Methane as a resource: can the methanotrophs add value?

Sustainable production of C50 carotenoid bacterioruberin from methane using soil-enriched microbial consortia

Bacterioruberin is widely used in medicine, food, and cosmetics owing to its prominent characteristics of antioxidants and bioactivities. Bioconversion of methane into bacterioruberin is a promising way to address biomanufacturing substrate costs and greenhouse gas emissions but has not been achieved yet. Herein, this study aimed to upcycle methane to bacterioruberin by microbial consortia. The microbial consortia consist of Methylomonas and Methylophilus capable of synthesizing carotenoids from methane was firstly enriched from paddy soil. Through this microbial community, methane was successfully converted into C50 bacterioruberin for the first time. The bioconversion process was then optimized by the response surface methodology. Finally, the methane-derived bacterioruberin reached a record yield of 280.88 ± 2.94 μg/g dry cell weight. This study presents a cost-effective and eco-friendly approach for producing long-chain carotenoids from methane, offering a significant advancement in the direct conversion of greenhouse gases into value-added products.

Microbial upcycling of methane to phytoene using metabolically engineered Methylocystis sp. MJC1 strain

Methane, a potent greenhouse gas, requires sustainable mitigation strategies. Here, the microbial upcycling of methane to phytoene, a valuable colorless carotenoid with applications in the cosmeceutical industry was demonstrated. To achieve this goal, a stepwise metabolic engineering approach was employed in Methylocystis sp. MJC1, a methane-oxidizing bacterium. The incorporation of crtE and crtB genes from Deinococcus radiodurans R1 established the phytoene biosynthetic pathway. This pathway was fine-tuned through promoter optimization, resulting in a phytoene production of 450 μg/L from 37 mmol/L methane. Disrupting the ackA gene reduced a by-product, acetate, by 50 % and increased phytoene production by 56 %. Furthermore, overexpressing the dxs gene boosted phytoene titer 3-fold. The optimized strain produced 15 mg/L phytoene from 2 mol/L methane in fed-batch fermentation, a 4-fold increase in phytoene titer and 4-fold in yield. This demonstrates Methylocystis sp. MJC1's potential for efficient phytoene production and presents a novel approach for greenhouse gas reduction.

Replacement of fishmeal with a microbial single-cell protein induced enteropathy and poor growth outcomes in barramundi (Lates calcarifer) fry

Fish meal (FM) replacement is essential for the sustainable expansion of aquaculture. This study focussed on the feasibility of replacing FM with a single-cell protein (SCP) derived from methanotrophic bacteria (Methylococcus capsulatus, Bath) in barramundi fry (Lates calcarifer). Three isonitrogenous and isoenergetic diets were formulated with 0%, 6.4% and 12.9% inclusion of the SCP, replacing FM by 0%, 25% and 50%. Barramundi fry (initial body weight 2.5 ± 0.1 g) were fed experimental diets for 21 days to assess growth performance, gut microbiome composition and gut histopathology. Our findings revealed that both levels of SCP inclusion induced detrimental effects in barramundi fry, including impaired growth and reduced survival compared with the control group (66.7% and 71.7% survival in diets replacing FM with SCP by 25% and 50%, respectively; p < .05). Both dietary treatments presented mild necrotizing enteritis with subepithelial oedema and accumulation of PAS positive, diastase resistant droplets within hepatocytes (ceroid hepatopathy) and pancreatic atrophy. Microbiome analysis revealed a marked shift in the gut microbial community with the expansion of potential opportunistic bacteria in the genus Aeromonas. Reduced overall performance in the highest inclusion level (50% SCP) was primarily associated with reduced feed intake, likely related to palatability issues, albeit pathological changes observed in gut and liver may also play a role. Our study highlights the importance of meticulous optimization of SCP inclusion levels in aquafeed formulations, and the need for species and life-stage specific assessments to ensure the health and welfare of fish in sustainable aquaculture practices.

