Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation

Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them

Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at cáhuil lagoon, chile.

Cáhuil Lagoon in central Chile harbors distinct microbial communities in various solar salterns that are arranged as interconnected ponds with increasing salt concentrations. Here, we report the metagenome of the 3.0- to 0.2-µm fraction of the microbial community present in a crystallizer pond with 34% salinity

The Smallest Known Genomes of Multicellular and Toxic Cyanobacteria: Comparison, Minimal Gene Sets for Linked Traits and the Evolutionary Implications

Cyanobacterial morphology is diverse, ranging from unicellular spheres or rods to multicellular structures such as colonies and filaments. Multicellular species represent an evolutionary strategy to differentiate and compartmentalize certain metabolic functions for reproduction and nitrogen (N2) fixation into specialized cell types (e.g. akinetes, heterocysts and diazocytes). Only a few filamentous, differentiated cyanobacterial species, with genome sizes over 5 Mb, have been sequenced. We sequenced the genomes of two strains of closely related filamentous cyanobacterial species to yield further insights into the molecular basis of the traits of N2 fixation, filament formation and cell differentiation. Cylindrospermopsis raciborskii CS-505 is a cylindrospermopsin-producing strain from Australia, whereas Raphidiopsis brookii D9 from Brazil synthesizes neurotoxins associated with paralytic shellfish poisoning (PSP). Despite their different morphology, toxin composition and disjunct geographical distribution, these strains form a monophyletic group. With genome sizes of approximately 3.9 (CS-505) and 3.2 (D9) Mb, these are the smallest genomes described for free-living filamentous cyanobacteria. We observed remarkable gene order conservation (synteny) between these genomes despite the difference in repetitive element content, which accounts for most of the genome size difference between them. We show here that the strains share a specific set of 2539 genes with >90% average nucleotide identity. The fact that the CS-505 and D9 genomes are small and streamlined compared to those of other filamentous cyanobacterial species and the lack of the ability for heterocyst formation in strain D9 allowed us to define a core set of genes responsible for each trait in filamentous species. We presume that in strain D9 the ability to form proper heterocysts was secondarily lost together with N2 fixation capacity. Further comparisons to all available cyanobacterial genomes covering almost the entire evolutionary branch revealed a common minimal gene set for each of these cyanobacterial traits

Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a Single Extrachromosomal Element.

Cylindrospermopsis raciborskii is a freshwater cyanobacterium producing bloom events and toxicity in drinking water source reservoirs. We present the first genome sequence for C. raciborskii CS505 (Australia), containing one 4.1-Mbp chromosome and one 110-Kbp plasmid having G+C contents of 40.3% (3933 genes) and 39.3% (111 genes), respectively

Table_2_Metaomics unveils the contribution of alteromonas bacteria to carbon cycling in marine oxygen minimum zones.xlsx

Gammaproteobacteria of the genus Alteromonas are prominent members of pelagic marine microbial communities, playing critical roles in the aerobic degradation of particulate organic matter. Comparative genomic studies of these microorganisms have mainly focused on the metabolic and genomic plasticity of strains isolated primarily from oxygenated environments. In this study, we show that Alteromonas significantly contribute to marine microbial communities from suboxic waters ([O2] < 5 uM) in both the free-living (FL) and particle-attached (PA) fractions, but considerably decrease in abundance in the anoxic waters. The highest proportion of Alteromonas transcripts was found within the secondary fluorescence maximum (SFM) of Oxygen Minimum Zones (OMZs). This metatranscriptomic information suggests an in situ coupling of Alteromonas iron (Fe) and carbon metabolisms, and a relevant role of the glyoxylate cycle across the different layers of the OMZs. This study demonstrates that Alteromonas is an abundant and active member of the OMZ microbial communities, with a potentially significant impact on the carbon cycling in these ecosystems. These results provide valuable environmental evidence to support previous culture-based studies assessing the physiology and ecology of these ubiquitous marine heterotrophs under low-oxygen conditions.</p

Table_3_Metaomics unveils the contribution of alteromonas bacteria to carbon cycling in marine oxygen minimum zones.xlsx

Gammaproteobacteria of the genus Alteromonas are prominent members of pelagic marine microbial communities, playing critical roles in the aerobic degradation of particulate organic matter. Comparative genomic studies of these microorganisms have mainly focused on the metabolic and genomic plasticity of strains isolated primarily from oxygenated environments. In this study, we show that Alteromonas significantly contribute to marine microbial communities from suboxic waters ([O2] < 5 uM) in both the free-living (FL) and particle-attached (PA) fractions, but considerably decrease in abundance in the anoxic waters. The highest proportion of Alteromonas transcripts was found within the secondary fluorescence maximum (SFM) of Oxygen Minimum Zones (OMZs). This metatranscriptomic information suggests an in situ coupling of Alteromonas iron (Fe) and carbon metabolisms, and a relevant role of the glyoxylate cycle across the different layers of the OMZs. This study demonstrates that Alteromonas is an abundant and active member of the OMZ microbial communities, with a potentially significant impact on the carbon cycling in these ecosystems. These results provide valuable environmental evidence to support previous culture-based studies assessing the physiology and ecology of these ubiquitous marine heterotrophs under low-oxygen conditions.</p

DataSheet_1_Metaomics unveils the contribution of alteromonas bacteria to carbon cycling in marine oxygen minimum zones.pdf

Gammaproteobacteria of the genus Alteromonas are prominent members of pelagic marine microbial communities, playing critical roles in the aerobic degradation of particulate organic matter. Comparative genomic studies of these microorganisms have mainly focused on the metabolic and genomic plasticity of strains isolated primarily from oxygenated environments. In this study, we show that Alteromonas significantly contribute to marine microbial communities from suboxic waters ([O2] < 5 uM) in both the free-living (FL) and particle-attached (PA) fractions, but considerably decrease in abundance in the anoxic waters. The highest proportion of Alteromonas transcripts was found within the secondary fluorescence maximum (SFM) of Oxygen Minimum Zones (OMZs). This metatranscriptomic information suggests an in situ coupling of Alteromonas iron (Fe) and carbon metabolisms, and a relevant role of the glyoxylate cycle across the different layers of the OMZs. This study demonstrates that Alteromonas is an abundant and active member of the OMZ microbial communities, with a potentially significant impact on the carbon cycling in these ecosystems. These results provide valuable environmental evidence to support previous culture-based studies assessing the physiology and ecology of these ubiquitous marine heterotrophs under low-oxygen conditions.</p