Methanogenic Archaea Research Articles

Effects on global warming by microbial methanogenesis in alkaline lakes during the Late Paleozoic Ice Age (LPIA)

Abstract Methane (CH4) is an important greenhouse gas, but its behavior and influencing factors over geological time scales are not sufficiently clear. This study investigated the Late Paleozoic Ice Age (LPIA), which is thought to have experienced an interval of rapid warming at ca. 304 Ma, that may have been analogous to modern warming. To explore possible causes of this warming event, we investigated ancient alkaline lakes in the Junggar Basin, northwestern China. Results show that microbial CH4 cycling here was strong, as evidenced by carbonate δ13C (δ13Ccarb) values of >5‰, ~+0.6‰ offsets between pristane δ13C (δ13CPr) and phytane δ13C (δ13CPh) values, a 3β-methylhopane index of 9.5% ± 3.0%, and highly negative δ13C values of hopanes (–44‰ to –61‰). Low sulfate concentrations in the alkaline lakes made methanogenic archaea more competitive than sulfate-reducing bacteria, and the elevated levels of dissolved inorganic carbon promoted methanogenesis. Biogenic CH4 emissions from alkaline lakes, in addition to CO2, may have contributed to rapid climate warming.

Metabolically diverse microorganisms mediate methylmercury formation under nitrate-reducing conditions in a dynamic hydroelectric reservoir

Brownlee Reservoir is a mercury (Hg)-impaired hydroelectric reservoir that exhibits dynamic hydrological and geochemical conditions and is located within the Hells Canyon Complex in Idaho, USA. Methylmercury (MeHg) contamination in fish is a concern in the reservoir. While MeHg production has historically been attributed to sulfate-reducing bacteria and methanogenic archaea, microorganisms carrying the hgcA gene are taxonomically and metabolically diverse and the major biogeochemical cycles driving mercury (Hg) methylation are not well understood. In this study, Hg speciation and redox-active compounds were measured throughout Brownlee Reservoir across the stratified period in four consecutive years (2016–2019) to identify the location where and redox conditions under which MeHg is produced. Metagenomic sequencing was performed on a subset of samples to characterize the microbial community with hgcA and identify possible links between biogeochemical cycles and MeHg production. Biogeochemical profiles suggested in situ water column Hg methylation was the major source of MeHg. These profiles, combined with genome-resolved metagenomics focused on hgcA-carrying microbes, indicated that MeHg production occurs in this system under nitrate- or manganese-reducing conditions, which were previously thought to preclude Hg-methylation. Using this multidisciplinary approach, we identified the cascading effects of interannual variability in hydrology on the redox status, microbial metabolic strategies, abundance and metabolic diversity of Hg methylators, and ultimately MeHg concentrations throughout the reservoir. This work expands the known conditions conducive to producing MeHg and suggests that the Hg-methylation mitigation efforts by nitrate or manganese amendment may be unsuccessful in some locations.

Methanogenic conversion of hydrogen to methane in reservoir rocks: An experimental study of microbial activity in water-filled pore space

Underground hydrogen storage can lead to the activation of methanogenic Archaea, demanding to quantify microbial activities within the pore space to evaluate potential hydrogen conversion rates. This study presents a method to determine microbial activities within various water-saturated reservoir rocks, inoculated media containing sand particles and rock fragments as well as bulk solution, by monitoring pressure and gas composition. Measured activities in water-saturated rock specimens with identical bulk volumes varied between 0.15 and 1.28 mM H2/h correlating with pore volume. Additionally, the results reveal that activities within intact rocks are 8–10 times higher than in corresponding bulk solutions. This observation demonstrates that the surface area available for microorganism colonization is another potential factor controlling microbial activity when the substance amount is held constant. This notion is supported by activities measured in inoculated media containing sand particles and rock fragments, as well as in rocks with similar pore volumes.