Optimization of methane gas-liquid mass transfer during biogas-based ectoine production in bubble column bioreactors

Nowadays, the utilization of biogas for energy generation is hindered by the declining production costs of solar and wind power. A shift towards the valorization of biogas into ectoine, a highly valuable bioproduct priced at 1000 €⸱kg-1, offers a novel approach to fostering a more competitive biogas market while contributing to carbon neutrality. This study evaluated the optimization of CH4 gas-liquid mass transfer in 10 L bubble column bioreactors for CH4 conversion into ectoine and hydroxyectoine using a mixed methanotrophic culture. The influence of the empty bed residence time (EBRTs of 27, 54, and 104 min) at different membrane diffuser pore sizes (0.3 and 0.6 mm) was investigated. Despite achieving CH4 elimination capacities (CH4-ECs) of 10-12 g⸱m-3⸱h-1, an EBRT of 104 min mediated CH4 limitation within the cultivation broth, resulting in a negligible biomass growth. Reducing the EBRT to 54 min entailed CH4-ECs of 21-24 g⸱m-3⸱h-1, concomitant to a significant increase in biomass growth (up to 0.17 g⸱L⸱d-1) and reaching maximum ectoine and hydroxyectoine accumulation of 79 and 13 mg⸱gVSS-1, respectively. Conversely, process operation at an EBRT of 27 min lead to microbial inhibition, resulting in a reduced biomass growth of 0.09 g⸱L⸱d-1 and an ectoine content of 47 mg⸱gVSS-1. While the influence of diffuser pore size was less pronounced compared to EBRT, the optimal process performance was observed with a diffuser pore size of 0.6 mm.

Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization

In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.

Agro-technologies for greenhouse gases mitigation in flooded rice fields for promoting climate smart agriculture

We investigated methane (CH4) and nitrous oxide (N2O), two important greenhouse gases (GHGs) emissions using the closed chamber method from a flooded rice field in Brahmaputra valley of Assam, northeast part of India. We tried to understand the factors responsible for the emission and identify appropriate agro-technologies for their mitigation. Various factors like water level, drainage management, soil organic carbon management, crop management, fertilizer amendment, cultivar type etc. affect the GHG production and emission from the flooded rice soil. In this study, six treatments were employed, namely, farmer's practice (FP), recommended fertilizer dosage (RDF), direct seeded rice (DSR), intermittent wetting drying (IWD), use of efficient methanotrophs (MTH), and use of ammonium sulfate as a nitrogen source for real-time nitrogen management using leaf color chart, (AS). GHG flux was measured through the static closed chamber technique. Soil temperature, pH, and redox potential (Eh) and other soil physico-chemical and biological properties that have a potential role in GHG emission were also assessed. The lowest CH4 flux was observed in IWD treatment. The highest CH4 but lowest N2O flux was observed in RDF thus portraying a tradeoff relationship among these two GHGs. The highest N2O flux was observed in AS. Changes in Eh strongly altered CH4 and N2O emissions. The CH4 flux for the growing season varied from 62.5 to 86.3 kg ha-1 with an average of 72.4 kg ha-1. The average N2O flux was 0.89 kg ha-1 with values fluctuating between 0.72 - and 1.08 kg ha-1. The findings of this study could assist in understanding the factors affecting the source, production, and sink of these two important GHGs. IWD, along with judicious N-based fertilizer use, could provide significant respite from GHG emissions in rice-based agriculture. These climate-smart strategies not only reduce emissions but also have the potential to improve yield.

Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss

Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d-1 and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d-1, respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.

Methylosinus trichosporium OB3b bioaugmentation unleashes polyhydroxybutyrate-accumulating potential in waste-activated sludge

BACKGROUND

Wastewater treatment plants contribute approximately 6% of anthropogenic methane emissions. Methanotrophs, capable of converting methane into polyhydroxybutyrate (PHB), offer a promising solution for utilizing methane as a carbon source, using activated sludge as a seed culture for PHB production. However, maintaining and enriching PHB-accumulating methanotrophic communities poses challenges.

