Thermococci-to-Clostridia Pathway for the Evolution of the Bacteria Domain

doi:10.21203/rs.3.rs-2461311/v1

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Thermococci-to-Clostridia Pathway for the Evolution of the Bacteria Domain

https://doi.org/10.21203/rs.3.rs-2461311/v1

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With the identification of an archaeal Last Universal Common Ancestor phylogenetically related to the archaeon Methanopyrus, the origin of Bacteria becomes a choice between independent emergence versus descent from Archaea. The similarity bitscores between paralogous valyl-tRNA synthetase (VARS) and isoleucyl-tRNA synthetase (IARS) indicated that an Ancestral Bacteria Cluster centred at clostridial Mahella australiensis (Mau) and Thermincola potens (Tpo) were the oldest bacteria. Overall, the high-bitscore bacteria dominated by Clostridia included a number of hydrogen producers. A search for archaea capable of hydrogen production that might be ancestral to the Bacteria domain yielded candidate Archaeal Progenitors led by Thermococci which, like Clostridia, form hydrogen through dark fermentation. A two-domain VARS tree based on Mahella, Thermincola, a broad spectrum of archaea together with a range of well known as well as newly detected species of Thermococci and Euryarchaeota allocated the two Clostridia to a minor-Thermococcal division on the tree containing Thermococi and Euryarchaeota species isolated from high-biodiversity environments. The kinship between Thermoccoci and Clostridia suggested by this allocation was substantiated by highly conserved oligopeptide segments on their VARS sequences, leading to the proposal that a Thermococci-to-Clostridia evolutionary pathway mediated the emergence of the Bacteria domain under conditions of elevated biodiversity.

Evolutionary Biology

Archaeal Progenitor

Bacteria domain

Clostridia

evolution pathway

Last Common Bacterial Ancestor

Thermococci

Search for the roots of the three biological domains of Archaea, Bacteria and Eukarya has been a multi-decade endeavor. According to the suggestion that bacteria were the earliest lifeforms, the Last Bacterial Common Ancestor (LBCA) would be identical to the Last Universal Common Ancestor (LUCA) of all living organisms¹. However, a series of different bacterial groups have also been suggested as the oldest bacteria, including Aquifex and Thermotoga²; Planctomycetales³; Gram-positive bacteria⁴; benthic cyanobacteria⁵; a bacterium between Gracilicutes and Terrabacteria near Fusobacteriota⁶; and Megasphaera elsdenii and Clostridium tartarivorum based on gene doubling⁷.

The search for LBCA is by necessity a two-step process, initiated by identifying the nature of the oldest bacteria, followed by determining their evolutionary precursor if any. Earlier, the identification of a Last Universal Common Ancestor (LUCA) proximal to Methanopyrus kandleri (Mka; see Supplementary Table S1 for names and abbreviations of microbes), an archaeal inhabitant of marine hydrothermal vents, based on the analysis of alloacceptor tRNAs⁸ was supported by the top ranking VARS-IARS bitscore of 473 of Mka among over 5,000 species of organisms⁹, which furnished evidence as well for the VARS-IARS bitscore as a measure of the relative ages of organisms; the invention of wobble rules for translation by Mka using the GNN and UNN anticodons to decode all family boxes of tetracodons, and two neighboring tRNAs in sequence space to read the well separated UCN and AGY Ser codons in the genetic code¹⁰; the oldest age of \(2.8 \text{G}\text{y}\text{a}\)of the Mka lineage among archaea¹¹; and the spontaneous high-yield synthesis of end products and intermediates of the ancient acetyl-CoA pathway in a hydrothermal-vent setting¹². The descent of bacteria from archaea was consistent with the location of an Ancestral Bacteria Cluster centred at clostridial Mahella australiensis (Mau) with a VARS-IARS bitscore of 378, well below the 473 bitscore of Mka.

