Omics-based characterization of complex anaerobic metabolism in methanogenic wastewater treatment

Below the familiar oxygenated biosphere lay ecosystems teeming with “anaerobic” prokaryotes thriving in the absence of O2. As anaerobes exhaust compounds for favorable respiration (e.g., NO3- and SO42-), microorganisms resort to fermentation and respiration of H+ and CO2. Across Earth, microbial communities under such environmental conditions are estimated to annually mineralize 1~2 GT of organic carbon to CH4 and CO2, thereby driving a critical step in the global carbon cycle. Since the discovery that we can tame such “methanogenic” (methane-generating) microbial communities to convert society’s organic waste to CH4 as a recoverable fuel, this biotechnology has become an essential component of managing municipal and industrial waste and development of sustainable energy. Driven by the environmental and technological significance, research has found four major niches form metabolic interactions to facilitate methanogenic degradation of organic carbon: hydrolyzers, fermenters, syntrophs, and methanogens. Despite this defined general ecological structure, many organisms and metabolism in methanogenic ecosystems remain uncharacterized due to challenges in handling and cultivating anaerobes. To tackle this issue, we can employ rapidly developing sequencing technology to recover genomes for uncultivated organisms directly from the environment (“metagenomics”), obtain insight into their physiology, and ultimately uncover hitherto overlooked ecological and biochemical processes taking place in methanogenic natural ecosystems and engineered systems. In the series of studies presented in this dissertation, we use methanogenic wastewater treatment bioreactors as model ecosystems and implement cutting-edge bioinformatics with rigorous annotation of anaerobic metabolic capacities to investigate the ecological roles of uncultured syntrophs, methanogens, and organisms from other bacterial lineages. For syntrophs, we characterize novel aromatic compound degradation pathways and find that syntrophic catabolism and interactions are much more diverse and flexible than previously anticipated, opening new possibilities for ecological niches that syntrophs can exploit. In investigating methanogens, we successfully recover the first genomes for a methanogen-related Euryarchaeota class WSA2 found across various anaerobic environments and discover that they encode unique H2-oxidizing methyl-compound-reducing methanogenesis, suggesting that this may be a major process in both natural and engineered methanogenic environments. As for uncharacterized bacterial lineages, we acquire genomes for populations spanning 15 phyla, of which 5 are bacterial phyla with no cultured representatives (“candidate phyla”). We find that these organisms may contribute to novel syntrophic, fermentative, and acetogenic processes and form intricate metabolic interactions to facilitate complete mineralization of organic matter to in methanogenic ecosystems. Finally, to expand the application of the approach used throughout these studies, we compile the accumulated insight into genomics and complex metabolism and perform an unprecedentedly large-scale comparative genomics analysis on a bacterial phylum that contains both uncultivated lineages affiliated with methanogenic ecosystems and poorly understood lineages prevalent across Earth: Bacteroidetes. This reveals novel relationships between phylogeny, metabolism, and habitats and unnoticed ecological roles that Bacteroidetes can take in methanogenic environments, marine ecosystems, and even the human gastrointestinal tract. In total, we demonstrate that integration of metagenomics, comparative genomics, and strict annotation of metabolic capacity can effectively characterize the ecophysiology of uncultivated organisms and reveal novel ecological niches in methanogenic environments and beyond

The Audiovisual Tau Effect in Infancy

Perceived spatial intervals between successive flashes can be distorted by varying the temporal intervals between them (the “tau effect”). A previous study showed that a tau effect for visual flashes could be induced when they were accompanied by auditory beeps with varied temporal intervals (an audiovisual tau effect).We conducted two experiments to investigate whether the audiovisual tau effect occurs in infancy. Forty-eight infants aged 5–8 months took part in this study. In Experiment 1, infants were familiarized with audiovisual stimuli consisting of three pairs of two flashes and three beeps. The onsets of the first and third pairs of flashes were respectively matched to those of the first and third beeps. The onset of the second pair of flashes was separated from that of the second beep by 150 ms. Following the familiarization phase, infants were exposed to a test stimulus composed of two vertical arrays of three static flashes with different spatial intervals. We hypothesized that if the audiovisual tau effect occurred in infancy then infants would preferentially look at the flash array with spatial intervals that would be expected to be different from the perceived spatial intervals between flashes they were exposed to in the familiarization phase. The results of Experiment 1 supported this hypothesis. In Experiment 2, the first and third beeps were removed from the familiarization stimuli, resulting in the disappearance of the audiovisual tau effect. This indicates that the modulation of temporal intervals among flashes by beeps was essential for the audiovisual tau effect to occur (Experiment 2).These results suggest that the cross-modal processing that underlies the audiovisual tau effect occurs even in early infancy. In particular, the results indicate that audiovisual modulation of temporal intervals emerges by 5–8 months of age

