Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil

Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87501, USA.
Science (Impact Factor: 33.61). 09/2005; 309(5739):1387-90. DOI: 10.1126/science.1112665
Source: PubMed


The complexity of soil bacterial communities has thus far confounded effective measurement. However, with improved analytical methods, we show that the abundance distribution and total diversity can be deciphered. Reanalysis of reassociation kinetics for bacterial community DNA from pristine and metal-polluted soils showed that a power law best described the abundance distributions. More than one million distinct genomes occurred in the pristine soil, exceeding previous estimates by two orders of magnitude. Metal pollution reduced diversity more than 99.9%, revealing the highly toxic effect of metal contamination, especially for rare taxa.

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Available from: Murray Wolinsky, Sep 29, 2015
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    • "The authors felt an imminent need for a robust and balanced scientific review that not only summarises the current state of knowledge regarding the subject but also highlights the key concerns that require further research. BIOCHAR AND SOIL BIOLOGY Soils form the most complicated biological system on the surface of earth (Young and Crawford, 2004), containing as many as a million taxa in a 10-g sample (Gans et al., 2005). The structure and function of biological communities within soils is highly complex , with its varied inhabitants categorised into bacteria , fungi, algae, archaea, arthropods, nematodes, protozoa and other invertebrates. "
    Pedosphere 09/2015; 25(5):639-653. · 1.50 Impact Factor
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    • "Soils are known to have higher taxonomic and functional diversity than any other environment ( Whitman et al . , 1998 ) . Earlier estimates suggested that 3 . 8 × 10 3 to 10 7 microbial species are present in a gram of soil ( Curtis et al . , 2002 ; Gans et al . , 2005 ) and 32 phyla have already been detected ( Janssen , 2006 ) . We reason that if one is interested in understanding how soil FIGURE 3 | Unrooted maximum likelihood tree of 750 sequences belonging to Verrucomicrobia 16S rRNA genes recovered from soils :"
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    Frontiers in Microbiology 08/2015; 6:779. DOI:10.3389/fmicb.2015.00779 · 3.99 Impact Factor
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    • "With an estimated total number of 4e6 Â 10 30 cells, prokaryotes are the most diverse and abundant cellular life forms on Earth [190]. For example, 1 g of soil may contain up to 10 9 bacterial cells [190], and mathematical treatment of the data suggests that 10 6 distinct prokaryotic taxa may be present [27] [54] [184]. Prokaryotes are small and undergo a rapid cell cycle coupled with a metabolic versatility that enables them to be key players in the functioning of all ecosystems, even the most extreme ones [190]. "
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    ABSTRACT: Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.
    Research in Microbiology 06/2015; DOI:10.1016/j.resmic.2015.06.001 · 2.71 Impact Factor
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