In the present study, the sequence divergence between VARS and IARS was further employed to measure the relative ages of different bacteria, which gave rise to the finding of Clostridia as one of the most primitive groups within an Ancestral Bacteria Cluster⁹ led by Mau and Tpo. An outstanding feature of this cluster was its prominent inclusion of glucose-metabolizing anaerobes with a propensity to produce hydrogen through glycolysis-linked dark fermentation. Accordingly, a search was performed for archaea capable of glycolysis-linked hydrogen production. The results pointed to Thermococci which included such active hydrogen-producers as Thermococcus kodakarensis and Pyrococcus furiosis. When a two-domain maximum parsimony tree for VARS based on a wide spectrum of archaea, a variety of Thermococci species and clostridial Mau and Tpo was built, it allocated the two clostridial species to a minor-Thermococcal division on the tree that also contained newly detected Thermococci and Euryarcheaota from the high-biodiversity Guaymas Basin and Crystal Geyser. Furthermore, alignment of the different species of VARS on the tree revealed strongly conserved amino acid residues in the archaeal and bacterial VARS sequences. Therefore it was proposed that a Thermococcus-to-Clostridia evolutionary pathway mediated the emergence of the Bacteria domain from the Archaea domain under conditions of elevated biodiversity.

Biological properties of LBCA

The list of 25 oldest bacteria indicated by their VARS-IARS bitscores were headed by Mau and Tpo, and dominated by Clostridia (Table 1). Among non-Firmicute bacteria, only Thermotogae appeared on the list. In comparison, Fusobacteria only attained a bitscore of 312 for F. ulcerans; and Cyanobacteria attained a bitscore of 269 for Synechococcus. The low bitscore of 148 for Aquifex aeolicus was not unexpected on account of its evolution of a substantial oxic network for aerobic metabolism¹³. While the primitive character of clostridial metabolism among bacteria was clearly regonized¹⁴, not all Clostridia exhibited high VARS-IARS bitscores: the pathogenic Clostridia were characterized by modest bitscores likely because of the tortuous evolution of their VARS and/or IARS in the course of adapting possibly to a variety of host organisms, which was in agreement with the phylogenetic tree of Firmicutes based on phosphoglycerate kinase where C. thermocellum clustered with Thermoanaerobacter tencongensis at a lower branching position than C. tetani and C. perfringens¹⁵. Since the G + C content, when estimated from genome sequence, varied by no more than 1% within species, it represented a useful taxonomic descriptor¹⁶; and the higher G + C contents of 55.5% for Mau and 45.9% for Tpo compared to the 28.6% for C. tetani, 28.6% for C. botulinum and 27.7–28.7% for C. perfringens were indicative of the latter species having to adapt to different hosts. Notably, among the top-bitscoring bacteria Halobacteroides halobius¹⁷, Halothermothrix orenii¹⁸, Carboxydocella thermautotrophica¹⁹, Caldicellulosiruptor, Themoanaerobacter and the non-Firmicute Thermotogae were hydrogen-producers²⁰. While growth with CO yielded acetate in most Moorella thermoacetica strains, such growth produced mainly hydrogen in its atypical AMP strain²¹; and the same-genus Moorella stamsii displayed an ability to ferment a range of sugars to form both hydrogen and acetate²². The major end products of pyruvate fermentation by Mau included H₂, CO₂ and acetate²³. Tpo contributed to a hydrogen producing biocathode²⁴; and Thermincola carboxydiphila, a close relative sharing 99% SSU rRNA identity with Tpo, could oxidize CO with H₂O to form CO₂ and H₂²⁵.

