Homo-Acetogens: Their Metabolism and Competitive Relationship with Hydrogenotrophic Methanogens

Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens

We examined the microbial populations present in fecal samples of macropods capable of utilizing a mixture of hydrogen and carbon dioxide (70:30) percent. The feces samples were cultured under anaerobic conditions, and production of methane or acetic acids characteristic for methanogenesis and homoacetogenesis was measured. While the feces of adult macropods mainly produced methane from the substrate, the sample from a 2-month-old juvenile kangaroo only produced acetic acid and no methane. The stable highly enriched culture of the joey kangaroo was sequenced to examine the V3 and V4 regions of the 16S rRNA gene. The results showed that over 70% of gene copies belonged to the Clostridia class, with Paraclostridium and Blautia as the most predominant genera. The culture further showed the presence of Actinomyces spp., a genus which has only been identified in the GI tract of macropods in a few studies, and where none, to our knowledge, have been classified as homoacetogenic. The joey kangaroo mixed culture showed a doubling time of 3.54 h and a specific growth rate of 0.199/h, faster than what has been observed for homoacetogenic bacteria in general.

IMPORTANCE

Enteric methane emissions from cattle are a significant contributor to greenhouse gas emissions worldwide. Methane emissions not only contribute to climate change but also represent a loss of energy from the animal's diet. However, methanogens play an important role as hydrogen sink to rumen systems; without it, the performance of hydrolytic organisms diminishes. Therefore, effective strategies of methanogen inhibition would be enhanced in conjunction with the addition of alternative hydrogen sinks to the rumen. The significance of our research is to identify homoacetogens present in the GI tract of kangaroos and to present their performance in vitro, demonstrating their capability to serve as alternatives to rumen methanogens.

Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome

BACKGROUND

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

RESULTS

Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified.

CONCLUSION

The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.

Archaeal community composition as key driver of H2 consumption rates at the start-up of the biomethanation process

The performance of hydrogen consumption by various inocula derived from mesophilic anaerobic digestion plants was evaluated under ex situ biomethanation. A panel of 11 mesophilic inocula was operated at a concentration of 15 gVS.L-1 at a temperature of 35 °C in batch system with two successive injections of H2:CO2 (4:1 mol:mol). Hydrogen consumption and methane production rates were monitored from 44 h to 72 h. Hydrogen consumption kinetics varies significantly based on the inoculum origin, with no accumulation of volatile fatty acids. Microbial community analyses revealed that microbial indicators such as the increase in Methanosarcina sp. abundance and the increase of the Archaea/Bacteria ratio were associated to high initial hydrogen consumption rates. The improvement in the hydrogen consumption rate between the two injections was correlated with the enrichment in hydrogenotrophic methanogens. This work provides new insights into the early response of microbial communities to hydrogen injection and on the microbial structures that may favor their adaptation to the biomethanation process.

Valorization of organic carbon in primary sludge via semi-continuous dark fermentation: First step to establish a wastewater biorefinery

In this study, lab-scale, bench-scale, and pilot-scale experiments were carried out to optimize short-chain fatty acids production from primary sludge. Batch tests showed the requirement of short retention times and semi-continuous operation mode showed a plateau of maximum daily productivity at 36-hours hydraulic retention time with minimal methanation. Optimization from pH 5 to pH 10 at 36 h-hydraulic retention time under long-term semi-continuous operating mode revealed that production of short-chain fatty acids was pH dependent and highest yields could be achieved at pH 7 by establishing optimum redox conditions for fermentation. Pilot-scale experiments at 32 °C showed that daily productivity (3.1 g∙Lreactor-1∙dHRT-1) and yields (150 mg∙gVS-1; OLR = 21 gVS∙Lreactor-1∙dHRT-1; pH 7) of short-chain fatty acids could be significantly improved, specifically for acetic and propionic acids. From these results, a robust dark fermentation step for recovery of valuable products from the solids treatment step in a biorefinery can be achieved.

Harnessing Fermentation May Enhance the Performance of Biological Sulfate-Reducing Bioreactors

Biological sulfate reduction (BSR) represents a promising strategy for bioremediation of sulfate-rich waste streams, yet the impact of metabolic interactions on performance is largely unexplored. Here, genome-resolved metagenomics was used to characterize 17 microbial communities in reactors treating synthetic sulfate-contaminated solutions. Reactors were supplemented with lactate or acetate and a small amount of fermentable substrate. Of the 163 genomes representing all the abundant bacteria, 130 encode 321 NiFe and FeFe hydrogenases and all genomes of the 22 sulfate-reducing microorganisms (SRM) encode genes for H2 uptake. We observed lactate oxidation solely in the first packed bed reactor zone, with propionate and acetate oxidation in the middle and predominantly acetate oxidation in the effluent zone. The energetics of these reactions are very different, yet sulfate reduction kinetics were unaffected by the type of electron donor available. We hypothesize that the comparable rates, despite the typically slow growth of SRM on acetate, are a result of the consumption of H2 generated by fermentation. This is supported by the sustained performance of a predominantly acetate-supplemented stirred tank reactor dominated by diverse fermentative bacteria encoding FeFe hydrogenase genes and SRM capable of acetate and hydrogen consumption and CO2 assimilation. Thus, addition of fermentable substrates to stimulate syntrophic relationships may improve the performance of BSR reactors supplemented with inexpensive acetate.