Role of Polysaccharides from Marine Seaweed as Feed Additives for Methane Mitigation in Ruminants: A Critical Review.

Given the increasing concerns regarding greenhouse gas emissions associated with livestock production, the need to discover effective strategies to mitigate methane production in ruminants is clear. Marine algal polysaccharides have emerged as a promising research avenue because of their abundance and sustainability. Polysaccharides, such as alginate, laminaran, and fucoidan, which are extracted from marine seaweeds, have demonstrated the potential to reduce methane emissions by influencing the microbial populations in the rumen. This comprehensive review extensively examines the available literature and considers the effectiveness, challenges, and prospects of using marine seaweed polysaccharides as feed additives. The findings emphasise that marine algal polysaccharides can modulate rumen fermentation, promote the growth of beneficial microorganisms, and inhibit methanogenic archaea, ultimately leading to decreases in methane emissions. However, we must understand the long-term effects and address the obstacles to practical implementation. Further research is warranted to optimise dosage levels, evaluate potential effects on animal health, and assess economic feasibility. This critical review provides insights for researchers, policymakers, and industry stakeholders dedicated to advancing sustainable livestock production and methane mitigation.

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

BackgroundArchaea 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.ResultsWe 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.

Model Organisms To Study Methanogenesis, a Uniquely Archaeal Metabolism.

Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments such as aquatic sediments, anaerobic digesters, inundated agricultural fields, the rumen of cattle, and the hindgut of termites, where they catalyze the terminal reactions in the degradation of organic matter. Methanogenesis is the only metabolism that is restricted to members of the domain Archaea. Here, we discuss the importance of model organisms in the history of methanogen research, including their role in the discovery of the archaea and in the biochemical and genetic characterization of methanogenesis. We also discuss outstanding questions in the field and newly emerging model systems that will expand our understanding of this uniquely archaeal metabolism.

Electromethanogenesis for the conversion of hydrothermal carbonization exhaust gases into methane

Hydrothermal carbonization (HTC) is a biomass conversion process that generates a CO2-rich gaseous phase that is commonly released directly into the atmosphere. Microbial electromethanogeneis (EM) can potentially use this off-gas to convert the residual CO2 into CH4, thus avoiding GHG emissions while adding extra value to the overall bioprocess. In the present work, the HTC gas phase was fed to two mixed-culture biocathodes (replicates) polarized at −1.0V vs. Ag/AgCl. Compared to pure CO2, HTC gas had a marked negative effect on the process, decreasing current density by 61%, while maximum CH₄ yield contracted up to 50%. HTC also had an unequal impact on the cathodic microbial communities, with the methanogenic hydrogenotrophic archaea Methanobacteriaceae experiencing the largest decline. Despite that, the present study demonstrates that HTC can be used in EM as a raw material to produce a biogas with a methane content of up to 70%.

Clay-associated microbial communities and their relevance for a nuclear waste repository in the Opalinus Clay rock formation.

Microorganisms are known to be natural agents of biocorrosion and mineral transformation, thereby potentially affecting the safety of deep geological repositories used for high-level nuclear waste storage. To better understand how resident microbial communities of the deep terrestrial biosphere may act on mineralogical and geochemical characteristics of insulating clays, we analyzed their structure and potential metabolic functions, as well as site-specific mineralogy and element composition from the dedicated Mont Terri underground research laboratory, Switzerland. We found that the Opalinus Clay formation is mainly colonized by Alphaproteobacteria, Firmicutes, and Bacteroidota, which are known for corrosive biofilm formation. Potential iron-reducing bacteria were predominant in comparison to methanogenic archaea and sulfate-reducing bacteria. Despite microbial communities in Opalinus Clay being in majority homogenous, site-specific mineralogy and geochemistry conditions have selected for subcommunities that display metabolic potential for mineral dissolution and transformation. Our findings indicate that the presence of a potentially low-active mineral-associated microbial community must be further studied to prevent effects on the repository's integrity over the long term.