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms, including those from candidate phyla with no cultivated representatives. Our previous metagenomic investigation proposed that Pelotomaculum and methanogens may interact with uncultivated organisms to degrade TA; however, many members of the community remained unaddressed because of past technological limitations. In further pursuit, this study employed state-of-the-art omics tools to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and reports the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments. Metabolic reconstruction revealed that these organisms perform fermentative, syntrophic and acetogenic catabolism facilitated by energy conservation revolving around H2 metabolism. Several of these organisms could degrade TA catabolism by-products (acetate, butyrate and H2) and syntrophically support Pelotomaculum. Other taxa could scavenge anabolic products (protein and lipids) presumably derived from detrital biomass produced by the TA-degrading community. The protein scavengers expressed complementary metabolic pathways indicating syntrophic and fermentative step-wise protein degradation through amino acids, branched-chain fatty acids and propionate. Thus, the uncultivated organisms may interact to form an intricate syntrophy-supported food web with Pelotomaculum and methanogens to metabolize catabolic by-products and detritus, whereby facilitating holistic TA mineralization to CO2 and CH4

Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph

Syntrophorhabdus aromaticivorans strain UI is a mesophilic bacterium capable of degrading aromatic substrates in syntrophic cooperation with a partner methanogen. The draft genome sequence is 3.7 Mb, with a G+C content of 52.0%

Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds

Methane-generating archaea drive the final step in anaerobic organic compound mineralization and dictate the carbon flow of Earth’s diverse anoxic ecosystems in the absence of inorganic electron acceptors. Although such Archaea were presumed to be restricted to life on simple compounds like hydrogen (H(2)), acetate or methanol, an archaeon, Methermicoccus shengliensis, was recently found to convert methoxylated aromatic compounds to methane. Methoxylated aromatic compounds are important components of lignin and coal, and are present in most subsurface sediments. Despite the novelty of such a methoxydotrophic archaeon its metabolism has not yet been explored. In this study, transcriptomics and proteomics reveal that under methoxydotrophic growth M. shengliensis expresses an O-demethylation/methyltransferase system related to the one used by acetogenic bacteria. Enzymatic assays provide evidence for a two step-mechanisms in which the methyl-group from the methoxy compound is (1) transferred on cobalamin and (2) further transferred on the C(1)-carrier tetrahydromethanopterin, a mechanism distinct from conventional methanogenic methyl-transfer systems which use coenzyme M as final acceptor. We further hypothesize that this likely leads to an atypical use of the methanogenesis pathway that derives cellular energy from methyl transfer (Mtr) rather than electron transfer (F(420)H(2) re-oxidation) as found for methylotrophic methanogenesis

A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism

Hydrogen gas, H2, is generated by alkaline hydrothermal vents through an ancient geochemical process called serpentinization in which water reacts with iron containing minerals deep within the Earth's crust. H2 is the electron donor for the most ancient and the only energy releasing route of biological CO2 fixation, the acetyl-CoA pathway. At the origin of metabolism, CO2 fixation by hydrothermal H2 within serpentinizing systems could have preceded and patterned biotic pathways. Here we show that three hydrothermal minerals—greigite (Fe3S4), magnetite (Fe3O4) and awaruite (Ni3Fe)—catalyse the fixation of CO2 with H2 at 100°C under alkaline aqueous conditions. The product spectrum includes formate (up to 200 mM), acetate (up to 100 µM), pyruvate (up to 10 µM), methanol (up to 100 µM), and methane. The results shed light on both the geochemical origin of microbial metabolism and on the nature of abiotic formate and methane synthesis in modern hydrothermal vents

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters

Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life