Community structure and metabolism through reconstruction of microbial genomes from the environment View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2004-02-01

AUTHORS

Gene W. Tyson, Jarrod Chapman, Philip Hugenholtz, Eric E. Allen, Rachna J. Ram, Paul M. Richardson, Victor V. Solovyev, Edward M. Rubin, Daniel S. Rokhsar, Jillian F. Banfield

ABSTRACT

Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment. More... »

PAGES

37-43

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nature02340

DOI

http://dx.doi.org/10.1038/nature02340

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1023089166

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/14961025


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51 community
52 community structure
53 complement
54 complete genome
55 composites
56 deletion
57 different individuals
58 ecosystems
59 energy generation
60 environment
61 existence
62 extreme environments
63 fixation
64 form
65 frequency
66 functioning
67 gene complement
68 gene insertion
69 generation
70 genome
71 genomic rearrangements
72 group II
73 heterogeneity
74 homologous recombination
75 individuals
76 insertion
77 insights
78 large population
79 levels
80 low-abundance variants
81 metabolism
82 microbial communities
83 microbial genomes
84 microorganisms
85 mosaic genomes
86 most microorganisms
87 natural systems
88 nitrogen fixation
89 nucleotide polymorphisms
90 number
91 organisms
92 partial recovery
93 pathway
94 polymorphism
95 population
96 predominant form
97 random shotgun sequencing
98 rearrangement
99 recombination
100 reconstruction
101 recovery
102 role
103 sequence
104 sequencing
105 shotgun sequencing
106 single nucleotide polymorphisms
107 small number
108 species populations
109 strain levels
110 strains
111 strategies
112 structure
113 survival strategies
114 system
115 type II
116 variants
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