Table 1

Bacteria with top VARS-IARS bitscores.
Species name	Phylum	Class	Bitscore
Mahella australiensis 50 − 1 BON	Firmicutes	Clostridia	378
Thermincola potens JR	Firmicutes	Clostridia	377
Halobacteroides halobius DSM 5150	Firmicutes	Clostridia	375
Halothermothrix orenii H 168	Firmicutes	Clostridia	373
Desulfosporosinus orientis DSM 765	Firmicutes	Clostridia	372
Caldicellulosiruptor lactoaceticus 6A	Firmicutes	Clostridia	368
Carboxydocella thermautotrophica	Firmicutes	Clostridia	366
Thermotoga sp. RQ7	Thermotogae	Thermotogae	363
Moorella thermoacetica ATCC 39073	Firmicutes	Clostridia	361
Marinitoga sp. 1137	Thermotogae	Thermotogae	355
Caldanaerobacter subterraneus subsp. tengcongensis MB4	Firmicutes	Clostridia	353
Carboxydothermus hydrogenoformans Z-2901	Firmicutes	Clostridia	353
Pelotomaculum thermopropionicum SI	Firmicutes	Clostridia	353
Thermosipho africanus TCF52B	Thermotogae	Thermotogae	352
Fervidobacterium pennivorans DSM 9078	Thermotogae	Thermotogae	350
Thermoanaerobacter mathranii subsp. mathranii str. A3	Firmicutes	Clostridia	349
Desulfitobacterium dehalogenans ATCC 51507	Firmicutes	Clostridia	347
Acidaminococcus fermentans DSM 20731	Firmicutes	Negativicutes	347
Thermoclostridium stercorarium	Firmicutes	Clostridia	345
Pseudothermotoga lettingae TMO	Thermotogae	Thermotogae	343
Desulfotomaculum ferrireducens	Firmicutes	Clostridia	343
Hungateiclostridium thermocellum ATCC 27405	Firmicutes	Clostridia	342
Kosmotoga olearia TBF 19.5.1	Thermotogae	Thermotogae	340
Halanaerobium hydrogeniformans	Firmicutes	Clostridia	340
Anoxybacter fermentans	Firmicutes	Clostridia	339

The attributes of Archaeal Progenitor

Since the primitive Clostridia were anaerobic chemoorganotrophs in possession of a glycolytic sequence and an inclination to produce hydrogen, the Archaeal Progenitor of bacteria might share some of these cellular traits. Microbial formation of hydrogen can proceed through biophotolysis as in cyanobacteria, photofermentation as in purple non-sulfur bacteria, electrohydrogenesis involving bacterial consortia and Proteobacteria with outer membrane c-type cytochromes, and dark fermentation as in Clostridia²⁶. Numerous archaeons are hydrogenotrophic methanogens²⁷, with the exception of hydrogen-cycling Methanosarcina where intracellular production of hydrogen is coupled to its extracellular participation in generating a transmembrane electrochemical gradient²⁸. The leading archaea in the development of glycolysis are Thermococcales and Desulfurococcales, which can degrade 100% of glucose via a modified Embden-Meyerhof-Parnas (EMP) pathway²⁹. Since Desulfurococcales employ hydrogen to reduce sulfur, whereas Thermococcales such as Pyrococcus furiosis and Thermococcus kodakarensis generate hydrogen through ferredoxin-NADH based on dark fermentation, Thermococcales would be more probable than Desulfurococcales as the origin of bacterial glycolysis. Thermococcus would be more probable than Pyrococcus as well due to the replacement of glyceraldehyde 3-phosphate (GAP) dehydrogenase by GAP:ferredoxin oxidoreductase in the latter’s glycolytic mechanism²⁰. Although Clostridia utilized an EMP pathway for glycolysis with ATP-dependent kinases, while Thermococci preferred to use ADP-dependent kinases, the ADP-dependent phosphofructokinase of Thermococcus kodakarensis retained 20% activity when ADP was replaced by ATP³⁰, suggesting that it might not be very difficult for Thermococci to switch to ATP-dependent kinases. Therefore Thermococci were faced with relatively few competing candidate Archaeal Progenitors capable of bequeathing to the bacteria both a modified EMP pathway and a dark fermentation mechanism for producing hydrogen. The comparable G + C contents of different Thermococcus clades at 45.5%-59.6%³¹, in the vicinity of the G + C contents of Mau and Tpo at 55.5% and 45.9% respectively, would remove any notion that Firmicutes are necessarily low in G + C, and facilitate a potential transformation of Thermococci as Archaeal Progenitor to form Clostridia.

Importance of high biodiversity sites

Mau was isolated from an oil reservoir²³, Clostridium kogasensis from the soil under a corroded gas pipeline³², and Thermococcus sibiricus from a high temperature oil reservoir³³. Thermococcus and Firmicutes were among the most plentiful archaea and bacteria respectively in reservoirs formed by the pressurized water employed to displace oil from the oil-bearing strata³⁴, and Thermincola were abundant in reservoirs above 90^oC³⁵. Thus geobiological sites favorable for a transition from Thermococci to Clostridia would include petroleum-bearing niches. Notably, a survey of fifteen Thermococcus species revealed that none of the species originating outside of hydrothermal vents metabolized maltose as energy substrate, while a majority of the species originating from hydrothermal vents, including T. aggregans, T. guaymasensis, T. fumicolans, T. hydrothermalis and T. profundus all metabolized maltose³⁶, suggesting that high biodiversity sites such as the vents would enhance divergence of the chemoorganotrophic Thermococcus from their cellular norm to develop breakthrough properties including bacterial-type sugar glycolysis based on a modified EMP pathway.

