Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-07-26

AUTHORS

J Kirk Harris, J Gregory Caporaso, Jeffrey J Walker, John R Spear, Nicholas J Gold, Charles E Robertson, Philip Hugenholtz, Julia Goodrich, Daniel McDonald, Dan Knights, Paul Marshall, Henry Tufo, Rob Knight, Norman R Pace

ABSTRACT

The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only ∼1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional ∼119,000 nearly full-length sequences and 28,000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life. More... »

PAGES

50-60

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ismej.2012.79

DOI

http://dx.doi.org/10.1038/ismej.2012.79

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1021240493

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22832344


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26 schema:description The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only ∼1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional ∼119,000 nearly full-length sequences and 28,000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life.
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34 California Sur
35 Culture-independent rRNA community
36 GN diversity
37 GN mat
38 Guerrero Negro
39 Guerrero Negro hypersaline microbial mat
40 Mexico
41 Negro
42 Negro hypersaline microbial mat
43 Phylogenetic stratigraphy
44 Previous shotgun metagenomic data
45 Sanger
46 Sur
47 abundance
48 bacteria
49 bacterial phylogenetic domain
50 bacterial phylogenetic tree
51 community
52 comprehensive survey
53 conclusion
54 congruent
55 coverage
56 cyanobacteria
57 data
58 depth
59 depth profiles
60 diverse environments
61 diversity
62 domain
63 environment
64 example
65 family-genus levels
66 full-length sequences
67 gene sequences
68 geochemical gradients
69 gradient
70 group
71 hypersaline microbial mats
72 known sequences
73 levels
74 life
75 lineages
76 long sequences
77 lower level taxa
78 lower taxonomic levels
79 mats
80 metagenome properties
81 metagenomic data
82 microbial mats
83 molecular survey
84 new phylogenetic diversity
85 new phylum-level groups
86 new sequences populate parts
87 novel lineage
88 nucleotide 454 reads
89 operational taxonomic units
90 part
91 patterns
92 phylogenetic diversity
93 phylogenetic domains
94 phylogenetic tree
95 phylum-level groups
96 populate parts
97 preliminary molecular survey
98 profile
99 properties
100 rRNA community
101 rRNA gene sequences
102 rRNA tree
103 reads
104 reference sequence
105 region
106 relevant regions
107 resolution
108 same depth profile
109 same stratified pattern
110 sequence
111 sequences populate parts
112 sequencing technologies
113 shotgun metagenomic data
114 simple environment
115 small subunit rRNA gene sequences
116 stratified pattern
117 stratigraphy
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119 sulfate-reducing bacteria
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126 technology
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