Confined aquifers as viral reservoirs

Smith, Renee J.; Jeffries, Thomas C.; Roudnew, Ben; Seymour, Justin R.; Fitch, Alison J.; Simons, Keryn L.; Speck, Peter; Newton, Kelly; Brown, Melissa H.; Mitchell, James G.

doi:10.1111/1758-2229.12072

Cited by 21 publications

(23 citation statements)

References 35 publications

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“…Considering that only four complete ssDNA viral genomes were identified in Ichetucknee Springs, our study supports the idea that in some aquatic environments, a few ssDNA viruses can be among the most abundant viruses contributing to the community composition (47). These findings are also consistent with a previous study that demonstrated elevated levels of ssDNA viruses in aquifer systems (22). However, the 2013 study by Smith et al used multiple-displacement amplification, which has a known bias toward small circular genomes such as those of ssDNA viruses, making it difficult to derive quantitative information from their sequence data (22,50).…”

Section: Figsupporting

confidence: 91%

“…These findings are also consistent with a previous study that demonstrated elevated levels of ssDNA viruses in aquifer systems (22). However, the 2013 study by Smith et al used multiple-displacement amplification, which has a known bias toward small circular genomes such as those of ssDNA viruses, making it difficult to derive quantitative information from their sequence data (22,50). Ichetucknee Springs is one of few environments reported where certain ssDNA viruses are more abundant than dsDNA viruses (47).…”

Section: Figsupporting

confidence: 87%

“…Almost half of the complete circular genomes were ssDNA viruses, mainly CRESS DNA viruses. Though it has been suggested previously that their small capsid size (15 to 38 nm in diameter) contributes to their elevated presence in aquifers (22), the abundance of these complete ssDNA genomes is also influenced by the fact that their small genome size increases the likelihood of complete genome assembly. Tailed phage with dsDNA genomes belonging to the order Caudovirales are ubiquitous in all aquatic environments examined to date, and their presence in our study is consistent with findings of other aquatic virome studies.…”

Section: Figmentioning

confidence: 99%

“…Aquifer systems host diverse microbial life and harbor a significant fraction (up to 40%) of the total microbial biomass on Earth (14)(15)(16)(17)(18)(19)(20)(21)(22). Prokaryotes play vital roles in mediating biogeochemical cycling and ultimately aid in maintenance of aquifers' water quality via removal of organic carbon, nitrates, and even micropollutants (23,24).…”

mentioning

confidence: 99%

“…Prokaryotes play vital roles in mediating biogeochemical cycling and ultimately aid in maintenance of aquifers' water quality via removal of organic carbon, nitrates, and even micropollutants (23,24). Viruses are also increasingly recognized as important members of aquatic environments, and yet only a small number of studies have looked at viruses in groundwater systems (19)(20)(21)(22), which represent a reservoir of unexplored viral diversity. However, despite their significance, little is known about the naturally occurring prokaryotic communities in the FAS or its associated springs.…”

mentioning

confidence: 99%

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Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA

Malki

Rosario

Sawaya

et al. 2020

mBio

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Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 103 ml−1 to 1.1 × 105 ml−1 and 2.2 × 103 ml−1 to 3.4 × 104 ml−1, respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) viruses. Sequences similar to those of ssDNA viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small viruses merit further investigation in groundwater systems. IMPORTANCE Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida’s first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida’s first-magnitude springs, providing a baseline against which to compare future ecosystem change.

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