Toward a Census of Bacteria in Soil

By Patrick D. Schloss, Jo Handelsman. PLoS Comput. Biol., 2006

466 citations recorded by the source corpus.

For more than a century, microbiologists have sought to determine the species richness of bacteria in soil, but the extreme complexity and unknown structure of soil microbial communities have obscured the answer. We developed a statistical model that makes the problem of estimating richness statistically accessible by evaluating the characteristics of samples drawn from simulated communities with parametric community distributions. We identified simulated communities with rank-abundance distributions that followed a truncated lognormal distribution whose samples resembled the structure of 16S rRNA gene sequence collections made using Alaskan and Minnesotan soils. The simulated communities constructed based on the distribution of 16S rRNA gene sequences sampled from the Alaskan and Minnesotan soils had a richness of 5,000 and 2,000 operational taxonomic units (OTUs), respectively, where an OTU represents a collection of sequences not more than 3% distant from each other. To sample each of these OTUs in the Alaskan 16S rRNA gene library at least twice, 480,000 sequences would be required; however, to estimate the richness of the simulated communities using nonparametric richness estimators would require only 18,000 sequences. Quantifying the richness of complex environments such as soil is an important step in building an ecological framework. We have shown that generating sufficient sequence data to do so requires less sequencing effort than completely sequencing a bacterial genome.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/528368f4c25facd9a8b6352da95365861a441dd0

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Citations in the corpus

A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies (2009, background): “16S rRNA gene sequences ranging in length between 60 and 1500 bp are generated to address interesting ecological questions”
Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets (2013, unknown): “The simplest approach is to define species based on a percentage cut-off rule, such as the 1% or 3% rule used to delimit bacterial species from 16S rDNA sequences (Schloss and Handelsman 2006) or cytochrome oxidase I for insect species (Brower 1994).”
Ecology and exploration of the rare biosphere (2015, background): “Our understanding of the metabolic and genomic potential of rare and uncharacterized organisms is lim ited by technical challenges: most notably, the extent of environmental metagenomes 127 and the estimated sequencing coverage required to access rare organ isms in some habitats 128 , 129 .”
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing (2008, background): “being explored across a great range of natural environments: in soils [3-5], air [6] and seas [7-10], on plants [11] and in animals [12,13] and in extreme environments such as the arctic [14], deep-sea vents[15], uranium-contaminated soil [16], and waste-water treatment discharge [17].”
Interactions between Diatoms and Bacteria (2012, background): “Microbial densities in the oceans (10(5) to 10(6) cells per gram of seawater) are orders of magnitude less than those found in sediments (10(8) cells/ g), humans (10(14) cells/g), or soil (10(9) cells/g) (157, 159, 185).”
Microbial Biogeography: Patterns in Microbial Diversity across Space and Time (2008, unknown): “We can model the taxon-abundance distribution of microbial communities using a variety of mathematical functions, including types of lognormal, logarithmic, or power-law functions (Angly et al., 2005; Curtis et al., 2002; Dunbar et al., 2002; Fierer et al., In Press; Hong et al., 2006; Schloss and H”
Assembling metagenomes, one community at a time (2017, background): “Estimates of the number of microbial species per gram of soil still vary substantially, with values ranging from 2000 [40] to more than 830,000 [37].”
Modeling Soil Processes: Review, Key Challenges, and New Perspectives (2016, background): “Even at very small scales, many thousands to millions of distinct genotypes (or operational taxonomic units, OTU) may inhabit a single gram of soil (Torsvik et al., 1990; Curtis et al., 2002; Schloss and Handelsman, 2006; Or et al., 2007).”
Pyrosequencing enumerates and contrasts soil microbial diversity (2007, methodology): “For example, for the Brazil data, we obtained separate rarefaction, ACE and Chao1 estimates for sample sizes of 500, 10 000, 15 000, 20 000, 25 000 and 26 140 sequences.”
Antibiotic resistance in the environment: a link to the clinic? (2010, background): “Schloss and Handelsmann [10] have shown that in an Alaskan soil sample, that 5.8% of the bacteria are actinobacteria.”