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: 31.48). 09/2005; 309(5739):1387-90. DOI: 10.1126/science.1112665
Source: PubMed

ABSTRACT 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, Jul 30, 2015
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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.
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    • "In addition to decomposition of natural organic matter, microorganisms are also capable of catalyzing oxidation and reduction reactions, and thus can influence the biogeochemical cycling of key metals and elements in the environment. It is estimated that in a single gram of a soil, there are *10 9 cells and over 10 6 individual taxa, reflecting the vast functional and taxonomic diversity in soil environments (Curtis and Sloan 2005; Gans et al. 2005). Thus the soil microbial community is one of the most diverse prokaryotic systems yet studied, which can pose technical challenges in detecting and isolating less numerous taxa (Delmont et al. 2011). "
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    ABSTRACT: Biological diagnostic tools are becoming an increasingly important aspect of geoenvironmental problems. Modern geoenvironmental professionals must be able to both understand and exploit biological processes for a variety of applications, ranging from contaminant biodegradation and removal to evaluation and monitoring of environmental quality in and around landfills and landfill cover systems. Advancements in genetics and environmental measurement have yielded a wealth of sophisticated tools to evaluate biological processes in soils, sediments and groundwater. Successful use of these tools requires a keen understanding of the limitations and advantages offered by each. This paper provides an overview of the currently available biological diagnostic tools with an emphasis on their application in geoenvironmental engineering. Limitations and unresolved challenges in successful applications of these tools are also discussed.
    Reviews in Environmental Science and Bio/Technology 06/2015; DOI:10.1007/s11157-014-9358-y · 2.26 Impact Factor
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    • "Soil microbial communities might display the highest level of bacterial diversity of any environment with a single gram reported to contain about a billion cells making up thousands to millions of different taxa (Torsvik et al., 2002; Gans et al., 2005; Roesch et al., 2007). "
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    ABSTRACT: Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.
    Frontiers in Microbiology 05/2015; 6. DOI:10.3389/fmicb.2015.00358 · 3.94 Impact Factor
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