RESULTS

This study investigated the potential of Methylosinus trichosporium OB3b to bioaugment PHB-accumulating methanotrophic consortium within activated sludge to enhance PHB production. Waste-activated sludges with varying ratios of M. trichosporium OB3b (1:0, 1:1, 1:4, and 0:1) were cultivated. The results revealed substantial growth and methane consumption in waste-activated sludge with M. trichosporium OB3b-amended cultures, particularly in a 1:1 ratio. Enhanced PHB accumulation, reaching 37.1% in the same ratio culture, indicates the dominance of Type II methanotrophs. Quantification of methanotrophs by digital polymerase chain reaction showed gradual increases in Type II methanotrophs, correlating with increased PHB production. However, while initial bioaugmentation of M. trichosporium OB3b was observed, its presence decreased in subsequent cycles, indicating the dominance of other Type II methanotrophs. Microbial community analysis highlighted the successful enrichment of Type II methanotrophs-dominated cultures due to the addition of M. trichosporium OB3b, outcompeting Type I methanotrophs. Methylocystis and Methylophilus spp. were the most abundant in M. trichosporium OB3b-amended cultures.

CONCLUSIONS

Bioaugmentation strategies, leveraging M. trichosporium OB3b could significantly enhance PHB production and foster the enrichment of PHB-accumulating methanotrophs in activated sludge. These findings contribute to integrating PHB production in wastewater treatment plants, providing a sustainable solution for resource recovery.

A rationally designed miniature of soluble methane monooxygenase enables rapid and high-yield methanol production in Escherichia coli

Soluble methane monooxygenase (sMMO) oxidizes a wide range of carbon feedstocks (C1 to C8) directly using intracellular NADH and is a useful means in developing green routes for industrial manufacturing of chemicals. However, the high-throughput biosynthesis of active recombinant sMMO and the ensuing catalytic oxidation have so far been unsuccessful due to the structural and functional complexity of sMMO, comprised of three functionally complementary components, which remains a major challenge for its industrial applications. Here we develop a catalytically active miniature of sMMO (mini-sMMO), with a turnover frequency of 0.32 s-1, through an optimal reassembly of minimal and modified components of sMMO on catalytically inert and stable apoferritin scaffold. We characterise the molecular characteristics in detail through in silico and experimental analyses and verifications. Notably, in-situ methanol production in a high-cell-density culture of mini-sMMO-expressing recombinant Escherichia coli resulted in higher yield and productivity (~ 3.0 g/L and 0.11 g/L/h, respectively) compared to traditional methanotrophic production.

Optimization of electroporation method and promoter evaluation for type-1 methanotroph, Methylotuvimicrobium alcaliphilum

Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, Methylotuvimicrobium alcaliphilum using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type M. alcaliphilum strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.

High production of ectoine from methane in genetically engineered Methylomicrobium alcaliphilum 20Z by preventing ectoine degradation

BACKGROUND

Methane is a greenhouse gas with a significant potential to contribute to global warming. The biological conversion of methane to ectoine using methanotrophs represents an environmentally and economically beneficial technology, combining the reduction of methane that would otherwise be combusted and released into the atmosphere with the production of value-added products.

RESULTS

In this study, high ectoine production was achieved using genetically engineered Methylomicrobium alcaliphilum 20Z, a methanotrophic ectoine-producing bacterium, by knocking out doeA, which encodes a putative ectoine hydrolase, resulting in complete inhibition of ectoine degradation. Ectoine was confirmed to be degraded by doeA to N-α-acetyl-L-2,4-diaminobutyrate under nitrogen depletion conditions. Optimal copper and nitrogen concentrations enhanced biomass and ectoine production, respectively. Under optimal fed-batch fermentation conditions, ectoine production proportionate with biomass production was achieved, resulting in 1.0 g/L of ectoine with 16 g/L of biomass. Upon applying a hyperosmotic shock after high-cell-density culture, 1.5 g/L of ectoine was obtained without further cell growth from methane.