In this regard, the marine hydrothermal vents at Guaymas Basin are known to release an abundance of CO₂, H₂ and low molecular-weight peptides, hydrocarbons and carbohydrates when magmatic sills intruded into organic-rich sediments up to 28 to 7 Kyr ago^37,38, and these compounds gave rise to elevated biodiversity^39,40. In a single study, five novel Thermococcus species were identified from these vents based on SSU rRNA, elongation factors EF-1alpha and EF-2, which was indicative of a rapid rate of Thermococus evolution⁴¹. More recently, based on 37 single-copy genes including the VARS and IARS genes, a series of metagenome-assembled genomes (MAGs) of Thermococci and Euryarchaeota from these vents were sequenced^42,43. The terrestrial subsurface has been revealed likewise as a hotspot of anaerobic biodiversity, where a single site was known to harbor much of the tree of life⁴⁴: the cold water CO₂-driven Crystal Geyser in Utah, originally an abandoned oil exploration well, allowed the sampling of 104 different phylum-level lineages of archaea and bacteria from different depths of the subsurface in the form of genome-resolved metagenomes and single amplified genomes (SAGs), including a novel Euryarchaeota archaeon genome with a VARS-IARS bitscore of 403 (viz. bit403)^45,46.

VARS tree and sequence alignment

Archaeal and bacterial species that produce hydrogen through dark fermentation are relatively limited. To examine whether the cellular resemblance between Thermococci and primitive Clostridia represented within regard convergent evolution or phylogenetic relatedness, a two-domain VARS tree was built using the maximum parsimony method⁴⁷, with the LUCA-proximal Methanopyrus kandleri as root (Fig. 1). There were a major-Thermococcal division consisting of familiar and novel species of Thermococci and Euyarchaeota such as T. litoralis, T. sibiricus and T. archaeon B45 G15, and a minor-Thermococcal division consisting of the novel species T. archaeon B48 G16 from Guaymas Basin, and Euryarchaeota archaeon bit403 from Crystal Geyser together with the clostridial Mahella and Thermincola. Different archaeal species with 300 or higher VARS-IARS bitscores were examined preferentially in the tree to minimize the impact of horizontal gene transfers (HGTs): since HGTs involving both the VARS and IARS genes would be unlikely, while HGTs involving either VARS or IARS alone would lower the similarity bitscore between VARS and IARS substantially, same-species VARS-IARS pairs that have managed to maintain a high bitscore between them could have been relatively protected against HGT perturbation.

In order to test further whether the allocation of Mau and Tpo to the minor-Thermococcal division on the VARS tree was the result of kinship or HGT, Fig. 2 shows oligopeptide segments I-V excerpted from the 49 aligned VARS sequences from Supplementary Figure S1. Their outstanding features were:

Oligo I. All eight of the amino acid positions of this Oligo in Thermincola were identical to those in Pyrococcus.

Oligo II. All nine of the amino acid positions in Thermincola were identical to those in Pyrococcus.

Oligo III. Eight of the nine amino acid positions in each of the Mahella and Thermincola nonapeptides were identical to those of Thermococcus sibiricus.

Oligo IV. The decapeptides in Mahella and Thermincola were identical to those in Paleococcus pacificus and T. archaeon B89 G9.

Oligo V. The heptapeptide in Mahella was identical to those in T. sibiricus, T. archaeon B45 G15, T. sp. 2319x1, T. litoralis, T. archaeon bit391, T. kodakarensis and P. furiosis.