Complexity of temperature dependence in methanogenic microbial environments.

There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH4, an important greenhouse gas. Microbial CH4 production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO2 and CH4. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH4 production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H2/CO2 as immediate CH4 precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH4 production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (Ea). Interestingly, CH4 release from defined microbial cultures, from environmental samples and from wetland field sites all show similar Ea values around 100 kJ mol-1 indicating that CH4 production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.

Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman.

Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H2 and CH4. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and "Mixed" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO2, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.

Surface electron-polarized biochar-enhanced anaerobic digestion mechanism revealed by metagenomic binning strategy

Inefficient electron transfer is a key bottleneck for anaerobic digestion (AD), which often leads to system instability. Here, we propose for the first time a new strategy to solve the problem by adding surface electron-polarized biochar to enhance methanogenesis by providing electrons to methanogens through surface electron-poor/rich regions. Pyrolysis conversion of pigeon manure to conductive materials (CM) containing electron-poor/rich regions is realized. Different levels of CM (2.5, 5 and 7.5 g/L) are used to enhance methane production from pig manure and rice straw co-digestion systems. It is found that the addition of 5 g/L CM results in the highest cumulative CH4 production (187.4 ± 8.0 mL/g VS substrate), 35.4% higher (P < 0.05) than the control (0 g/L). Methanogenic archaea are enriched. Synergistic metabolic mechanisms between the functional microorganism bin.CM52.160 (cellulose degradation) and bin.CM03.101 (methane production) are revealed by the metagenomic binning strategy. A large number of potentially unculturable electroactive microorganisms have been identified. This work provides important insights into the construction of micro-electric fields on material surfaces and offers a practical approach to improving AD performance.

Evaluation of the controlled hydrodynamic cavitation as gas mass transfer system for ex-situ biological hydrogen methanation

The present work represents the first study focused on controlled hydrodynamic cavitation applied as gas transfer system to supply the methanogenic archaea with exogenous H2 and CO2. Starting from a generic mixed inoculum sampled from a thermophilic full-scale anaerobic digester, a bubble column bioreactor was coupled with a rotating hydrodynamic cavitator and fed with different H2/CO2 loading rates. Process efficiency and long-term effects on process stability and microbial population were evaluated. Gas sparging through the controlled hydrodynamic cavitation device is feasible under the operating conditions tested, resulting in almost 100% efficiency in H2 utilization and recording a CH4 volumetric content more than 99% in the gas leaving the reactor, without any gas recirculation from the headspace. The experimental trials lasted about 160 days and the behavior of the bioreactor showed a substantial stability over the time. Metagenomic and FISH analyses were carried out at the end of the experimental trials, revealing a remarkable increase of hydrogenotrophic methanogens species, related to the selection-effect of H2 on community composition. The findings provide previously unidentified insights into long-term effect on process stability and microbial community diversity in the biological hydrogenotrophic methanation process coupled with a gas–liquid mass transfer system based on controlled hydrodynamic cavitation technology.

Biodiversity and Potential Activity of Microorganisms in Underground Gas Storage Horizons

The share of molecular hydrogen as a source of “green energy” is currently significantly increasing. It is proposed to use existing underground natural gas storage facilities to store large volumes of hydrogen. In Russia, depleted oil and gas fields (DOGFs) and deep aquifers are used for natural gas storage. The purpose of this work was to determine microbial diversity in DOGF and deep aquifers by cultural and 16S rRNA gene-based approaches and the effect of H2 on the growth of microorganisms from the underground gas storage (UGS) horizons. The composition of the microbial community inhabiting the formation water of the Peschano–Umetskoe depleted oil and gas reservoir was typical for microbial communities of oil reservoirs and included bacteria of the phyla Bacillota (Dethiosulfatibacter, Defluviitalea, Acetobacterium, Syntrophobotulus), Actinobacteriota (Dietzia, Rhodococcus), Spirochaetota (Sphaerochaeta), Pseudomonadota (Shewanella), and Bacteroidota (Petrimonas), together with methanogenic archaea of the phylum Euryarchaeota (Methanobacterium). In some formation water samples, the share of methanogens of the genus Methanobacterium reached 61.6% of the total community; these hydrogen-utilizing organisms may contribute to the formation of methane in the reservoirs used for the storage of molecular hydrogen. Microbial communities of UGSs located in aquifers were less diverse and abundant. Cultivable hydrogenotrophic sulfate-reducing, homoacetogenic, and methanogenic prokaryotes were retrieved from the studied aquifers and from the DOGF used for gas storage. Microorganisms present in the condensation and reservoir waters of the UGS facilities can influence the composition of the water and gas phase, and affect the host rocks and borehole equipment.