CONCLUSIONS

This study suggests the optimization of a method for the high production of ectoine from methane by preventing ectoine degradation. To our knowledge, the final titer of ectoine obtained by M. alcaliphilum 20ZDP3 was the highest in the ectoine production from methane to date. This is the first study to propose ectoine production from methane applying high cell density culture by preventing ectoine degradation.

The fundamental role of pH in CH4 bioconversion into polyhydroxybutyrate in mixed methanotrophic cultures

Climate change and plastic pollution are likely the most relevant challenges for the environment in the 21st century. Developing cost-effective technologies for the bioconversion of methane (CH4) into polyhydroxyalkanoates (PHAs) could simultaneously mitigate CH4 emissions and boost the commercialization of biodegradable polymers. Despite the fact that the role of temperature, nitrogen deprivation, CH4:O2 ratio or micronutrients availability on the PHA accumulation capacity of methanotrophs has been carefully explored, there is still a need for optimization of the CH4-to-PHA bioconversion process prior to becoming a feasible platform in future biorefineries. In this study, the influence of different cultivation broth pH values (5.5, 7, 8.5 and 10) on bacterial biomass growth, CH4 bioconversion rate, PHA accumulation capacity and bacterial community structure was investigated in a stirred tank bioreactor under nitrogen deprivation conditions. Higher CH4 elimination rates were obtained at increasing pH, with a maximum value of 50.4 ± 2.7 g CH4·m-3·h-1 observed at pH 8.5. This was likely mediated by an increased ionic strength in the mineral medium, which enhanced the gas-liquid mass transfer. Interestingly, higher PHB accumulations were observed at decreasing pH, with the highest PHB contents recorded at a pH 5.5 (43.7 ± 3.4 %w·w-1). The strong selective pressure of low pH towards the growth of Type II methanotrophic bacteria could explain this finding. The genus Methylocystis increased its abundance from 34 % up to 85 and 90 % at pH 5.5 and 7, respectively. On the contrary, Methylocystis was less abundant in the community enriched at pH 8.5 (14 %). The accumulation of intracellular PHB as energy and carbon storage material allowed the maintenance of high CH4 biodegradation rates during 48 h after complete nitrogen deprivation. The results here obtained demonstrated for the first time a crucial and multifactorial role of pH on the bioconversion performance of CH4 into PHA.

Unlocking synergies: Harnessing the potential of biological methane sequestration through metabolic coupling between Methylomicrobium alcaliphilum 20Z and Chlorella sp. HS2

A halotolerant consortium between microalgae and methanotrophic bacteria could effectively remediate in situ CH4 and CO2, particularly using saline wastewater sources. Herein, Methylomicrobium alcaliphilum 20Z was demonstrated to form a mutualistic association with Chlorella sp. HS2 at a salinity level above 3.0%. Co-culture significantly enhanced the growth of both microbes, independent of initial inoculum ratios. Additionally, increased methane provision in enclosed serum bottles led to saturated methane removal. Subsequent analyses suggested nearly an order of magnitude increase in the amount of carbon sequestered in biomass in methane-fed co-cultures, conditions that also maintained a suitable cultural pH suitable for methanotrophic growth. Collectively, these results suggest a robust metabolic coupling between the two microbes and the influence of the factors other than gaseous exchange on the assembled consortium. Therefore, multi-faceted investigations are needed to harness the significant methane removal potential of the identified halotolerant consortium under conditions relevant to real-world operation scenarios.

The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter

BACKGROUND

Moonmilk represents complex secondary structures and model systems to investigate the interaction between microorganisms and carbonatic rocks. Grotta Nera is characterized by numerous moonmilk speleothems of exceptional size hanging from the ceiling, reaching over two meters in length. In this work we combined microbiological analyses with analytical pyrolysis and carbon stable isotope data to determine the molecular composition of these complex moonmilk structures as well as the composition of the associated microbiota.

