Fervidicoccus fontis

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1. Classification

a. Higher order taxa

Archaea; Crenarchaeota; Thermoprotei; Fervidicoccales; Fervidicoccaceae; Genus

2. Description and significance

Fervidicoccus fontis is a thermophilic archaeon and the sole documented species within its taxonomic order, Fervidococcales [1]. Initially discovered in the Uzon Caldera geothermal springs in Russia, F. fontis is a coccus-shaped obligate anaerobic organotroph capable of pyruvate catabolism, but its main distinguishing feature is its ability to hydrolyze lipids including keratin [2]. F. fontis’ discovery greatly expanded the known diversity of its phylum, as F. fontis was the first discovered crenarchaeon able to grow on lipids and the first to acquire energy through lipid hydrolysis [3]. This capability of F. fontis has numerous applications, including detoxifying arsenic, sulfur, and iron cycling in hot springs [4]: its lipid hydrolysis can be useful for both commercial cleaning products as well as wastewater treatment and refined products [3]. Ultimately, F. fontis’ special ability to conduct lipid hydrolysis can be instrumental in both biotechnology and environmental sustainability, but it is unclear exactly what mechanism allows specific F. fontis strains and not closely related lineages of F. fontis to hydrolyze lipids.

3. Genome structure

The genome of F. fontis comprises a single circular chromosome containing 1,319,216 base pairs, with a G+C content of 37.5% and lacking extrachromosomal elements. Within this genome, researchers have identified 42 tRNA genes—of which 9 contain introns—along with a single 16S-23S rRNA operon and a distantly located 5S rRNA gene [5]. The genome of F. fontis contains 1,385 protein-coding genes, averaging 829 bp in length and covering 87.1% of the genome [5]. Of these, 911 genes (65.8%) have predicted functions related to survival in extreme environments. These include roles in energy metabolism, amino acid transamination, oxidative decarboxylation, and protein degradation. The genome encodes both membrane-bound and cytoplasmic [NiFe]-hydrogenases, essential for proton translocation and NADPH-dependent hydrogen production. Regarding peptidase activity, the genome of F. fontis encodes 35 peptidases, including metallopeptidases, serine peptidases, and aspartic peptidases, which facilitate protein metabolism [5]. A genome analysis of strain 3639Fd found a gene encoding for 𝛼/𝛽-hydrolases, an enzyme responsible for lipid degradation, which showed 30-33% similarity of amino acid sequences at 60% coverage with eukaryotic monoacylglycerol lipases [3]. Among the 474 (34.2%) uncharacterized genes in the F. fontis genome, 345 are unique to F. fontis and show no similarities to any known sequences [5]. Additionally, the genome contains five CRISPR loci and several associated Cas proteins, which likely play a significant role in the organism's defense against mobile genetic elements and enhance its survival in extreme conditions. Initiation of DNA replication occurs between genes FFONT_0896 and FFONT_0897. This region is characterized by ORB motifs, which are previously identified conserved DNA elements in archaea responsible for initiation of replication [6]. However, GC-skew analysis revealed a rearrangement event that has affected nucleotide distribution across the genome, indicating a dynamic evolutionary history [5].

4. Cell structure

F. fontis cells are non-motile, owing to the absence of flagella, and have sizes ranging from 1 to 3 micrometers. This lack of motility limits their movement in extreme environments but aligns with their adaptation to stable geothermal ecosystems [1].

5. Metabolic processes

While F. fontis possesses enzymes for amino acid catabolism, the organism appears to lack complete pathways for carbohydrate metabolism, such as glycolysis or oxidative pentose phosphate pathway [5]. As a result, they cannot rely on common biochemical processes, such as glycolysis or the oxidative pentose phosphate pathway, to break down sugars for energy. Instead, they depend on alternative substrates, such as proteins, peptides, or lipids, which are metabolized to generate energy and cellular building blocks. Notably, there are no genes encoding the necessary enzymes for the oxidative pentose phosphate pathway. Although some genes related to carbohydrate transport and the ribulose monophosphate pathway are present, the absence of key enzymes for sugar breakdown suggests that F. fontis primarily relies on protein and peptide hydrolysis for its energy needs [5]. In terms of metabolic byproducts, the organism generates acetate, hydrogen, and carbon dioxide through the catabolism of pyruvate. It utilizes acetyl-CoA synthetase to convert acetate into ATP [5]. Remarkably, strain 3639Fd possesses a gene for carboxylesterase, which allows it to grow on various triglycerides, and is related to encoded 𝛼/𝛽-hydrolases involved in lipid degradation. This ability to metabolize triglycerides represents a novel feature for the genus, opening new avenues for research into its ecological roles and potential biotechnological applications [3].

6. Ecology

F. fontis is relatively endemic as it thrives in extreme geothermal environments, primarily terrestrial hot springs. F. fontis has been found between 55–84°C in the hot springs of Yellowstone National Park, Iceland, New Zealand, and the Kamchatka peninsula in Far East Russia [7]. Using an isolated colony in Uzon Caldera, it was determined that F. fontis has optimal growth at 65–70°C [5] and thrives in moderately acidic conditions with a pH range of 6.0–7.5​ [8]. F. fontis is adapted to anaerobic environments, feeding on organic material and contributing to nutrient cycling, particularly in carbon and sulfur-rich geothermal ecosystems ​[8]. F. fontis is geographically tied to volcanic regions, especially in Russia and Iceland, where geothermal activity creates ideal habitats ​(1,8).

7. Pathology

F. fontis has not been reported as a pathogen in humans, animals, or plants [1]. As a member of the phylum Crenarchaeota, it exists primarily as an extremophile with multiple environmental functions [5]. No known pathogenic mechanisms have been identified, and their interactions are mostly linked to nutrient cycling in hot springs ​[3]. Studies on the organism focus on its role as an extremophile in ecosystems rather than any pathogenicity or disease-causing behaviors​ [9].

