Methanogenesis on Early Stages of Life: Ancient but Not Primordial

Metabolic and physiological adaptations of microalgal growth-promoting bacterium Azospirillum brasilense growing under biogas atmosphere: a microarray-based transcriptome analysis

Using microalgal growth-promoting bacteria (MGPB) to improve the cultured microalga metabolism during biotechnological processes is one of the most promising strategies to enhance their benefits. Nonetheless, the culture condition effect used during the biotechnological process on MGPB growth and metabolism is key to ensure the expected positive bacterium growth and metabolism of microalgae. In this sense, the present research study investigated the effect of the synthetic biogas atmosphere (75% CH4-25% CO2) on metabolic and physiological adaptations of the MGPB Azospirillum brasilense by a microarray-based transcriptome approach. A total of 394 A. brasilense differentially expressed genes (DEGs) were found: 201 DEGs (34 upregulated and 167 downregulated) at 24 h and 193 DEGs (140 upregulated and 53 downregulated) under the same conditions at 72 h. The results showed a series of A. brasilense genes regulating processes that could be essential for its adaptation to the early stressful condition generated by biogas. Evidence of energy production is shown by nitrate/nitrite reduction and activation of the hypothetical first steps of hydrogenotrophic methanogenesis; signal molecule modulation is observed: indole-3-acetic acid (IAA), riboflavin, and vitamin B6, activation of Type VI secretion system responding to IAA exposure, as well as polyhydroxybutyrate (PHB) biosynthesis and accumulation. Moreover, an overexpression of ipdC, ribB, and phaC genes, encoding the key enzymes for the production of the signal molecule IAA, vitamin riboflavin, and PHB production of 2, 1.5 and 11 folds, respectively, was observed at the first 24 h of incubation under biogas atmosphere Overall, the ability of A. brasilense to metabolically adapt to a biogas atmosphere is demonstrated, which allows its implementation for generating biogas with high calorific values and the use of renewable energies through microalga biotechnologies.

Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions

BACKGROUND

Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains.

RESULTS

Here, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12 exchanges could enable them to occupy ecological niches that possibly alter the direction of H2 utilization.

CONCLUSIONS

We provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2 flow.

Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea

BACKGROUND

Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination.

RESULTS

We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.

Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges

Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a slim LCA based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life.

The reductive carboxylation activity of heterotetrameric pyruvate synthases from hyperthermophilic archaea

Pyruvate synthase (pyruvate:ferredoxin oxidoreductase, PFOR) catalyzes the interconversion of acetyl-CoA and pyruvate, but the reductive carboxylation activities of heterotetrameric PFORs remain largely unknown. In this study, we cloned, expressed, and purified selected six heterotetrameric PFORs from hyperthermophilic archaea. The reductive carboxylation activities of these heterotetrameric PFORs were measured at 70 °C and the ratio of reductive carboxylation activity to oxidative decarboxylation activity (red/ox ratio) were calculated. Four out of six showed reductive decarboxylation activities. Among them, the PFOR_pfm from Pyrolobus fumarii showed the highest reductive carboxylation activities and the highest red/ox ratio, which were 54.32 mU/mg and 0.51, respectively. The divergence of the reductive carboxylation activities and the red/ox ratios of heterotetrameric PFORs in hyperthermophilic archaea indicate the diversity of the functions of PFOR over long-term evolution. This can help us better understand the autotrophic CO₂ fixation process in thermal vent, or in other CO₂-rich high temperature habitat.

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000-6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.

Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways

Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.

The activity of RubisCO and energy demands for its biosynthesis. Comparative studies with CO2-reductases

Most CO₂ on Earth is fixed into organic matter via reactions catalysed by enzymes called carboxylases. CO₂-fixation via carboxylases occurs in the Calvin-Benson-Bassham (CBB) cycle, and the crucial role in this cycle is played by RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase). CO₂ can also be fixed by pathways, where a reduction of CO₂ to formate or carbon monoxide (CO) occurs. The latter reactions are performed by so-called CO₂-reductases e.g. formate dehydrogenase (FDH), carbon-monooxide (CO) dehydrogenase (CODH), and crotonyl-CoA reductase/carboxylase (CCR). In general, a simple model of enzymatic activity based only on a turnover rate of an enzyme for an appropriate substrate (k_cat) is insufficient. Based on estimated metabolic costs of each amino acid, the average energetic costs of amino acid biosynthesis (E_aa), and the total costs (E_T) for selected CO₂-fixing enzymes were analyzed concerning 1) k_cat for CO₂ (k_C), and 2) specificity factor (S_rel) for RubisCO. A comparison of E_aa and E_T to their k_C showed that CODH and FDHs do not need to be more efficient enzymes in CO₂ capturing pathways than some forms of RubisCO. CCR was the only both low-cost and highly active CO₂-fixing enzyme. The obtained results showed also that there exists an evolutionarily conserved trade-off between S_rel of RubisCOs and the energetic demands needed for their biosynthesis. Phylogenetic analysis demonstrated that RubisCO, CODH, FDH, and CCR are enzymes formed as a result of parallel evolution. Moreover, the kinetic parameters (k_C) of CO₂-fixing enzymes were plausibly optimized already at the early stages of life evolution on Earth.

Simulating Serpentinization as It Could Apply to the Emergence of Life Using the JPL Hydrothermal Reactor

The molecules feeding life's emergence are thought to have been provided through the hydrothermal interactions of convecting carbonic ocean waters with minerals comprising the early Hadean oceanic crust. Few laboratory experiments have simulated ancient hydrothermal conditions to test this conjecture. We used the JPL hydrothermal flow reactor to investigate CO₂ reduction in simulated ancient alkaline convective systems over 3 days (T = 120°C, P = 100 bar, pH = 11). H₂-rich hydrothermal simulant and CO₂-rich ocean simulant solutions were periodically driven in 4-h cycles through synthetic mafic and ultramafic substrates and Fe>Ni sulfides. The resulting reductants included micromoles of HS^- and formate accompanied possibly by micromoles of acetate and intermittent minor bursts of methane as ascertained by isotopic labeling. The formate concentrations directly correlated with the CO₂ input as well as with millimoles of Mg²⁺ ions, whereas the acetate did not. Also, tens of micromoles of methane were drawn continuously from the reactor materials during what appeared to be the onset of serpentinization. These results support the hypothesis that formate may have been delivered directly to a branch of an emerging acetyl coenzyme-A pathway, thus obviating the need for the very first hydrogenation of CO₂ to be made in a hydrothermal mound. Another feed to early metabolism could have been methane, likely mostly leached from primary CH₄ present in the original Hadean crust or emanating from the mantle. That a small volume of methane was produced sporadically from the ¹³CO₂-feed, perhaps from transient occlusions, echoes the mixed results and interpretations from other laboratories. As serpentinization and hydrothermal leaching can occur wherever an ocean convects within anhydrous olivine- and sulfide-rich crust, these results may be generalized to other wet rocky planets and moons in our solar system and beyond.