Genetic and Physiological Probing of Cytoplasmic Bypasses for the Energy-Converting Methyltransferase Mtr in Methanosarcina acetivorans.

Methanogenesis is a unique energy metabolism carried out by members of the domain Archaea. Unlike most other methanogens, which reduce CO2 to methane with hydrogen as the electron donor, Methanosarcina acetivorans is able to grow on methylated compounds, on acetate, and on carbon monoxide (CO). These substrates are metabolized via distinct yet overlapping pathways. For the use of any single methanogenic substrate, the membrane-integral, energy-converting N5-methyl-tetrahydrosarcinapterin (H4SPT):coenzyme M (HS-CoM) methyltransferase (Mtr) is required. It was proposed that M. acetivorans can bypass the methyl transfer catalyzed by Mtr via cytoplasmic activities. To address this issue, conversion of different energy substrates by an mtr deletion mutant was analyzed. No significant methyl transfer from H4SPT to HS-CoM could be detected with CO as the electron donor. In contrast, formation of methane and CO2 in the presence of methanol or trimethylamine was indicative of an Mtr bypass in the oxidative direction. As methane thiol and dimethyl sulfide were transiently produced during methylotrophic methanogenesis in the mtr mutant, involvement in this process of methyl sulfide-dependent methyltransferases (Mts) was analyzed in a strain lacking both the Mts system and Mtr. It could be unequivocally demonstrated that the Mts system is not involved in bypassing Mtr, thereby ruling out previous proposals. Conversion of [13C]methanol indicated that in the absence of Mtr M. acetivorans provides the reducing equivalents for methyl-S-CoM reduction to methane by oxidizing (an) intracellular compound(s) to CO2 rather than disproportioning the source of methyl groups. Thus, no in vivo Mtr bypass appears to exist in M. acetivorans. IMPORTANCE Methanogenic archaea possess only a limited number of chemiosmotic coupling sites in their respiratory chains. Among them, N5-methyl-H4SPT:HS-CoM methyltransferase (Mtr) is the most widely distributed. Previous observations led to the conclusion that Methanosarcina acetivorans is able to bypass this reaction via methyl sulfide-dependent methyltransferases (Mts). However, strains lacking Mtr are not able to produce methane from CO. Also, these strains are unable to oxidize methylated substrates to CO2, in contrast to observations in the close relative Methanosarcina barkeri. The results also highlight the sole function of the Mts system in methyl sulfide metabolism. Thus, no in vivo Mtr bypass appears to exist in M. acetivorans.

Oil Has a Higher Methanogenic Potential than Coal in an Oil-Bearing Coal Seam.

