Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater

Bell, Emma; Lamminmäki, Tiina; Alneberg, Johannes; Andersson, Anders F.; Chen, Qian; Xiong, Weili; Hettich, Robert L.; Balmer, Louise; Frutschi, Manon; Sommer, Guillaume; Bernier‐Latmani, Rizlan

doi:10.3389/fmicb.2018.02129

Cited by 42 publications

(32 citation statements)

References 78 publications

(102 reference statements)

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“…The relative abundances of bacterial and archaeal 16S rRNA gene sequences in the springs were similar to the abundances found in other aquifer studies, and some similar taxa have also been reported previously (41)(42)(43)(44). Proteobacteria and Cyanobacteria composed a large portion of the 16S rRNA gene sequences from all of the Florida springs investigated here.…”

Section: Figsupporting

confidence: 89%

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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Section: Figsupporting

confidence: 89%

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

Malki

Rosario

Sawaya

et al. 2020

mBio

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“…The concentration of acetate in the Olkiluoto fracture fluids is often below the detection limit [40], as it was also in both studied fracture fluids (Table 1). However, it seems that detectable and even relatively high amounts of acetate can be found sporadically in the Olkiluoto fracture water [41] Nevertheless, acetate production is likely in these subsurface fluids, as both autotrophic and heterotrophic acetogens have been cultivated from many Olkiluoto fracture fluids [42], and an active pathway for acetogenesis has been detected in the studied OL-KR6/125-130 m fracture fluid by metagenomic and metatranscriptomic sequencing [18]. In addition to utilising acetate, some of the SRB also produce acetate as a by-product of sulphate reduction when organic compounds are incompletely degraded to acetate, such as Desulfovibrionaceae and Desulfovibrio species [43].…”

Section: Discussionmentioning

confidence: 98%

Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland

Miettinen

Bomberg

2018

Geosciences

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Crystalline bedrock has been chosen for deep geologic long-term storage of used nuclear fuel in Finland. The risks generated by the deep subsurface microbial communities in these disposal sites need to be well characterised in advance to ensure safety. Deep subsurface microbial communities in a steady state are unlikely to contribute to known risk factors, such as corrosion or gas production. However, the construction of the geological final-disposal facility, bedrock disturbances, and hydraulic gradients cause changes that affect the microbial steady-state. To study the induced metabolism of deep microbial communities in changing environmental conditions, the activating effect of different electron donors and acceptors were measured with redox sensing fluorescent dyes (5-Cyano-2,3-ditolyl tetrazolium chloride, CTC and RedoxSensor™ Green, RSG). Fluids originating from two different fracture zones of the Finnish disposal site in Olkiluoto were studied. These fracture fluids were very dissimilar both chemically and in terms of bacterial and archaeal diversity. However, the microbial communities of both fracture fluids were activated, especially with acetate, which indicates the important role of acetate as a preferred electron donor for Olkiluoto deep subsurface communities.

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“…The genome of strain F-1 T possessed all genes for glycolysis via the Embden-Meierhoff-Parnas pathway. Surprisingly, the reductive pentose phosphate pathway in the genome of strain F-1 T is absent, although ribulose biphosphate carboxylase, key enzyme of rPP, was present in the proteomes of several Pseudodesulfovibrio strains (Bell et al 2018). Strain F-1 T is capable of utilizing molecular hydrogen as an energy source.…”

Section: Genome Analysismentioning

confidence: 99%

Pseudodesulfovibrio alkaliphilus, sp. nov., an alkaliphilic sulfate-reducing bacterium isolated from a terrestrial mud volcano

Frolova

Merkel

Kuchierskaya

et al. 2021

Antonie van Leeuwenhoek

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The diversity of anaerobic microorganisms in terrestrial mud volcanoes is largely unexplored. Here we report the isolation of a novel sulfate-reducing alkaliphilic bacterium (strain F-1 T ) from a terrestrial mud volcano located at the Taman peninsula, Russia. Cells of strain F-1 T were Gram--negative motile vibrios with a single polar agellum; 2.0-4.0 µm in length and 0.5 µm in diameter. The temperature range for growth was 6-37°C, with an optimum at 24°C. The pH range for growth was 7.0-10.5, with an optimum at pH 9.5. Strain F-1 T utilized lactate, pyruvate, and molecular hydrogen as electron donors and sulfate, sul te, thiosulfate, elemental sulfur, fumarate or arsenate as electron acceptors. In the presence of sulfate the end products of lactate oxidation were acetate, H 2 S and CO 2 . Lactate and pyruvate could also be fermented. The major product of lactate fermentation was acetate. The main cellular fatty acids were anteiso-С 15:0 , С 16:0 , С 18:0 , and iso-С 17:1 ω8. Phylogenetic analysis revealed that strain F-1 T was most closely related to Pseudodesulfovibrio aespoeensis (98.05% similarity). The total size of the genome of the novel isolate was 3.23Mb and the genomic DNA G + C content was 61.93 mol%. The genome contained all genes essential for dissimilatoty sulfate reduction. We propose to assign strain F-1 T to the genus Pseudodesulfovibrio, as a new species, Pseudodesulfovibrio alkaliphilus sp. nov. The type strain is F-1 T (= KCTC 15918 T = VKM B-3405 T ).

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Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater

Cited by 42 publications

References 78 publications

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

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

Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland

Pseudodesulfovibrio alkaliphilus, sp. nov., an alkaliphilic sulfate-reducing bacterium isolated from a terrestrial mud volcano

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