Methanogenesis is the primary biogenic source of methane in the atmosphere and a key contributor to climate change. The long-standing dogma that methanogenesis originated within the Euryarchaeota was recently challenged by the discovery of putative methane-metabolizing genes in members of the Bathyarchaeota, suggesting that methanogenesis may be more phylogenetically widespread than currently appreciated. Here, we present the discovery of divergent methylcoenzyme M reductase genes in population genomes recovered from anoxic environments with high methane flux that belong to a new archaeal phylum, the Verstraetearchaeota. These archaea encode the genes required for methylotrophic methanogenesis, and may conserve energy using a mechanism similar to that proposed for the obligate H 2 -dependent methylotrophic Methanomassiliicoccales and recently described Candidatus 'Methanofastidiosa'. Our findings indicate that we are only beginning to understand methanogen diversity and support an ancient origin for methane metabolism in the Archaea, which is changing our understanding of the global carbon cycle.

A replicate long-term experiment was conducted using anaerobic digestion (AD) as a model process to determine the relative role of niche and neutral theory on microbial community assembly, and to link community dynamics to system performance. AD is performed by a complex network of microorganisms and process stability relies entirely on the synergistic interactions between populations belonging to different functional guilds. In this study, three independent replicate anaerobic digesters were seeded with the same diverse inoculum, supplied with a model substrate, a-cellulose, and operated for 362 days at a 10-day hydraulic residence time under mesophilic conditions. Selective pressure imposed by the operational conditions and model substrate caused large reproducible changes in community composition including an overall decrease in richness in the first month of operation, followed by synchronised population dynamics that correlated with changes in reactor performance. This included the synchronised emergence and decline of distinct Ruminococcus phylotypes at day 148, and emergence of a Clostridium and Methanosaeta phylotype at day 178, when performance became stable in all reactors. These data suggest that many dynamic functional niches are predictably filled by phylogenetically coherent populations over long time scales. Neutral theory would predict that a complex community with a high degree of recognised functional redundancy would lead to stochastic changes in populations and community divergence over time. We conclude that deterministic processes may play a larger role in microbial community dynamics than currently appreciated, and under controlled conditions it may be possible to reliably predict community structural and functional changes over time.

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Anaerobic digestion of waste activated sludge (WAS) is currently enjoying renewed interest due to the potential for methane production. However, methane production is often limited by the slow hydrolysis rate and/or poor methane potential of WAS. This study presents a novel pretreatment strategy based on free nitrous acid (FNA or HNO2) to enhance methane production from WAS. Pretreatment of WAS for 24 h at FNA concentrations up to 2.13 mg N/L substantially enhanced WAS solubilization, with the highest solubilization (0.16 mg chemical oxygen demand (COD)/mg volatile solids (VS), at 2.13 mg HNO2-N/L) being six times that without FNA pretreatment (0.025 mg COD/mg VS, at 0 mg HNO2-N/L). Biochemical methane potential tests demonstrated methane production increased with increased FNA concentration used in the pretreatment step. Model-based analysis indicated FNA pretreatment improved both hydrolysis rate and methane potential, with the highest improvement being approximately 50% (from 0.16 to 0.25 d(-1)) and 27% (from 201 to 255 L CH4/kg VS added), respectively, achieved at 1.78-2.13 mg HNO2-N/L. Further analysis indicated that increased hydrolysis rate and methane potential were related to an increase in rapidly biodegradable substrates, which increased with increased FNA dose, while the slowly biodegradable substrates remained relatively static.

Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities.

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Anaerobic co-digestion has been widely investigated, but there is limited analysis of interaction between substrates. The objective of this work was to assess the role of carbohydrates, protein and lipids in co-digestion behaviour separately, and together. Two sets of batch tests were done, each set consisting of the mono-digestion of three substrates, and the co-digestion of seven mixtures. The first was done with pure substrates--cellulose, casein and olive oil--while in the second slaughterhouse waste--paunch, blood and fat--were used as carbohydrate, protein and lipid sources, respectively. Synergistic effects were mainly improvement of process kinetics without a significant change in biodegradability. Kinetics improvement was linked to the mitigation of inhibitory compounds, particularly fats dilution. The exception was co-digestion of paunch with lipids, which resulted in an improved final yield with model based analysis indicating the presence of paunch improved degradability of the fatty feed.

Polyhydroxyalkanoate (PHA) biopolymers are widely recognised as outstanding candidates to replace conventional petroleum-derived polymers. Their mechanical properties are good and can be tailored through copolymer composition, they are biodegradable, and unlike many alternatives, they do not rely on oil-based feedstocks. Further, they are the only commodity polymer that can be synthesised intracellularly, ensuring stereoregularity and high molecular weight. However, despite offering enormous potential for many years, they are still not making a significant impact. This is broadly because commercial uptake has been limited by variable performance (inconsistent polymer properties) and high production costs of the raw polymer. Additionally, the main type of PHA produced naturally is poly-3-hydroxybutyrate (PHB), which has limited scope due to its brittle nature and low thermal stability, as well as its tendency to embrittle over time. Production cost is strongly impacted by the type of the feedstock used. In this article we consider: the production of PHAs from methanotrophs using methane as a cost-effective substrate; the use of mixed cultures, as opposed to pure strains; and strategies to generate a poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer (PHBV), which has more desirable qualities such as toughness and elasticity.