Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments

Abstract

Studies of hypersaline ecosystems often yield novel organisms and contribute to our understanding of extreme environments. Soils and sediments from La Sal del Rey, a previously uncharacterized, hypersaline lake located in southern Texas, USA, were surveyed to characterize the structure and diversity of their microbial communities. Samples were collected along a transect that spanned vegetated uplands, exposed lakebed sediments, and water-logged locations, capturing a wide range of environments and physical and chemical gradients. Community quantitative PCR (qPCR) was used in combination with tag-encoded pyrosequencing, 16S rRNA gene cloning, and Sanger sequencing to characterize the lake's soil and sediment microbial communities. Further, we used multivariate statistics to identify the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa, and sharing significant correlations with site water content, phosphorus and total organic carbon concentrations, and pH. Some individual populations, especially of Archaea, also correlated with sodium concentration and electrical conductivity salinity. Across the transect, Bacteria were numerically dominant relative to Archaea, and among them, three phyla-the Proteobacteria, Bacteroidetes, and Firmicutes-accounted for the majority of taxa detected. Although these taxa were detected with similar abundances to those described in other hypersaline ecosystems, the greater depth of sequencing achieved here resulted in the detection of taxa not described previously in hypersaline sediments. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of highthroughput sequencing in the study of complex ecosystems.

A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data

“…Module 1 shows an association between coral samples and photosystem-related pathways, unsurprising given that corals are high-light environments where microbial photosynthesis is common. Module 3 shows an association between high-salinity samples and archaeal pathways, consistent with prior work showing archaea associated with high-salinity environments (Hollister et al 2010). Module 2 shows a larger group of specific pathways, but these are less specific than those associated with the two smaller modules-many of them overlap the samples associated with these modules.…”

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

“…This indicates that biogeochemical function can be enhanced by species adaptation to local conditions. Indeed, a plethora of literature demonstrates that environmental features such as pH [25], nutrients [51], and salinity [26,27] impact microbial community structure and biogeochemical function, and our results indicate that the linkage between community structure and function is due to microbial adaptation to local conditions. Our results also indicate that when immigrating microorganisms are derived from environments that differ from the receiving community (e.g., dispersal across steep geochemical gradients), biogeochemical function may be suppressed.…”

Reproducibility and quantitation of amplicon sequencing-based detection

“…Therefore, about half of the available information is not used (Acosta-Martinez et al, 2008;Hollister et al, 2010). As demonstrated in this study, combining sequences from both forward and reverse primers alleviates the problem of random sampling because it doubles the sampling effort.…”