The presence of oil in coal seams from coal-oil symbiosis areas poses a serious threat to the safe and efficient mining of coal. However, the information about the application of microbial technology in oil-bearing coal seams was insufficient. In this study, the biological methanogenic potential of coal and oil samples in an oil-bearing coal seam was analyzed by anaerobic incubation experiments. The results showed that the biological methanogenic efficiency of the coal sample increased from 0.74 to 1.06 from day 20 to day 90, and the biological methanogenic potential of the oil sample was about twice as high as that of the coal sample after 40 days of incubation. The Shannon diversity and observed operational taxonomic unit (OTU) number of oil were lower than those in coal. The major genera in coal were Sedimentibacter, Lysinibacillus, Brevibacillus, etc., and the major genera in oil mainly included Enterobacter, Sporolactobacillus, and Bacillus. The methanogenic archaea in coal mainly belonged to the order Methanobacteriales, Methanocellales, Methanococcales, etc., and the methanogenic archaea in oil mainly belonged to the genera Methanobacterium, Methanobrevibacter, Methanoculleus, and Methanosarcina. In addition, metagenome analysis showed that functional genes belonging to processes such as methane metabolism, microbial metabolism in different environments, and benzoate degradation were in a higher abundance in the oil culture system, while genes belonging to sulfur metabolism, biotin metabolism, and glutathione metabolism were in a higher abundance in the coal culture system. The metabolites specific to coal samples mainly belonged to phenylpropanoids, polyketides, lipids, and lipid-like molecules; meanwhile, the metabolites specific to oil were mainly organic acids and their derivatives. In summary, this study has a reference value for the elimination of oil from coal in oil-bearing coal seams and can be used to separate oil from oil-bearing coal seams and reduce the hazard brought by oil for coal seam mining.

Stable Carbon Isotope Signature of Methane Released From Phytoplankton

AbstractAquatic ecosystems play an important role in global methane cycling and many field studies have reported methane supersaturation in the oxic surface mixed layer (SML) of the ocean and in the epilimnion of lakes. The origin of methane formed under oxic condition is hotly debated and several pathways have recently been offered to explain the “methane paradox.” In this context, stable isotope measurements have been applied to constrain methane sources in supersaturated oxygenated waters. Here we present stable carbon isotope signatures for six widespread marine phytoplankton species, three haptophyte algae and three cyanobacteria, incubated under laboratory conditions. The observed isotopic patterns implicate that methane formed by phytoplankton might be clearly distinguished from methane produced by methanogenic archaea. Comparing results from phytoplankton experiments with isotopic data from field measurements, suggests that algal and cyanobacterial populations may contribute substantially to methane formation observed in the SML of oceans and lakes.

In situ field experiment shows the potential of methanogenic archaea for biomethane production from underground gas storage in natural rock environment

Biological methanation occurs naturally in the specific rock environment of some underground gas reservoirs. To use the natural potential of hydrogenotrophic methanogenic archaea in the underground gas reservoirs environment in the future for any type of energy conversion, better knowledge of these systems is required. Most studies investigating the potential for biological methane production from hydrogen and carbon dioxide have been conducted in laboratory-scale systems, making it impossible to evaluate the process under realistic environmental conditions. A unique field experiment of biomethanation in an underground gas reservoir confirmed the feasibility of these facilities for targeted production of biologically produced methane. The experiment followed data previously obtained from long-term experiments carried out in the laboratory, including 300 days lasting operation of reactor and cultivation experiments, which led to repeated isolation of Methanothermobacter sp. This species was the dominant methanogen, which raised from 1% to 43% of all microbial population after 22 days of field experiment, while the complete conversion of hydrogen took place. In addition, the study is supported by metagenomic analysis to gain deep insight into the microbiome of the underground gas reservoir.

Different microplastics in anaerobic paddy soils: Altering methane emissions by influencing organic matter composition and microbial metabolic pathways

