Microbial Community Structure and Functional Potential Along a Hypersaline Gradient

Abstract

Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.

Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India

“…In general, sediments exhibited a greater diversity in terms of OTU to sequence ratio compared to brine. This is in support of the view that sediments support a broad range of microorganisms because of the availability of a wide range of organic nutrients and hypersaline soils are no exception to this pattern (Sander and Kalff, 1993;Kimbrel et al, 2018). Though the statistical analysis indicated that the taxonomic composition between the brine and sediments during different salt production phases are similar, we acknowledge the low statistical power involved in the analysis due to the composite sampling approach resulting in single sample per sampling location.…”

“…Though the occurrence of halophilic archaea in the low salinity environments has been documented before, the large number of sequences observed in the salterns of Siridao is unprecedented. Recently, Kimbrel et al (2018) have shown that at 7.5% salinity, there were about 20% and 18% of archaeal sequences in brine and sediments obtained from a solar saltern respectively. Similarly, Elshahed et al (2004) have reported the isolation of halophilic archaeal clones belonging to Halogeometricum, Natronomonas, Halococcus, and Haloferax from low salinity (0.7 -1%) brine and sediment samples.…”

“…In our study, we could also detect a significant proportion of Archaea at intermediate salinities albeit at a higher rate than previously reported ranging between 55% and 85% in brine and sediments, respectively. As the saltern compartments are interconnected and the prevalent Archaea in RP could provide a microbial seed bank, microorganisms could be transported from RP to CP via EP through a constant influx of brine (Lennon and Jones, 2011;Kimbrel et al, 2018).This could provide Archaea a head start over Bacteria to rapidly colonize and dominate in EP and CP.…”

Comparative Genomics of Two New HF1-like Haloviruses

“…depositum Y78, is flanked by two annotated tRNA-thr genes (FGM06_RS03355 and FGM06_RS03870), and has an integrase gene close to one end (FGM06_RS03360). The second provirus we designated ELPmg-prov1, and was described as part of a metagenomic study of the Eden Landing Ponds, San Francisco, USA [19]. It is 77.7 kb long, has an integrase gene near one end, and has recombined into a tRNA-Thr gene present on an 82.4 kb contig.…”

Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences

“…Eiler et al (2014) characterized microbial communities using metagenomic data for various freshwater samples (lakes in the USA and Sweden) and marine locations. For hypersaline settings, we used metagenomic data from the Santa Pola salterns in Spain (Ghai et al, 2011;Fernandez et al, 2013), natural soda lakes of the Kulunda Steppe in Serbia (Vavourakis et al, 2016), and South Bay salterns in California, USA (Kimbrel et al, 2018). The compositional analysis reveals a relatively low n H2O of proteins inferred from the marine metagenomes compared to freshwater samples in the Eiler et al dataset (Fig.…”