Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

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.

Trade-offs between microbiome diversity and productivity in a stratified microbial mat

“…Of these include the comparable microbial mats of Guerrero Negro (Baja California Sur, Mexico), which have historically been of keen interest as spatially stratified, highly diverse model microbial ecosystems (Canfield and Des Marais, 1993;Risatti et al, 1994;Ley et al, 2006). A previous study reported increasing OTU counts with depth over the first 3 mm of the Guerrero Negro mat (Harris et al, 2013). Although depth profiles of productivity were not explicitly measured, higher-species richness presumably corresponded with lower rates of photosynthesis than would be observed at the mat's surface.…”

Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed

“…Strain SCBM T shared only 91.7 % pairwise 16S rRNA gene sequence identity with its closest cultured phylogenetic relative, Desulfarculus baarsii DSM 2075 T , while similarities to other recognized species in the class Deltaproteobacteria were ¡87 %. The next most closely related, described relatives of strain SCBM T were Desulfatibacillum alkenivorans AK-01 (87 % similarity), Desulfomonile tiedjei DSM 6799 T (87 %), Desulfatibacillum aliphaticivorans CV2803 T (87 %), Desulfovibrio cavernae H1M (87 %), Desulfobacterium anilini Ani1 T (86 %), Desulfococcus oleovorans Hxd3 (86 %), Desulfosalsimonas propionicica PropA T (86 %) and Desulfatitalea tepidiphila (Harris et al, 2013); 65-OC-8 (93 %; HE797781), retrieved from an anoxic brackish photosynthetic biofilm at Berre Pond, France; UASB-TL19 (93 %; AF254400), recovered from a 4-methylbenzoatedegrading methanogenic consortium (Wu et al, 2001);and 624H2B-13, 624H2B-24 and 624H2B-36 (93 %;KC408551, KC408562 and KC408572, respectively), retrieved from coalbed water from Qinshui Basin, China. We suggest that the unique coal environment from which our isolate was retrieved may have enriched microorganisms such as strain SCBM T and that such bacteria may be important members of the microbial community involved in anaerobic carbon metabolism in coal beds.…”

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

“…A current synthesis of the available data suggests that JS1 is a characteristic denizen of subseafloor environments, and is particularly abundant in sediments associated with methane hydrates and hydrocarbon seeps, and on continental margins and shelves (Inagaki et al, 2006;Orcutt et al, 2011;Parkes et al, 2014). Sequences related to JS1 have also been detected in environments such as petroleum reservoirs (Pham et al, 2009;Kobayashi et al, 2012), hypersaline microbial mats (Harris et al, 2013), and landfill leachates (Liu et al, 2011). The phylogenetic relationships between OP9, JS1 and other bacterial phyla have not been fully resolved (McDonald et al, 2012), and to date, no axenic cultures have been reported for either of these lineages, although enrichment cultures containing JS1 have been successfully obtained (Webster et al, 2011).…”