RESULTS

Three moonmilk structures were dissected into the apical, lateral, and core parts, which shared similar values of microbial abundance, richness, and carbon isotopes but different water content, microbiota composition, and organic matter. Moonmilk parts/niches showed higher values of microbial biomass and biodiversity compared to the bedrock (not showing moonmilk development signs) and the waters (collected below dripping moonmilk), indicating the presence of more complex microbial communities linked to carbonate rock interactions and biomineralization processes. Although each moonmilk niche was characterized by a specific microbiota as well as a distinct organic carbon profile, statistical analyses clustered the samples in two main groups, one including the moonmilk lateral part and the bedrock and the other including the core and apical parts of the speleothem. The organic matter profile of both these groups showed two well-differentiated organic carbon groups, one from cave microbial activity and the other from the leaching of vascular plant litter above the cave. Correlation between organic matter composition and microbial taxa in the different moonmilk niches were found, linking the presence of condensed organic compounds in the apical part with the orders Nitrospirales and Nitrosopumilales, while different taxa were correlated with aromatic, lignin, and polysaccharides in the moonmilk core. These findings are in line with the metabolic potential of these microbial taxa suggesting how the molecular composition of the preserved organic matter drives the microbiota colonizing the different moonmilk niches. Furthermore, distinct bacterial and archaeal taxa known to be involved in the metabolism of inorganic nitrogen and C1 gases (CO2 and CH4) (Nitrospira, Nitrosopumilaceae, Nitrosomonadaceae, Nitrosococcaceae, and novel taxa of Methylomirabilota and Methanomassiliicoccales) were enriched in the core and apical parts of the moonmilk, probably in association with their contribution to biogeochemical cycles in Grotta Nera ecosystem and moonmilk development.

CONCLUSIONS

The moonmilk deposits can be divided into diverse niches following oxygen and water gradients, which are characterized by specific microbial taxa and organic matter composition originating from microbial activities or deriving from soil and vegetation above the cave. The metabolic capacities allowing the biodegradation of complex polymers from the vegetation above the cave and the use of inorganic nitrogen and atmospheric gases might have fueled the development of complex microbial communities that, by interacting with the carbonatic rock, led to the formation of these massive moonmilk speleothems in Grotta Nera.

Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields

Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and 13CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, 13CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating 13C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of 13C-metagenome-assembled genomes and 13C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.

Diverse type I and type II methanotrophs cultivated from an Indian freshwater wetland habitat

Wetlands are the main natural sources of methane emissions, which make up a significant portion of greenhouse gas emissions. Such wetland patches serve as rich habitats for aerobic methanotrophs. Limited knowledge of methanotrophs from tropical wetlands widens the scope of study from these habitats. In the present study, a freshwater wetland in a tropical region in India was sampled and serially diluted to obtain methanotrophs in culture. This was followed by the isolation of methanotrophs on agarose-containing plates, incubated under methane: air atmosphere. Methanotrophs are difficult to cultivate, and very few cultures of methanotrophs are available from tropical wetlands. Our current study reports the cultivation of a diverse community of methanotrophs from six genera, namely, Methylomonas, Methylococcus, Methylomagnum, Methylocucumis (type I methanotrophs) along with Methylocystis, Methylosinus (type II methanotrophs). A high abundance of methanotrophs (106-1010 methanotrophs/g fresh weight) was observed in the samples. A Methylococcus strain could represent a putative novel species that was also isolated. Cultures of Methylomagnum and Methylocucumis, two newly described type I methanotrophs exclusively found in rice fields, were obtained. A large number of Methylomonas koyamae strains were cultured. Our study is pioneering in the documentation of culturable methanotrophs from a typical tropical wetland patch. The isolated methanotrophs can act as models for studying methanotroph-based methane mitigation from wetland habitats and can be used for various mitigation and valorization applications.