Microplastics are widespread in farmland and threaten soil ecology. However, how different microplastics affect methane emission in paddy soil are still unclear. To address this knowledge gap, three typical microplastics, polyethylene, polypropylene, and polyvinyl chloride were added to paddy soil with different doses (0.01%, 0.1%, and 1%), and a 50-day incubation experiment was conducted. Compared with polyethylene and polypropylene microplastics, 1% of polyvinyl chloride microplastic resulted in the highest increase in methane production. According to the integrated liquid phase analysis, all three microplastics contributed to the accumulation of humus in the soil solution. Differential microbial taxa analysis indicated that some denitrifying bacteria such as Gemmatimonadetes and Omnitrophicaeota were significantly enriched in 1% polyethylene and polypropylene microplastics groups on day 30, and Rice Cluster I methanogens archaea were enriched specially in the 1% polyvinyl chloride microplastic group. The predicted soil metabolic functions suggested that polyethylene and polyvinyl chloride microplastics enhanced oxidative phosphorylation and amino acid reduction pathways. Macromolecular humus induced by microplastics may play a critical role in the dynamic equilibrium of anaerobic systems in paddy soils. These findings highlighted the threat of microplastics in agricultural fields greenhouse gas emissions. The identified quinone reductive metabolic pathways may provide potential strategies to reduce methane emissions.

Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics.

Omnivorous cockroaches host a complex hindgut microbiota comprised of insect-specific lineages related to those found in mammalian omnivores. Many of these organisms have few cultured representatives, thereby limiting our ability to infer the functional capabilities of these microbes. Here we present a unique reference set of 96 high-quality single cell-amplified genomes (SAGs) from bacterial and archaeal cockroach gut symbionts. We additionally generated cockroach hindgut metagenomic and metatranscriptomic sequence libraries and mapped them to our SAGs. By combining these datasets, we are able to perform an in-depth phylogenetic and functional analysis to evaluate the abundance and activities of the taxa in vivo. Recovered lineages include key genera within Bacteroidota, including polysaccharide-degrading taxa from the genera Bacteroides, Dysgonomonas, and Parabacteroides, as well as a group of unclassified insect-associated Bacteroidales. We also recovered a phylogenetically diverse set of Firmicutes exhibiting a wide range of metabolic capabilities, including-but not limited to-polysaccharide and polypeptide degradation. Other functional groups exhibiting high relative activity in the metatranscriptomic dataset include multiple putative sulfate reducers belonging to families in the Desulfobacterota phylum and two groups of methanogenic archaea. Together, this work provides a valuable reference set with new insights into the functional specializations of insect gut symbionts and frames future studies of cockroach hindgut metabolism.

Fertilization Enhances Grain Inorganic Arsenic Assimilation in Rice

To investigate how soil fertilization/amendments alters arsenic speciation grain off-take in paddy rice, rice was grown to maturity in growth chambers fertilized with standard mineral fertilizer, wood ash (rich in silica), pig slurry (rich in organic matter), and non-amended control. The soil was sourced from a Chinese paddy field. The primary fertilized elements (nitrogen, phosphorus, potassium) were kept constant across treatments. Porewater chemistry and soil microbiology were monitored throughout the experiments. Total grain arsenic, sum of inorganic arsenic and dimethylarsinic acid (DMA), was significantly different between treatments (P = 0.024), with inorganic arsenic varying from 0.025 to 0.08 mg/kg and DMA from 0.08 to 0.16 mg/kg for control compared to fertilized, respectively. Fertilizer source made no difference to arsenic speciation concentration in grain. Porewater analysis found that as anaerobism set in, inorganic arsenic, phosphorus and manganese greatly lowered in concentration. Methylated arsenic species concentrations increased over time, concurrent with an increase in pH, decrease in Eh, and increase in total organic carbon and iron, with no strong treatment effects, except for pig slurry that enhanced pH and decreased Eh. Methanogenic archaea, sulfate-reducing bacteria and Acidobacteria increased with time and some Actinobacteria and Firmicutes increased due to slurry, but then decreased with time (P < 0.01). Methanogenic archaea and sulphate-reducing bacteria correlated positively with porewater DMA and negatively with porewater inorganic arsenic (P < 0.05). Genera within the Actinobacteria and Burkholderiaceae correlated negatively with DMA, while genera with iron-reducing capacity (Clostridiales) correlated positively with porewater inorganic arsenic and DMA (P < 0.05).