Search for: All records

ABSTRACT We report the full genome sequence ofHalomonassp. strain M1, isolated from a continental high pH serpentinizing spring in northern California, USA. The 3.7 Mb genome has a G + C content of 54.13%, encodes 3,354 protein-coding genes, and provides insights into the metabolic potential for sulfur oxidation. 

Groundwater-surface water interaction (hyporheic exchange) is critical in numerous hydrogeochemical processes; however, hyporheic exchange is difficult to characterize due to the various spatial (e.g., sedimentary architecture) and temporal (e.g., stage fluctuations) variables that influence it. This interdisciplinary study brings forth novel insights by integrating various methodologies including geophysical surveys, physical and chemical sediment characterization, and water chemistry analysis to explore the interplay of the numerous facets governing hyporheic zone processes within a compound bar deposit. The findings reveal distinct sedimentary facies and geochemical zones within the compound bar, driven by the sedimentary architecture. Cross-bar channel fills are identified as critical structures influencing hydrogeochemical dynamics, acting as baffles to groundwater flow and modulating nutrient transformations. Geophysical imaging and hydrogeochemical analyses highlight the complex interplay between sediment characteristics and subsurface hydraulic connectivity, emphasizing the role of sediment heterogeneity in controlling hyporheic exchange and solute mixing. The study concludes that sediment heterogeneity, particularly the presence of cross-bar channel fills, plays a pivotal role in the hydrogeochemical dynamics of the hyporheic zone. These structures significantly influence hyporheic flow paths, solute residence times, and nutrient cycling, underscoring the necessity to consider the fine-scale sedimentary architecture in models of hyporheic exchange. The findings contribute to a deeper understanding of riverine ecosystem processes, offering insights that can inform management strategies for water quality and ecological integrity. 

ABSTRACT Here, we report the complete genome sequence forRoseinatronobactersp. S2, a sulfur-oxidizing heterotroph isolated from a serpentinizing system in Northern California. The S2 genome is 4.4 Mb and contains 4,570 protein-encoding genes. This organism contains the genes necessary for sulfur species oxidation and complete ethylmalonyl and pentose phosphate pathways. 

Terrestrial serpentinizing systems allow us insight into the realm of alkaliphilic microbial communities driven by geology in a way that is frequently more accessible than their deep subsurface or marine counterparts. However, these systems are also marked by geochemical and microbial community variation due to the interactions of serpentinized fluids with host geology and the surface environment. To separate the transient from the endemic microbes in a hyperalkaline environment, we assessed the Ney Springs terrestrial serpentinizing system microbial community and geochemistry at six time points over the span of a year. Using 16S rRNA gene surveys we observed 93 amplicon sequence variants (ASVs) that were found at every sampling event. This is compared to ~17,000 transient ASVs that were detected only once across the six sampling events. Of the resident community members, 16 of these ASVs were regularly greater than 1% of the community during every sampling period. Additionally, many of these core taxa experienced statistically significant changes in relative abundance with time. Variation in the abundance of some core populations correlated with geochemical variation. For example, members of the Tindallia group, showed a positive correlation with variation in levels of ammonia at the spring. Investigating the metagenome assembled genomes of these microbes revealed evidence of the potential for ammonia generation via Stickland reactions within Tindallia . This observation offers new insight into the origin of high ammonia concentrations (>70 mg/L) seen at this site. Similarly, the abundance of putative sulfur-oxidizing microbes like Thiomicrospira , Halomonas , and a Rhodobacteraceae species could be linked to changes observed in sulfur-oxidation intermediates like tetrathionate and thiosulfate. While these data supports the influence of core microbial community members on a hyperalkaline spring’s geochemistry, there is also evidence that subsurface processes affect geochemistry and may impact community dynamics as well. Though the physiology and ecology of these astrobiologically relevant ecosystems are still being uncovered, this work helps identify a stable microbial community that impacts spring geochemistry in ways not previously observed in serpentinizing ecosystems. 

Extracellular electron transfer (EET), the process that allows microbes to exchange electrons in a redox capacity with solid interfaces such as minerals or electrodes, has been predominantly described in microbes that use iron during respiration. In this work, we characterize the physiology, genome, and electrochemical properties of two obligately heterotrophic marine microbes that were previously isolated from marine sediment cathode enrichments. Phylogenetic analysis of isolate 16S rRNA genes showed two strains, SN11 and FeN1, belonging to the genus Idiomarina. Strain SN11 was found to be nearly identical to I. loihiensis L2-TRT, and strain FeN1 was most closely related to I. maritima 908087T. Each strain had a relatively small genome (~2.8–2.9 MB). Phenotypic similarities among FeN1, SN11, and the studied strains include being Gram-negative, motile, catalase- and oxidase-positive, and rod-shaped. Physiologically, all strains appeared to exclusively use amino acids as a primary carbon source for growth. This was consistent with genomic observations. Each strain contained 17 to 22 proteins with heme-binding motifs. None of these were predicted to be extracellular, although seven were of unknown localization and lacked functional annotation beyond cytochrome. Despite the lack of homology to known EET pathways, both FeN1 and SN11 were capable of sustained electron uptake over time in an electrochemical system linked to respiration. Given the association of these Idiomarina strains with electro-active biofilms in the environment and their lack of autotrophic capabilities, we predict that EET is used exclusively for respiration in these microbes.