Unique architecture of microbial snottites from a methane driven biofilm revealed by confocal microscopy

Microbial biofilms occur in many shapes and different dimensions. In natural and semi-artificial caves they are forming pendulous structures of 10 cm and more. In this study a methane driven microbial community of a former medicinal spring was investigated. The habitat was completely covered by massive biofilms and snottites with a wobbly, gelatinous appearance. By using fluorescence techniques in combination with confocal laser scanning microscopy the architecture of these so far unknown snottites was examined. The imaging approaches applied comprised reflection of geogenic and cellular origin, possible autofluorescence, nucleic acid staining for bacterial cells, protein staining for bacteria and extracellular fine structures, calcofluor white for β 1 → 3, β 1 → 4 polysaccharide staining for possible fungi as well as lectin staining for the extracellular biofilm matrix glycoconjugates. The results showed a highly complex, intricate structure with voluminous, globular, and tube-like glycoconjugates of different dimensions and densities. In addition, filamentous bacteria seem to provide additional strength to the snottites. After screening with all commercially available lectins, by means of fluorescence lectin barcoding and subsequent fluorescence lectin binding analysis, the AAL, PNA, LEA, and Ban lectins identified α-Fuc, β-Gal, β-GlcNAc, and α-Man with α-Fuc as a major component. Examination of the outer boundary with fluorescent beads revealed a potential outer layer which could not be stained by any of the fluorescent probes applied. Finally, suggestions are made to further elucidate the characteristics of these unusual microbial biofilms in form of snottites. RESEARCH HIGHLIGHTS: The gelatinous snottites revealed at the microscale a highly complex structure not seen before. The extracellular matrix of the snottite biofilm was identified as clusters of different shape and density. The matrix of snottites was examined by taking advantage of 78 fluorescently-labeled lectins. The extracellular matrix glycoconjugates of snottites identified comprised: α-Fuc, β-Gal, β-GlcNAc, and α-Man. Probing the snottite outer surface indicated an additional unknown stratum.

Linking methanotroph phenotypes to genotypes using a simple spatially resolved model ecosystem

Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental context in laboratory settings. Laboratory-based model ecosystems offer a means to better account for environmental conditions compared with standard planktonic cultures and can help link genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs) within the methane-oxygen counter gradient typically found in the natural environment of these organisms. Culturing the methanotroph Methylomonas sp. strain LW13 in this system resulted in the formation of a distinct horizontal band at the intersection of the counter gradient, which we discovered was not due to increased numbers of bacteria at this location but instead to an increased amount of polysaccharides. We also discovered that different methanotrophic taxa form polysaccharide bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this band, we identified genes upregulated within the band and validated their involvement in growth and band formation within the model ecosystem using knockout strains. Notably, deletion of these genes did not negatively affect growth using standard planktonic culturing methods. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover bacterial phenotypes missing from standard laboratory conditions, and to link these phenotypes with their genetic determinants.

Microaerobic methane-driven denitrification in a biotrickle bed - Investigating the active microbial biofilm community composition using RNA-stable isotope probing

A microaerobic (2% O2 v/v) biotrickle bed reactor supplied continuously with 2% methane to drive nitrate removal (MAME-D) was investigated using 16S rDNA and rRNA amplicon sequencing in combination with RNA-stable isotope probing (RNA-SIP) to identify the active microorganisms. Methane removal rates varied from 500 to 1000 mmol m-3h-1 and nitrate removal rates from 25 to 58 mmol m-3h-1 over 55 days of operation. Biofilm samples from the column were incubated in serum bottles supplemented with 13CH4. 16S rDNA analysis indicated a simple community structure in which four taxa accounted for 45% of the total relative abundance (RA). Dominant genera included the methanotroph Methylosinus and known denitrifiers Nubsella and Pseudoxanthomonas; along with a probable denitrifier assigned to the order Obscuribacterales. The 16S rRNA results revealed the methanotrophs Methylocystis (15% RA) and Methylosinus (10% RA) and the denitrifiers Arenimonas (10% RA) and Pseudoxanthomonas (7% RA) were the most active genera. Obscuribacterales was the most active taxa in the community at 22% RA. Activity was confirmed by the Δ buoyant density changes with time for the taxa, indicating most of the community activity was associated with methane oxidation and subsequent consumption of methanotrophic metabolic intermediates by the denitrifiers. This is the first report of RNA stable isotope probing within a microaerobic methane driven denitrification system and the active community was markedly different from the full community identified via 16S-rDNA analysis.

