desulforudis audaxviator from 2.8 km beneath earth's surface

A more complete picture of life on Earth, and even life in the Earth, has recently become possible through the application of environmental genomics. We have obtained the complete genome sequence of a new genus of the Finnicutes, the uncultivated sulfate reducing bacterium Desulforudis audaxviator, by filtering fracture water from a borehole at 2.8 km depth in a South African gold mine. The DNA was sequenced using a combination of Sanger sequencing and 454 pyrosequencing, and asserrlbled into just one genome, indicating the planktonic community is extremely low in diversity. We analyzed the genome of D. audaxviator using the MicrobesOnline annotation pipeline and toolkit (http://www.microbesonline.org), which offers powerful resources for comparative genome analysis, including operon predictions and treebased comparative genome browsing. MicrobesOnline allowed us to compare the D. audaxviator genome with other sequenced members of the Firmicutes in the same clade (primarily Pelotomaculum thennoproprionicum, Desulfotomaculum reducens, Carboxydothennus hydrogenoformans, and Moorella thennoacetica), as well as other known sulfate reducers and thermophilic organisms. D. audaxviator gives a view to the set of tools necessary for what appears to be a self-contained, independent lifestyle deep in the Earth's crust. The genome is not very streamlined, and indicates a motile, endospore forming sulfate reducer with pili that can fix its own nitrogen and carbon. D. audaxviator is an obligate anaerobe, and lacks obvious homologs of many of the traditional 02 tolerance genes, consistent with the low concentration of O2 in the fracture water and its long-term isolation from the surface. D. audaxviator provides a complete genome representative of the Gram-positive bacteria to further our understanding of dissimilatory sulfate reducing bacteria and archaea. Additionally, study of the deep subsurface has offered access to the simplest community yet studied by environmental genomics, perhaps consisting of just a single species that is capable of performing all of the tasks necessary for life