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

Abstract

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.

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

“…On 6/12/17, 7/17/17, 8/8/17, 8/21/17, 9/11/17, 9/25/17, 10/30/17, and 5/7/18 the iron chloride procedure was used on the pond water after sequential 1 μm and 0.2 μm filtration, with the 0.2 μm a common pore size used in virome generation to prevent cellular contamination [ 33 , 37 , 42 ]. A 1 mL solution of FeCl 3 (4.83 g FeCl 3 into 100 ml H 2 O) was added to the filtered pond water and incubated in the dark for 1 h. The samples were then filtered onto 142-mm 1 μm polycarbonate filters (Sigma-Aldrich, MO, United States) to capture flocculated viral particles [ 43 ].…”

“…Using metagenomics previous studies have identified that within the viral community of surface freshwater sites bacteriophages (phage) dominate [33][34][35][36][37]. Phages are critical components in shaping the evolution, diversity, abundance, and genetic composition of bacteria [38].…”

Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation

“…For the amplified DNA dataset, Cenote-Taker2 detected more total calls (5.2X all other tools combined) and more unique calls (23.8X all other tools combined), all of which have at least one type of hallmark gene. Single-stranded DNA viruses are highly abundant members of many microbial communities 12,37,38 making Cenote-Taker2’s discovery module a particular advance for researchers interested in these viruses.…”

Influence of Environmental Factors on the Variability of Archaeal Communities in a Karst Wetland

“…Prokaryotic microbes have important roles in global biochemistry cycles, affect water quality (Mermillod-Blondin et al, 2015;Malki et al, 2020) and the dynamics of karst processes (Lian et al, 2011). However, archaea, a significant portion of the prokaryotic community in the karst environment, have not been well studied, especially for spatial and temporal variation.…”