Strategies for the biological production of ectoine by using different chassis strains

As an amino acid derivative and a typical compatible solute, ectoine can assist microorganisms in resisting high osmotic pressure. Own to its long-term moisturizing effects, ectoine shows extensive applications in cosmetics, medicine and other fields. With the rapid development of synthetic biology and fermentation engineering, many biological strategies have been developed to improve the ectoine production and simplify the production process. Currently, the microbial fermentation has been widely used for large scaling ectoine production. Accordingly, this review will introduce the metabolic pathway for ectoine synthesis and also comprehensively evaluate both wild-type and genetically modified strains for ectoine production. Furthermore, process parameters affecting the ectoine production efficiency and adoption of low cost substrates will be evaluated. Lastly, future prospects on the improvement of ectoine production will be proposed.

Iron and nitrogen regulate carbon transformation in a methanotroph-microalgae system

Nutrient supply is important for maintaining a methanotroph and microalgae (MOB-MG) system for biogas valorization. However, there is a lack of understanding regarding how key elements regulate the growth of a MOB-MG coculture. In this study, a MOB-MG coculture with high protein content (0.47 g/g biomass) was established from waste activated sludge using synthetic biogas. An increase in iron availability substantially stimulated the specific growth rate (from 0.18 to 0.62 day-1) and biogas conversion rate (from 26.81 to 106.57 mg-C L-1 day-1) of the coculture. Moreover, the protein content remained high (0.51 g/g biomass), and the total lipid content increased (from 0.09 to 0.14 g/g biomass). Nitrogen limitation apparently constrained the specific growth rate (from 0.64 to 0.28 day-1) and largely reduced the protein content (from 0.51 to 0.31 g/g biomass) of the coculture. Intriguingly, the lipid content remained unchanged after nitrogen was depleted. The eukaryotic community was consistently dominated by MG belonging to Chlorella, while the populations of MOB shifted from Methylococcus/Methylosinus to Methylocystis due to iron and nitrogen amendment. In addition, diverse non-methanotrophic heterotrophs were present in the community. Their presence neither compromised the performance of the coculture system nor affected the protein content of the biomass. However, these heterotrophs may contribute to high carbon conversion efficiency by utilizing the dissolved organic carbon released by MOB and MG. Overall, the findings highlight the vital roles of iron and nitrogen in achieving efficient conversion of biogas, fast growth of cells, and optimal biomass composition in a MOB-MG coculture system.

Regulation of potential denitrification rates in sediments by microbial-driven elemental coupled metabolisms

Microbial driven coupled processes between denitrification and methane/sulfur metabolism play a very substantial role in accelerating nitrogen removal in river sediments. Until now, little is known about how element coupling processes alter nitrogen metabolism by the microbial functional communities. The primary objective of this research was to clarify the contributory role of microbial-mediated coupled processes in controlling denitrification. Specifically, the study sought to identify the key bioindicators (or metabolic pathway) for preferably regulating and predicting potential denitrification rate (PDR). Here, a total of 40 sediment samples were collected from the inflow rivers of Chaohu Lake under nitrogen stress. The results revealed the ecological importance of methanogens and sulfate reducing bacteria in the microbial interaction network. Correlations between quantitative or predicted genes showed that the methanogenic gene (mcrA) was synergistic with denitrifying genes, further unraveling that the key role of methanogenesis in denitrification process for facilitating nitrogen removal. The PDR of sediments ranged from 0.03 to 133.21 μg N·g-1·h-1. The study uncovered specific environmental factors (NH4+ and OM) and microbial indicators (nosZ, mcrA, Paracoccus, Thauera, Methanobrevibacter and Desulfomicrobium) as potential contributors to the variations in PDR. Structural Equation Model (SEM) analysis revealed a significant direct effect of NH4+ on PDR, evidenced by a standardized coefficient (λ) of 0.77 (P < 0.001). Additionally, the findings also emphasized the salient role of methanogens (Methanobrevibacter) and methanogenic gene (mcrA) in indicating PDR. The research's aforementioned findings shed light on the substantial consequences of methanogenesis on nitrogen metabolism in coupled processes, enabling improved control of nitrogen pollution in river sediments. This study provided fresh perspectives on the effects of multiple functional taxa on denitrification, and reinforces the significance of coupling processes for nitrogen removal.