A Review of Potential Feed Additives Intended for Carbon Footprint Reduction through Methane Abatement in Dairy Cattle

Eight rumen additives were chosen for an enteric methane-mitigating comparison study including garlic oil (GO), nitrate, Ascophyllum nodosum (AN), Asparagopsis (ASP), Lactobacillus plantarum (LAB), chitosan (CHI), essential oils (EOs) and 3-nitrooxypropanol (3-NOP). Dose-dependent analysis was carried out on selected feed additives using a meta-analysis approach to determine effectiveness in live subjects or potential efficacy in live animal trials with particular attention given to enteric gas, volatile fatty acid concentrations, and rumen microbial counts. All meta-analysis involving additives GO, nitrates, LAB, CHI, EOs, and 3-NOP revealed a reduction in methane production, while individual studies for AN and ASP displayed ruminal bacterial community improvement and a reduction in enteric CH4. Rumen protozoal depression was observed with GO and AN supplementation as well as an increase in propionate production with GO, LAB, ASP, CHI, and 3-NOP rumen fluid inoculation. GO, AN, ASP, and LAB demonstrated mechanisms in vitro as feed additives to improve rumen function and act as enteric methane mitigators. Enzyme inhibitor 3-NOP displays the greatest in vivo CH4 mitigating capabilities compared to essential oil commercial products. Furthermore, this meta-analysis study revealed that in vitro studies in general displayed a greater level of methane mitigation with these compounds than was seen in vivo, emphasising the importance of in vivo trials for final verification of use. While in vitro gas production systems predict in vivo methane production and fermentation trends with reasonable accuracy, it is necessary to confirm feed additive rumen influence in vivo before practical application.

Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle

Background

Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission.

Results

The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate.

Conclusion

Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.

Assessing feasible H2-CO2 sources in the US as Feedstocks for Sustainable Aviation Fuel Precursors: Acetic Acid and Ethanol Production via Hydrogenotrophic Pathways

The environmental impact of carbon dioxide emissions is significant, and research is focused on mitigating these emissions and developing eco-friendly technologies in line with green chemistry principles. Waste-to-energy technologies play a crucial role in converting waste into renewable energy and valuable biofuels and bioproducts. This study specifically explores the utilization of waste gas emissions, particularly carbon dioxide, from various sources in the United States for the production of sustainable aviation fuel (SAF) precursors, such as ethanol and acetic acid. The study categorizes and quantifies the volumes of carbon dioxide emissions into three types: non-biogenic, biogenic, and biogenic emissions from ethanol production facilities. Stoichiometric calculations are applied to compare the amounts of carbon dioxide from each category with the available hydrogen production capacity, determining if sufficient hydrogen is present for converting carbon dioxide into SAF precursors. The study reveals two key findings. Firstly, there is a significant reserve of carbon dioxide, approximately 1648 million metric tons per year (MMTy), combining all three categories, which would require a substantial increase of approximately 35-40 times in the existing hydrogen production capacity of 4.988 MMTy. This increased hydrogen production has the potential to yield approximately 1067.82 MMTy of acetic acid and 189.19 MMTy of ethanol annually. Secondly, upon analyzing the quality and application of the three sources of carbon dioxide with the currently available hydrogen production capacity, it is found that biogenic carbon dioxide from ethanol plants is the most suitable choice for immediate production of SAF precursors. This would theoretically result in an annual production of 1.36 MMTy of ethanol and 1.772 MMTy of acetic acid. The other two sources of carbon dioxide can be considered potential reserves for future utilization when additional hydrogen production facilities are established. The study provides a foundation for assessing the aggregation potential required for acetic acid and ethanol production. By optimizing the use of waste gases as raw materials, the study not only enables the production of SAF precursors but also contributes to the passive reduction of greenhouse gas emissions.

Influence of pH, Heat Treatment of Inoculum, and Selenium Oxyanions on Concomitant Selenium Bioremediation and Volatile Fatty Acid Production from Food Waste

