Correlation between viral production and carbon mineralization under nitrate-reducing conditions in aquifer sediment

Abstract

A variety of microbially mediated metabolic pathways impact biogeochemical cycling in terrestrial subsurface environments. However, the role that viruses have in influencing microbial mortality and microbial community structure is poorly understood. Here we investigated the production of viruses and change in microbial community structure within shallow alluvial aquifer sediment slurries amended with 13 C-labeled acetate and nitrate. Biostimulation resulted in production of viruses concurrent with acetate oxidation, 13 CO 2 production and nitrate reduction. Interestingly, change in viral abundance was positively correlated to acetate consumption (r 2 ¼ 0.6252, Po0.05) and 13 CO 2 production (r 2 ¼ 0.6572, Po0.05); whereas change in cell abundance was not correlated to acetate consumption or 13 CO 2 production. Viral-mediated cell lysis has implications for microbial community structure. Betaproteobacteria predominated microbial community composition (62% of paired-end reads) upon inoculation but decreased in relative abundance and was negatively correlated to changes in viral abundance (r 2 ¼ 0.5036, Po0.05). As members of the Betaproteobacteria decreased, Gammaproteobacteria, specifically Pseudomonas spp., increased in relative abundance (82% of paired-end reads) and was positively correlated with the change in viral abundance (r 2 ¼ 0.5368, Po0.05). A nitrate-reducing bacterium, Pseudomonas sp. strain Alda10, was isolated from these sediments and produced viral-like particles with a filamentous morphology that did not result in cell lysis. Together, these results indicate that viruses are linked to carbon biogeochemistry and community structure in terrestrial subsurface sediments. The subsequent cell lysis has the potential to alter available carbon pools in subsurface environments, additionally controlling microbial community structure from the bottom-up.

Deciphering the virus‐to‐prokaryote ratio (VPR): insights into virus–host relationships in a variety of ecosystems

“…Initially, archaeal communities were thought to be typical of (or limited to) extreme environments; reports on the omnipresence of archaea in other environments became available only fairly recently (Chaban, Ng & Jarrell, 2006). This led to the introduction of terms such as 'virus-to-prokaryote ratio (VPR)' (De Corte et al, 2012) and 'virus-to-cell ratio' (Engelhardt et al, 2014;Pan et al, 2014). Herein, we suggest adoption of the term 'virus-to-prokaryote ratio' (VPR), as the most appropriate when considering the relative importance of bacterial and archaeal communities and the related virosphere, as compared to eukaryotic communities and their viruses [although use of 'prokaryote' to designate 'non-eukaryotes' remains controversial (Pace, 2006)].…”

Filamentous phage SW1 is active and influences the transcriptome of the host at high‐pressure and low‐temperature

“…Filamentous phages infect a variety of mostly Gram-negative bacteria without killing the host, and they play a significant role in the host's physiological characteristics such as growth, fragility, acid resistance, swarming motility, toxin production, biofilm formation and lateral gene transfer (Mai-Prochnow et al, 2015). Several reports have identified filamentous phages in the subsurface sediment, which was suggested to be linked to carbon mineralization and to confer a competitive advantage to the nitrate-reducing Pseudomonas host (Pan et al, 2014). Moreover, the Pseudoalteromonas phage f327 was shown to be prevalent in Arctic sea ice and to enhance motility and chemotaxis for improved host survival (Yu et al, 2015).…”

How Deep Can Surface Signals Be Traced in the Critical Zone? Merging Biodiversity with Biogeochemistry Research in a Central German Muschelkalk Landscape

“…Traditionally it has been assumed that subsurface microbial processes are dependent on reduced C originating from photosynthesis (represented by "Marilyn" in Figure 4A). Hence the surface would necessarily dictate subsurface characteristics (Culver et al, 1985;Baker et al, 2000;Foulquier et al, 2010;Akob and Küsel, 2011;Foulquier et al, 2011;Pan et al, 2014; Figure 4A). However, reduced carbon can also enter soils via microbial non-photoautotrophic CO 2 fixation (represented by "Elvis" in Figure 4B) and this carbon can be important to soil microenvironments despite its relatively small contribution to fixed C (0.05% of soil organic carbon; Miltner et al, 2004Miltner et al, , 2005.…”