8. Current Research

Over the last few years, research on F. fontis has focused on several aspects, including its metabolic capabilities, environmental adaptations, and applications to the biotechnology industry. Unique lipid degradation capability possessed by strain 3639Fd isolated from a hot spring in Kamchatka, Russia [3]. Other strains and hyperthermophilic archaea studied in the past did not show any capabilities of growing on lipids, but in a genome analysis of 3639Fd, a gene encoding for 𝛼/𝛽-hydrolases (lipid degradation), which are closely related to carboxylesterases (fatty acid degradation), was found. A genomic analysis comparison was performed between strain 3639Fd and Kam940, another known strain capable of lipid metabolism, and revealed 99.63% genomic similarity, yet strain 3639Fd still possessed its unique lipolytic proteins. This research demonstrated that F. fontis, specifically strain 3639fd, can be a useful model organism for further studying its lipid metabolism capabilities and potential applications for biotechnology industries requiring robust enzymes for high-temperature processes [3].

With regards to environmental adaptations of F. fontis, Zeng et al., 2019 studied the structure of glycerol dialkyl glycerol tetraethers (GDGTs) in archaea and its possible role in changing with different environmental factors, most importantly temperature [10]. GDGTs are lipids that span the cell membrane of archaea, including F. fontis [10], helping with structural rigidity. Archaea can modify GDGTs by adding up to 8 cyclopentane rings and/or 1 cyclohexane ring into its chain. Comparative genomics and lipid analysis revealed that there are two GDGT ring synthase proteins, GrsA and GrsB, that are responsible for the addition of a specific number of rings. This helps researchers look for homologs in other crenarchaeota genomes to identify similarities and differences to F. fontis and how their environmental factors can explain the potential adaptations to different temperatures.

References

[1] [Perevalova, Anna A, et al. “Fervidicoccus Fontis Gen. Nov., Sp. Nov., an Anaerobic, Thermophilic Crenarchaeote from Terrestrial Hot Springs, and Proposal of Fervidicoccaceae Fam. Nov. And Fervidicoccales Ord. Nov.” INTERNATIONAL JOURNAL of SYSTEMATIC and EVOLUTIONARY MICROBIOLOGY, vol. 60, no. 9, 3 Nov. 2009, pp. 2082–2088, https://doi.org/10.1099/ijs.0.019042-0.]

[2] [Kublanov, Ilya V, et al. “Biodiversity of Thermophilic Prokaryotes with Hydrolytic Activities in Hot Springs of Uzon Caldera, Kamchatka (Russia).” Applied and Environmental Microbiology, vol. 75, no. 1, 1 Jan. 2009, pp. 286–291, https://doi.org/10.1128/aem.00607-08. Accessed 27 Oct. 2023.]

[3] [Karaseva, A. I., et al. “Fervidicoccus Fontis Strain 3639Fd, the First Crenarchaeon Capable of Growth on Lipids.” Microbiology, vol. 90, no. 4, July 2021, pp. 435–442, https://doi.org/10.1134/s002626172104007x.]

[4] [Jiang, Zhou, et al. “Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China.” PLOS ONE, vol. 11, no. 1, 13 Jan. 2016, p. e0146331, https://doi.org/10.1371/journal.pone.0146331. Accessed 21 Oct. 2022.] [5] [Lebedinsky, Alexander V, et al. “Analysis of the Complete Genome of Fervidococcus Fontis Confirms the Distinct Phylogenetic Position of the Order Fervidicoccales and Suggests Its Environmental Function.” Extremophiles, vol. 18, no. 2, 23 Dec. 2013, pp. 295–309, https://doi.org/10.1007/s00792-013-0616-7.]

[6] [Robinson, Nicholas P, et al. “Identification of two origins of replication in the single chromosome of the archaeon sulfolobus solfataricus.” Cell, vol. 116, no. 1, Jan. 2004, pp. 25–38, https://doi.org/10.1016/s0092-8674(03)01034-1.]

[7] [Wemheuer, Bernd, et al. “Microbial Diversity and Biochemical Potential Encoded by Thermal Spring Metagenomes Derived from the Kamchatka Peninsula.” Archaea, vol. 2013, 2013, pp. 1–13, https://doi.org/10.1155/2013/136714. Accessed 18 Oct. 2024]

[8] [Perevalova, Anna A., et al. “Distribution of Crenarchaeota Representatives in Terrestrial Hot Springs of Russia and Iceland.” Applied and Environmental Microbiology, vol. 74, no. 24, 15 Dec. 2008, pp. 7620–7628, https://doi.org/10.1128/aem.00972-08.]

[9] [Mirete, Salvador, et al. “Diversity of Archaea in Icelandic Hot Springs Based on 16S RRNA and Chaperonin Genes.” FEMS Microbiology Ecology, vol. 77, no. 1, 15 Apr. 2011, pp. 165–175, https://doi.org/10.1111/j.1574-6941.2011.01095.x. Accessed 9 Nov. 2021.]

[10] [Zeng, Zhirui, et al. “GDGT Cyclization Proteins Identify the Dominant Archaeal Sources of Tetraether Lipids in the Ocean.” Proceedings of the National Academy of Sciences, vol. 116, no. 45, 7 Oct. 2019, pp. 22505–22511,https://doi.org/10.1073/pnas.1909306116.]

[11] [OpenAI. ChatGPT. Version 4, 2023, www.openai.com/chatgpt]


Edited by Christian, Kota, Ananya, Mihika, Kenneth, students of Jennifer Bhatnagar for BI 311 General Microbiology, 2020, Boston University.