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Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR - ISME J (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, CO, USA.

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.

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Abundance of some prominent phyla and taxonomic subgroups by depth in the mat. (a) Cyanobacteria, (b) Bacteroidetes, (c) Proteobacteria, (d) Chloroflexi, (e) Planctomycetes, (f) Spirochetes, (g) and (h) other low-abundance phyla.
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fig2: Abundance of some prominent phyla and taxonomic subgroups by depth in the mat. (a) Cyanobacteria, (b) Bacteroidetes, (c) Proteobacteria, (d) Chloroflexi, (e) Planctomycetes, (f) Spirochetes, (g) and (h) other low-abundance phyla.

Mentions: There are many possible correlations between the depths of different phylotypes in the mat and physiological attributes of known, albeit distant relatives of the GN microbes. Figure 2 illustrates the distribution of some of the most abundant (>5% overall) subphylum groups and a few of the more rare phylum-level groups of sequences. The upper ∼5 mm, which includes the photic zone and oxic/sulfide boundary (zones A and B in Figure 1), clearly demarcates the main gradient of variation. All the groups of cyanobacterial sequences (Figure 2a), for instance, are highly enriched, ∼35% of total, in the upper few millimeters and diminish drastically below that. We note that rRNA gene abundance does not translate directly into cellular abundance because of variable gene contents, growth rates, and so on. Subgroups of other phyla, for instance Bacteroidetes or Proteobacteria (Figures 2b and c), are abundant in both zones and so consist of more physiologically cosmopolitan organisms than the obligately photosynthetic Cyanobacteria. Many of the representatives of Bacteroidetes seen deeper in the mat have relatives among human fecal bacteria, consistent with the expected fermentative nature of the mat physiology below the photic zone. The persistence of Delta-proteobacteria throughout the deep mat (Figure 2c) including relatives of organisms known for hydrogen metabolism and sulfate reduction, also is consistent with a fermentative environment deep in the mat. Many groups with unknown physiological properties are restricted to the anoxic portion of the mat (for example, Chloroflexi (Figure 2d), Planctomycetes (Figure 2e)). Although the deeper mat seems more uniform in composition than the upper portion, some stratification is seen even at the phylum level, including candidate phyla with abundance peaks at various positions in the lower portion of the mat (Figures 2g and h). These gradients of variation deep in the mat may represent unidentified biochemical gradients or intrinsic patchiness in the organismal structure of the mat. Overall, however, the deeper portion of the mat, >10 mm, is more homogeneous in composition than the upper few millimeters.


Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR - ISME J (2012)

Abundance of some prominent phyla and taxonomic subgroups by depth in the mat. (a) Cyanobacteria, (b) Bacteroidetes, (c) Proteobacteria, (d) Chloroflexi, (e) Planctomycetes, (f) Spirochetes, (g) and (h) other low-abundance phyla.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3526174&req=5

fig2: Abundance of some prominent phyla and taxonomic subgroups by depth in the mat. (a) Cyanobacteria, (b) Bacteroidetes, (c) Proteobacteria, (d) Chloroflexi, (e) Planctomycetes, (f) Spirochetes, (g) and (h) other low-abundance phyla.
Mentions: There are many possible correlations between the depths of different phylotypes in the mat and physiological attributes of known, albeit distant relatives of the GN microbes. Figure 2 illustrates the distribution of some of the most abundant (>5% overall) subphylum groups and a few of the more rare phylum-level groups of sequences. The upper ∼5 mm, which includes the photic zone and oxic/sulfide boundary (zones A and B in Figure 1), clearly demarcates the main gradient of variation. All the groups of cyanobacterial sequences (Figure 2a), for instance, are highly enriched, ∼35% of total, in the upper few millimeters and diminish drastically below that. We note that rRNA gene abundance does not translate directly into cellular abundance because of variable gene contents, growth rates, and so on. Subgroups of other phyla, for instance Bacteroidetes or Proteobacteria (Figures 2b and c), are abundant in both zones and so consist of more physiologically cosmopolitan organisms than the obligately photosynthetic Cyanobacteria. Many of the representatives of Bacteroidetes seen deeper in the mat have relatives among human fecal bacteria, consistent with the expected fermentative nature of the mat physiology below the photic zone. The persistence of Delta-proteobacteria throughout the deep mat (Figure 2c) including relatives of organisms known for hydrogen metabolism and sulfate reduction, also is consistent with a fermentative environment deep in the mat. Many groups with unknown physiological properties are restricted to the anoxic portion of the mat (for example, Chloroflexi (Figure 2d), Planctomycetes (Figure 2e)). Although the deeper mat seems more uniform in composition than the upper portion, some stratification is seen even at the phylum level, including candidate phyla with abundance peaks at various positions in the lower portion of the mat (Figures 2g and h). These gradients of variation deep in the mat may represent unidentified biochemical gradients or intrinsic patchiness in the organismal structure of the mat. Overall, however, the deeper portion of the mat, >10 mm, is more homogeneous in composition than the upper few millimeters.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, CO, USA.

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.

Show MeSH
Related in: MedlinePlus