These amino acid identities between the Oligos I-V of clostridial Mahella, Thermincola and some of the Thermococci were in accord with the association of the two primitive clostridial species only with Thermococci and no other archaeal group on the VARS tree⁴⁸. Since HGTs occur most frequently between closely related species⁴⁹, inter-domain HGTs would be rare. Furthermore, because Oligos I-V were scattered over different regions of the VARS sequence, five separate HGT events would be required for their horizontal transfer between the two microbial groups, even without counting the numerous additional oligopeptides in the VARS sequence that also exhibited significant Thermococci-Clostridia identities (as marked by red underline in Supplementary Figure S1). Therefore, the probability of Oligos I-V stemming from inter-domain HGTs was vanishingly small, establishing thereby the phylogenetic proximity between primitive Clostridia and a Thermococci-related LBCA.

Few archaeon-bacterium pairs are so comparable in their biologies or genomes that they would be suggestive of an evolutionary precursor-product relationship between them. The pairings between Thermococcus and primitive clostridial species constituted important exceptions. The high VARS-IARS similarity bitscores of primitive Clostridia attested to their antiquity among bacteria, in agreement with the ancient clostridial metabolic network¹⁴; the modified EMB pathway in Thermococci contained the same intermediates as bacterial glycolysis; and both groups utilized dark fermentation to produce hydrogen. In view of these concordant properties between them, a two-domain maximum parsimony phylogenetic VARS tree was built based on a wide spectrum of archaea together with the clostridial Mau and Tpo. Comparisons of five different oligopeptide sequences of VARS in some of the species on the tree were also performed.

The VARS tree showed that primitive Clostridia formed sister clades in the minor-Thermococcal division with novel Thermococci and Euryarcheaeota isolated from the high-biodiversity environments of Guaymas Basin and Crystal Geyser (Fig. 1), which together with the striking amino acid identities in Oligos I-V between the primitive clostridial and some thermococcal sequences (Fig. 2) provided strong evidence for the emergence of Bacteria from Archaea through a Thermococci-to-Clostridia evolutionary pathway expedited by the exceptionally innovative evolution of Thermococci at high biodiversity sites.

Such an evolutionary pathway had to bridge many fundamental divergences between the two biological domains through deep-seated genomic alterations. The deciphering of these alterations would necessitate the application of multiple approaches. Further searches of novel Thermococci and Euryarchaeota, especially from high-biodiversity sites, may uncover additional species with increasingly close phylogenetic relationships with the Archaeal Progenitor. Complementary searches of primitive Clostridia/Firmicutes with elevated VARS-IARS similarity bitscores may likewise lead to species with increasingly close phylogenetic relationships with LBCA. Moreover, in view of the privotal roles played by both ectosymbiotic and endosymbiotic gene transfers from prokaryotes to eukaryotes in eukaryogenesis⁵⁰, it would be useful to examine whether such transfers might have contributed exogenous prokaryotic genes to facilitate the maturation of either the Archaeal Progenitor or the Last Bacterial Common Ancestor. Altogether, a combination of multiple approaches will be required to meet the unique challenge of understanding how the complex transformation of an archaeal genome into a bacterial one could be achieved.

VARS sequences were obtained from refs. 9, 43 and 46, and sequence alignment was performed with CLUSTALX. A maximum parsimony VARS phylogenetic tree was constructed using PAUP* version 4.0a169 win32⁴⁹, with application of heuristic searches with 10 random taxon addition replicates and tree bisection-reconnection swapping.

Data availability

All data analysed in this study are retrieved from the National Center for Biotechnology Information at https://www.ncbi.nlm.nih.gov and shown in the supplementary materials, with GenBank Accession numbers provided in Supplementary Table S1.

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Acknowledgements

We thank Ms Si Chen for server management. This research was funded by grant number 5112-703-0110D-42002 of the University Grants Council of Hong Kong to Applied Genomics Center of Hong Kong University of Science and Technology.

Author contributions

Conceptualization T.F.W.; data analysis C.K.C. and H.X.; writing, T.F.W., C.K.C. and H.X. All authors have read and agreed to the published version of the manuscript.

Competing interests

The authors declare no conflict of interest.

Additional Information

All data generated or analysed during this study are included in this published article and its supplementary information files.

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Thermococci-to-Clostridia Pathway for the Evolution of the Bacteria Domain

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Abstract

Figures

Introduction

Results

Biological properties of LBCA

The attributes of Archaeal Progenitor

Importance of high biodiversity sites

VARS tree and sequence alignment

Discussion

Methods

References

Declarations

Supplementary Files

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