Expression patterns of elemental cycling genes in the Amazon River Plume.
ISME J
; 11(8): 1852-1864, 2017 08.
Article
in En
| MEDLINE
| ID: mdl-28387773
ABSTRACT
Metatranscriptomics and metagenomics data sets benchmarked with internal standards were used to characterize the expression patterns for biogeochemically relevant bacterial and archaeal genes mediating carbon, nitrogen, phosphorus and sulfur uptake and metabolism through the salinity gradient of the Amazon River Plume. The genes were identified in 48 metatranscriptomic and metagenomic data sets summing to >500 million quality-controlled reads from six locations in the plume ecosystem. The ratio of transcripts per gene copy (a direct measure of expression made possible by internal standard additions) showed that the free-living bacteria and archaea exhibited only small changes in the expression levels of biogeochemically relevant genes through the salinity and nutrient zones of the plume. In contrast, the expression levels of genes in particle-associated cells varied over orders of magnitude among the stations, with the largest differences measured for genes mediating aspects of nitrogen cycling (nifH, amtB and amoA) and phosphorus acquisition (pstC, phoX and phoU). Taxa varied in their baseline gene expression levels and extent of regulation, and most of the spatial variation in the expression level could be attributed to changes in gene regulation after removing the effect of shifting taxonomic composition. We hypothesize that changes in microbial element cycling along the Amazon River Plume are largely driven by shifting activities of particle-associated cells, with most activities peaking in the mesohaline regions where N2 fixation rates are elevated.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Bacteria
/
Archaea
/
Rivers
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Metagenomics
Language:
En
Journal:
ISME J
Journal subject:
MICROBIOLOGIA
/
SAUDE AMBIENTAL
Year:
2017
Document type:
Article
Affiliation country: