Regulation of the methanogenesis pathways by hydrogen at transcriptomic level in time.

The biomethane formation from 4 H2 + CO2 by pure cultures of two methanogens, Methanocaldococcus fervens and Methanobacterium thermophilum, has been studied. The goal of the study was to understand the regulation of the enzymatic steps associated with biomethane biosynthesis by H2, using metagenomic, pan-genomic, and transcriptomic approaches. Methanogenesis in the autotrophic methanogen M. fervens could be easily "switched off" and "switched on" by H2/CO2 within about an hour. In contrast, the heterotrophic methanogen M. thermophilum was practically insensitive to the addition of the H2/CO2 trigger although this methanogen also converted H2/CO2 to CH4. From practical points of view, the regulatory function of H2/CO2 suggests that in the power-to-gas (P2G) renewable excess electricity conversion and storage systems, the composition of the biomethane-generating methanogenic community is essential for sustainable operation. In addition to managing the specific hydrogenotrophic methanogenesis biochemistry, H2/CO2 affected several, apparently unrelated, metabolic pathways. The redox-regulated overall biochemistry and symbiotic relationships in the methanogenic communities should be explored in order to make the P2G technology more efficient. KEY POINTS : • Hydrogenotrophic methanogens may respond distinctly to H2/CO2 in bio-CH4 formation. • H2/CO2 can also activate metabolic routes, which are apparently unrelated to methanogenesis. • Sustainable conversion of the fluctuating renewable electricity to bio-CH4 is an option.

Genetic polymorphism in European and African sheep breeds reared in Hungary based on 48 SNPs associated with resistance to gastrointestinal parasite infection using KASP-PCR technique.

This pilot study used an alternative and economically efficient technique, the Kompetitive Allele-Specific Polymerase Chain Reaction (KASP-PCR) to examine 48 SNPs from 11 parasite-resistance genes found on 8 chromosomes in 110 animals from five sheep breeds reared in Hungary; Hungarian Tsigai, White Dorper, Dorper, Ile de France, and Hungarian Merino. Allele and genotype frequencies, fixation index, observed heterozygosity, expected heterozygosity, F statistic, and their relationship with the Hardy-Weinberg equilibrium (WHE) and the polymorphic information content (PIC) were determined, followed by principal component analysis (PCA). As much as 32 SNPs out of the 48 initially studied were successfully genotyped. A total of 9 SNPs, 4 SNPs in TLR5, 1 SNP in TLR8, and 4 SNPs in TLR2 genes, were polymorphic. The variable genotype and allele frequency of the TLRs gene indicated genetic variability among the studied sheep breeds, with the Hungarian Merino exhibiting the most polymorphisms, while Dorper was the population with the most SNPs departing from the HWE. According to the PIC value, the rs430457884-TLR2, rs55631273-TLR2, and rs416833129-TLR5 were found to be informative in detecting polymorphisms among individuals within the populations, whereas the rs429546187-TLR5 and rs424975389-TLR5 were found to have a significant influence in clustering the population studied. This study reported a moderate level of genetic variability and that a low to moderate within-breed diversity was maintained in the studied populations.

Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics.

BACKGROUND: The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies. RESULTS: The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria. CONCLUSIONS: External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.

Regenerative medicine: characterization of human bone matrix gelatin (BMG) and folded platelet-rich fibrin (F-PRF) membranes alone and in combination (sticky bone).

During the last two decades autologous platelet and leukocyte rich products (PRP; PRF), opened new perspectives in regenerative medicine. In particular regenerative dentistry played a pioneer role in the application of these products in bone regenerative cases. Many aspects of cytokines, such as, growth factor release, blood cell content and its characterization were reported, but some practical questions are still unanswered in the preparation of PRF membranes and sticky bones. A new folding technique was introduced that created a good quality, pliable, and strong F-PRF membrane with a dense fibrin network and more homogenous blood cell distribution. F-PRF produced a very promising sticky bone combined with human freeze-dried cortical bone matrix gelatin (BMG). There hasn't been much focus on the quality and character of the applied bone and the optimal membrane/bone particle ratio has not been reported. A 0.125 g BMG/ml plasma (1 g/8 ml) seems like the ideal combination with maximal BMG adhesion capacity of the membrane. Particle distribution of BMG showed that 3/4 of the particles ranged between 300-1000 µ, the remnant 1/4 was smaller than 300 µ. The whole F-PRF membrane and its parts were compared with conventional A-PRF membrane concerning their resistance against proteolytic digestion. The F-PRF was superior to A-PRF, which dissolved within 4-5 days, while F-PRF was destroyed only after 11 days, so this provides a better chance for local bone morphogenesis. The F-PRF pieces had similar resistance to the whole intact one, so they can be ideal for surgical procedures without risk of fast disintegration.

Anaerobic gaseous biofuel production using microalgal biomass - A review.

Most photosynthetic organisms store and convert solar energy in an aerobic process and produce biomass for various uses. Utilization of biomass for the production of renewable energy carriers employs anaerobic conditions. This review focuses on microalgal biomass and its use for biological hydrogen and methane production. Microalgae offer several advantages compared to terrestrial plants. Strategies to maintain anaerobic environment for biohydrogen production are summarized. Efficient biogas production via anaerobic digestion is significantly affected by the biomass composition, pretreatment strategies and the parameters of the digestion process. Coupled biohydrogen and biogas production increases the efficiency and sustainability of renewable energy production.

Adaptation of continuous biogas reactors operating under wet fermentation conditions to dry conditions with corn stover as substrate.

Corn stover (CS) is the agricultural by-product of maize cultivation. Due to its high abundance and high energy content it is a promising substrate for the bioenergy sector. However, it is currently neglected in industrial scale biogas plants, because of its slow decomposition and hydrophobic character. To assess the maximum biomethane potential of CS, long-term batch fermentations were carried out with various substrate concentrations and particle sizes for 72 days. In separate experiments we adapted the biogas producing microbial community in wet fermentation arrangement first to the lignocellulosic substrate, in Continuous Stirred Tank Reactor (CSTR), then subsequently, by continuously elevating the feed-in concentration, to dry conditions in solid state fermenters (SS-AD). In the batch tests, the <10 mm fraction of the grinded and sieved CS was amenable for biogasification, but it required 10% more time to produce 90% of the total biomethane yield than the <2 mm sized fraction, although in the total yields there was no significant difference between the two size ranges. We also observed that increasing amount of substrate added to the fermentation lowered the specific methane yield. In the CSTR experiment, the daily substrate loading was gradually increased from 1 to 2 gvs/L/day until the system produced signs of overloading. Then the biomass was transferred to SS-AD reactors and the adaptation process was studied. Although the specific methane yields were lower in the SS-AD arrangement (177 mL CH4/gvs in CSTR vs. 105 mL in SS-AD), the benefits of process operational parameters, i.e. lower energy consumption, smaller reactor volume, digestate amount generated and simpler configuration, may compensate the somewhat lower yield.

Pretreatment of poultry manure for efficient biogas production as monosubstrate or co-fermentation with maize silage and corn stover.

Water extraction of raw chicken manure elevated the carbon-to-nitrogen ratio 2.7-fold, i.e. from 7.48 to 19.81. The treated chicken manure (T-CM) thus became suitable for biogas fermentation as monosubstrate. Improved methane production was achieved in co-fermentations with either maize silage (24% more methane) or corn stover (19% more methane) relative to T-CM monosubstrate. The standardized biogas potential assay indicated that the methane yields varied with the organic loading rate between 160 and 250 mL CH4/g organic total solid (oTS). Co-fermentation with maize silage was sustainable in continuous anaerobic digestion for at least 4 months.

Bioaugmentation of the thermophilic anaerobic biodegradation of cellulose and corn stover.

Two stable, thermophilic mixed cellulolytic consortia were enriched from an industrial scale biogas fermenter. The two consortia, marked as AD1 and AD2, were used for bioaugmentation in laboratory scale batch reactors. They enhanced the methane yield by 22-24%. Next generation sequencing method revealed the main orders being Thermoanaerobacterales and Clostridiales and the predominant strains were Thermoanaerobacterium thermosaccharolyticum, Caldanaerobacter subterraneus, Thermoanaerobacter pseudethanolicus and Clostridium cellulolyticum. The effect of these strains, cultivated in pure cultures, was investigated with the aim of reconstructing the defined cellulolytic consortium. The addition of the four bacterial strains and their mixture to the biogas fermenters enhanced the methane yield by 10-11% but it was not as efficient as the original communities indicating the significant contribution by members of the enriched communities present in low abundance.

Biomethane: The energy storage, platform chemical and greenhouse gas mitigation target.

Results in three areas of anaerobic microbiology in which methane formation and utilization plays central part are reviewed. a.) Bio-methane formation by reduction of carbon dioxide in the power-to-gas process and the various possibilities of improvement of the process is a very intensively studied topic recently. From the numerous potential methods of exploiting methane of biological origin two aspects are discussed in detail. b.) Methane can serve as a platform chemical in various chemical and biochemical synthetic processes. Particular emphasis is put on the biochemical conversion pathways involving methanotrophs and their methane monooxygenase-catalyzed reactions leading to various small molecules and polymeric materials such as extracellular polysaccharides, polyhydroxyalkanoates and proteins. c.) The third area covered concerns methane-consuming reactions and methane emission mitigation. These investigations comprise the anaerobic microbiology of ruminants and approaches to diminishing methane emissions from ruminant animals.

Buzzing with Intelligence: Current Issues in Apiculture and the Role of Artificial Intelligence (AI) to Tackle It.

Honeybees (Apis mellifera L.) are important for agriculture and ecosystems; however, they are threatened by the changing climate. In order to adapt and respond to emerging difficulties, beekeepers require the ability to continuously monitor their beehives. To carry out this, the utilization of advanced machine learning techniques proves to be an exceptional tool. This review provides a comprehensive analysis of the available research on the different applications of artificial intelligence (AI) in beekeeping that are relevant to climate change. Presented studies have shown that AI can be used in various scientific aspects of beekeeping and can work with several data types (e.g., sound, sensor readings, images) to investigate, model, predict, and help make decisions in apiaries. Research articles related to various aspects of apiculture, e.g., managing hives, maintaining their health, detecting pests and diseases, and climate and habitat management, were analyzed. It was found that several environmental, behavioral, and physical attributes needed to be monitored in real-time to be able to understand and fully predict the state of the hives. Finally, it could be concluded that even if there is not yet a full-scale monitoring method for apiculture, the already available approaches (even with their identified shortcomings) can help maintain sustainability in the changing apiculture.

A Review on Indigenous Goats of East Africa: A Case for Conservation and Management.

Indigenous goats are important in the livelihoods of rural households in East African countries. This is due to their ability to produce and reproduce in different environments and climatic conditions. Even though these indigenous goats are important, there is little available information on the genetic characterization of these breeds in Africa and at the international level. This paper reviews the status of indigenous goats, highlighting their production systems, phenotypic and genetic characteristics, and genetic diversity, and proposes potential ways for sustainable improvement and conservation in East African countries. Most households use traditional production systems with various uncharacterized goat breeds and ecotypes, which are hence named after the tribe or locality in which they are found. Most of these goats are classified as small East African breeds, with significant variability in morphological features. Some of the challenges to goat production in this region are indiscriminate crossbreeding, lack of pedigree records, parasites and disease incidences, low-quality pastures, and low levels of management. There is a need for a collaborative approach amongst the actors in goat breeding value chains as well as integrating modern genomic tools into breeding programs to enhance selection. This will ensure the resilience and sustainability of these unique indigenous goat populations in East Africa.

Application potential of chicken DNA chip in domestic pigeon species - Preliminary results.

Introducing the SNP technology to pigeon breeding will enhance the competitiveness of a sector that produces one of the healthiest and best quality meats. The present study aimed to test the applicability of the Illumina Chicken_50K_CobbCons array on 24 domestic pigeon individuals from the Mirthys hybrids and Racing pigeon breeds. A total of 53,313 SNPs were genotyped. Principal component analysis shows a significant overlap between the two groups. The chip performed poorly in this data set, with a call rate per sample of 0.474 (49%). The low call rate was likely due to an increase in the evolutionary distance. A total of 356 SNPs were retained after a relatively strict quality control. We have demonstrated that it is technically feasible to use a chicken microarray chip on pigeon samples. Presumably, with a larger sample size and by assigning phenotypic data, efficiency would be improved, allowing more thorough analyses, such as genome-wide association studies.

Effect of ad libitum feeding of Holstein Friesian calves on immunological parameters and molecular stress on a transcriptional level.

Our aim was to compare the health and performance of ad libitum (ADLIB) and restrictedly fed Holstein Friesian heifer calves. Calves were selected to ADLIB (n = 13) and control (n = 13) groups randomly. The period of ADLIB feeding lasted for 3 weeks after colostrum supplementation. The calves in the control group received the same milk replacer, which was supplied according to the restrained feeding schedule of the farm. There was no difference between the two groups in weight, weight gain or movement activity, furthermore in the values of glucose, albumin, total protein, BHB, AST, oxidant and antioxidant status incl. dROM, PAT and OSI. The IL8 gene had higher levels (non significant, p > 0.05) of expression in the ADLIB group during the first 20 days of life, which indicates that ADLIB feeding might potentiate a stronger immune response to environmental stress. The IGF1 gene showed increased expression in the ADLIB fed group at almost all time points, however the difference was already detected on the first day of the study, indicating the importance of individual differences even within the same breed. During the first 10 days INS expression was higher in the restricted group, followed by a shift by day 20 and after, when the ADLIB group showed a higher relative expression level. The observed values describe a trend that, although not significant (p > 0.05), would seem to indicate that ADLIB feeding might potentiate a stronger immune response to environmental stress.

Hungarian indigenous Tsigai, a promising breed for excellent heat tolerance and immunity.

The adverse effects of climate change on sheep farming have become more noticeable in recent decades. Extensive efforts have been made to untangle the complex relationship between heat tolerance, animal health, and productivity, also to identify a resilient and economically suitable breed for selection that can be resilient to future climate change conditions. Using quantitative real-time polymerase chain reaction (qRT-PCR), we observed the seasonal variations in the expression of several important genes related to heat stress and immunity (HSP70, IL10, TLR2, TLR4, and TLR8) in three of the most widely kept sheep breeds in Hungary: The indigenous Tsigai, Hungarian Merino, and White Dorper. We found that the seasonal stressor affected the relative gene expression of all genes in this study. Notably, The Hungarian indigenous Tsigai was the most robust breed adapted to the Hungarian continental (hot summer, cold winter) environment, with excellent thermotolerance and immunity. Furthermore, despite suffering from heat stress in the summer, Hungarian Merino maintained their robust immune system well throughout the year.

A review on the potential effects of environmental and economic factors on sheep genetic diversity: Consequences of climate change.

Climate change has a significant effect on the productivity of livestock including milk, meat, and reproduction. This could be attributed to the internal diversion of energy resources towards adaptive mechanisms. Among the climate change variables, thermal stress seems to be the major limiting factor in animal agriculture. A better understanding of the effects of climate change-influenced ecological factors on the genetic diversity of livestock species is warranted. Sheep is an ideal livestock species to be used in investigating environmental adaptation due to its wide range of agroecological habitats, genetic and phenotypic variability. There is a heavy reliance on sheep genetic diversity for future animal protein security, but the implications of climate change on their genetic diversity receive less attention. Here, the potential environmental factors influencing natural selection in sheep populations are presented. We argue that prolonged exposure to these factors plays a major role in influencing the development of adaptation traits in indigenous sheep breeds, consequently leading to the alteration of genetic diversity at specific loci. The factors discussed include hot temperatures (heat stress), insufficient water, low quantity and quality of forage, and prevalence of parasites, pests, and diseases. In addition, genetic diversity, some signatures of selection for adaptation and economic angles of selection are also briefly discussed. A better understanding of environmental factors influencing the genetic diversity of sheep populations will inform breeding and management programs and may offer an opportunity for greater production efficiency with low input costs.

Assessing the Genomics Structure of Dorper and White Dorper Variants, and Dorper Populations in South Africa and Hungary.

Dorper sheep was developed for meat production in arid and semi-arid regions under extensive production systems in South Africa. Two variants with distinct head and neck colors were bred during their development process. White Dorper have a white coat while Dorper have a black head and neck. Both variants have grown in popularity around the world. Therefore, understanding the genomic architecture between South African Dorpers and Dorper populations adapted to other climatic regions, as well as genomic differences between Dorper and White Dorper variants is vital for their molecular management. Using the ovine 50K SNP chip, this study compared the genetic architecture of Dorper variants between populations from South Africa and Hungary. The Dorper populations in both countries had high genetic diversity levels, although Dorper in Hungary showed high levels of inbreeding. White Dorpers from both countries were genetically closely related, while Dorpers were distantly related according to principal component analysis and neighbor-joining tree. Additionally, whereas all groups displayed unique selection signatures for local adaptation, Dorpers from Hungary had a similar linkage disequilibrium decay. Environmental differences and color may have influenced the genetic differentiation between the Dorpers. For their molecular management and prospective genomic selection, it is crucial to understand the Dorper sheep's genomic architecture, and the results of this study can be interpreted as a step in this direction.

Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants.

Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H2/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.

Association study between relative expression levels of eight genes and growth rate in Hungarian common carp (Cyprinus carpio).

One of the most important issues in improving the competitiveness of the fish production sector is to improve the growth rate of fish. The genetic background to this trait is at present poorly understood. In this study, we compared the relative gene expression levels of the Akt1s1, FGF, GH, IGF1, MSTN, TLR2, TLR4 and TLR5 genes in blood in groups of common carps (Cyprinus carpio), which belonged to different growth types and phenotypes. Fish were divided into groups based on growth rate (normal group: n = 6; slow group: n = 6) and phenotype (scaled group: n = 6; mirror group: n = 6). In the first 18 weeks, we measured significant differences (p < 0.05) between groups in terms of body weight and body length. Over the next 18 weeks, the fish in the slow group showed more intense development. In the same period, the slow group was characterized by lower expression levels for most genes, whereas GH and IGF1 mRNA levels were higher compared to the normal group. We found that phenotype was not a determining factor in differences of relative expression levels of the genes studied.

Genes and elements involved in the regulation of the nervous system and growth affect the development of spinal deformity in Cyprinus carpio.

Spinal deformity is a serious economic and animal welfare problem in intensive fish farming systems, which will be a significant unsolved problem for the fish sector. The aim of this study was to determine the relative expression of genes (Akt1 substrate 1, Calreticulin, Collagen type I alpha 2 chain, Corticotropin-releasing hormone, Chromodomain-Helicase DNA-binding, Growth hormone, Insulin like growth factor 1, Myostatin, Sine oculis-related homeobox 3, Toll-like receptor 2) in different tissues associated with spinal deformity and to determine the macroelement (calcium, magnesium, phosphorus, potassium, sodium, sulfur) and microelement (barium, copper, iron, manganese, strontium, zinc) content of spine in healthy and deformed common carps (Cyprinus carpio) in Hungary. The mRNA levels of the genes were measured in 7 different tissues (abdominal fat, blood, brain, dorsal muscle, genitals, heart, liver) by qRT-PCR. Correlations between gene expression and element content were analyzed by using linear regression and Spearman rank correlation. In a total of 15 cases, we found a statistically significant connection between gene expression in a tissue and the macro- or microelement content of the spine. In these contexts, the genes Akt1 substrate 1 (3), Collagen type I alpha 2 chain (2), Corticotropin-releasing hormone (4), Insulin-like growth factor 1 (4), and Myostatin (2), the tissue's blood (3), brain (6), heart (5), and liver (1), the macroelements sodium (4), magnesium (4), phosphorus (1) and sulfur (2) as well as the microelement iron (4) were involved. We also found statistically significant mRNA level differences between healthy and deformed common carps in tissues that were not directly affected by the deformation. Based on our results, genes regulating the nervous system and growth, elements, and tissues are the most associated components in the phenomenon of spinal deformity. With our study, we wish to give direction to and momentum for the exploration of these complex processes.

Pretreatment of lignocellulosic biogas substrates by filamentous fungi.

Decomposition of lignocellulosic plant biomass by four filamentous fungi was carried out to facilitate subsequent anaerobic degradation and biogas formation. Agricultural side products, wheat straw and corn stover and forestry energy plant willow chips were selected as plant biomass sources. The substrates were confronted by pure cultures of Penicillium aurantiogriseum (new isolate from rumen), Trichoderma reesei (DSM768), Gilbertella persicaria (SZMC11086) and Rhizomucor miehei (SZMC11005). In addition to total cellulolytic filter paper degradation activity, the production of endoglucanase, cellobiohydrolase, ß-glucosidase enzymes were followed during the pretreatment period, which lasted for 10 days at 37 °C. The products of pretreatments were subsequently tested for mesophilic biogas production in batch reactors. All 4 strains effectively pretreated the lignocellulosic substrates albeit in varying degrees, which was related to the level of the tested hydrolytic enzyme activities. Penicillium aurantiogriseum showed outstanding hydrolytic enzyme production and highest biogas yield from the partially degraded substrates. Corn stover was the best substrate for biomass decomposition and biogas production. Scanning electron microscopy confirmed the deep penetration of fungal hyphae into the lignocellulosic substrate in all cases.