Developing novel strategies to enhance volatile fatty acid (VFA) yield from abundant waste resources is imperative to improve the competitiveness of biobased VFAs over petrochemical-based VFAs. This study hypothesized to improve the VFA yield from food waste via three strategies, viz., pH adjustment (5 and 10), supplementation of selenium (Se) oxyanions, and heat treatment of the inoculum (at 85 °C for 1 h). The highest VFA yield of 0.516 g COD/g VS was achieved at alkaline pH, which was 45% higher than the maximum VFA production at acidic pH. Heat treatment resulted in VFA accumulation after day 10 upon alkaline pretreatment. Se oxyanions acted as chemical inhibitors to improve the VFA yield at pH 10 with non-heat-treated inoculum (NHT). Acetic and propionic acid production was dominant at alkaline pH (NHT); however, the VFA composition diversified under the other tested conditions. More than 95% Se removal was achieved on day 1 under all the conditions tested. However, the heat treatment was detrimental for selenate reduction, with less than 15% Se removal after 20 days. Biosynthesized Se nanoparticles were confirmed by transmission and scanning electron microscopy and and energy dispersive X-ray analyses. The heat treatment inhibited the presence of nonsporulating bacteria and methanogenic archaea (Methanobacteriaceae). High-throughput sequencing also revealed higher relative abundances of the bacterial families (such as Clostridiaceae, Bacteroidaceae, and Prevotellaceae) that are capable of VFA production and/or selenium reduction.

The evolving role of methanogenic archaea in mammalian microbiomes

Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.

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.

Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.

Prevotella: A Key Player in Ruminal Metabolism

Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. Prevotella is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in P. ruminicola strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus Prevotella have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of Prevotella in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice Prevotella researchers and as an update to others more conversant with the topic.

Draft Genome Sequence of the Extremely Haloalkaliphilic and Homoacetic Bacterium Natroniella acetigena Z-7937 T

Natroniella acetigena Z-7937^T (= DSM 9952^T) is a heterotrophic homoacetogenic natronophile. The draft genome sequence is 2.6 Mb in 116 contigs, with a G+C content of 34.1%.

Comparisons of Ramie and Corn Stover Silages: Effects on Chewing Activity, Rumen Fermentation, Microbiota and Methane Emissions in Goats

The study aimed to investigate the nutritional value of ramie (Boehmeria nivea) silage, and its consequences for chewing activity, rumen fermentation, and enteric methane (CH4) emissions in goats, by comparing it with corn stover (CS) silage. An in vitro ruminal experiment was firstly performed to investigate the substrate degradation and fermentation of CS and ramie silage. The ramie silage diet was formulated by replacing 60% of CS silage with ramie silage (dry matter (DM) basis). Eight female Xiangdong Black goats (a local breed in Southern China, 1 to 1.2 years of age) with BW of 21.0 ± 1.05 kg were used for this experiment and were randomly assigned to either one of the two dietary treatments in a cross-over design. The ramie silage had higher crude protein (CP) and ash content and lower hemicellulose content, together with decreased (p < 0.05) nutrient degradation and methane production and increased (p < 0.05) acetate molar percentage and acetate to propionate ratio through in vitro ruminal fermentation. Feeding the ramie silage diet did not alter feed intake (p > 0.05), decreased (p < 0.05) nutrient digestibility, and increased (p < 0.05) chewing activity and rumination activity, with reductions (p < 0.05) in eating activity and idle activity. Although feeding the ramie silage diet caused a greater (p < 0.05) molar percentage of acetate and lower molar percentage of propionate, it decreased the rumen-dissolved CH4 concentration and enteric CH4 emissions (p < 0.05). Feeding the ramie silage diet did not alter (p > 0.05) the population of bacteria, protozoa, and fungi; it increased the 16S rRNA gene copies of Ruminococcus flavefaciens (p < 0.05). Further 16SrRNA gene amplicon analysis indicated a distinct bacterial composition between the two treatments (p < 0.05). Feeding the ramie silage diet led to a lower abundance of genera Lawsonibacter, Sedimentibacter, Saccharofermentans, Sediminibacterium, and Bifidobacterium (p < 0.05). Ramie can be an alternative forage resource to stimulate chewing activity and reduce CH4 emissions in ruminants.

Microorganisms as New Sources of Energy

The use of fossil energy sources has a negative impact on the economic and socio-political stability of specific regions and countries, causing environmental changes due to the emission of greenhouse gases. Moreover, the stocks of mineral energy are limited, causing the demand for new types and forms of energy. Biomass is a renewable energy source and represents an alternative to fossil energy sources. Microorganisms produce energy from the substrate and biomass, i.e., from substances in the microenvironment, to maintain their metabolism and life. However, specialized microorganisms also produce specific metabolites under almost abiotic circumstances that often do not have the immediate task of sustaining their own lives. This paper presents the action of biogenic and biogenic–thermogenic microorganisms, which produce methane, alcohols, lipids, triglycerides, and hydrogen, thus often creating renewable energy from waste biomass. Furthermore, some microorganisms acquire new or improved properties through genetic interventions for producing significant amounts of energy. In this way, they clean the environment and can consume greenhouse gases. Particularly suitable are blue-green algae or cyanobacteria but also some otherwise pathogenic microorganisms (E. coli, Klebsiella, and others), as well as many other specialized microorganisms that show an incredible ability to adapt. Microorganisms can change the current paradigm, energy–environment, and open up countless opportunities for producing new energy sources, especially hydrogen, which is an ideal energy source for all systems (biological, physical, technological). Developing such energy production technologies can significantly change the already achieved critical level of greenhouse gases that significantly affect the climate.