Microbial gas fermentation technology for sustainable food protein production

The development of novel, sustainable, and robust food production technologies represents one of the major pillars to address the most significant challenges humanity is going to face on earth in the upcoming decades - climate change, population growth, and resource depletion. The implementation of microfoods, i.e., foods formulated with ingredients from microbial cultivation, into the food supply chain has a huge potential to contribute towards energy-efficient and nutritious food manufacturing and represents a means to sustainably feed a growing world population. This review recapitulates and assesses the current state in the establishment and usage of gas fermenting bacteria as an innovative feedstock for protein production. In particular, we focus on the most promising representatives of this taxon: the hydrogen-oxidizing bacteria (hydrogenotrophs) and the methane-oxidizing bacteria (methanotrophs). These unicellular microorganisms can aerobically metabolize gaseous hydrogen and methane, respectively, to provide the required energy for building up cell material. A protein yield over 70% in the dry matter cell mass can be reached with no need for arable land and organic substrates making it a promising alternative to plant- and animal-based protein sources. We illuminate the holistic approach to incorporate protein extracts obtained from the cultivation of gas fermenting bacteria into microfoods. Herein, the fundamental properties of the bacteria, cultivation methods, downstream processing, and potential food applications are discussed. Moreover, this review covers existing and future challenges as well as sustainability aspects associated with the production of microbial protein through gas fermentation.

Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF

Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.

Valorization of protein-rich waste and its application

Energy shortages present significant challenges with the rising population and dramatic urbanization development. The effective utilization of high-value products generated from massive protein-rich waste has emerged as an excellent solution for mitigating the growing energy crisis. However, the traditional disposal and treatment of protein-rich waste, have been proven to be ineffective in resource utilization, which led to high chemical oxygen demand and water eutrophication. To effectively address this issue, hydrolysate and bioconversion products from protein-rich waste have been widely investigated. Herein, we aim to provide an overview of the valorization of protein-rich waste based on a comprehensive analysis of publicly available literature. Firstly, the sources of protein-rich waste with various quantities and qualities are systematically summarized. Then, we scrutinize and analyze the hydrolysis approaches of protein-rich waste and the versatile applications of hydrolyzed products. Moreover, the main factors influencing protein biotransformation and the applications of bioconversion products are covered and extensively discussed. Finally, the potential prospects and future directions for the valorization of protein-rich waste are proposed pertinently.

A bio-augmented system with Methylosarcina sp. LC-4 immobilized on bio-carriers: Towards an integrated approach to mitigate and valorize methane emissions from landfills to biodiesel

Bio-augmented systems based on methanotrophs are indispensable in curbing anthropogenic methane emissions from engineered landfills or dumpsites to curtail rising levels of greenhouse gases. Using a defined methanotroph culture immobilized on an inert material-based bio-carrier makes it possible to harness these methane emissions for creating value-added products, thus contributing to the circular bio-economy. The methane oxidation capacity of the model methanotroph Methylosarcina sp. LC-4, a prospective organism for biodiesel production using methane present in landfill gas, immobilized on several inert bio-carriers, was evaluated to identify a bio-carrier that provided optimum conditions for the process. Among the several bio-carriers evaluated, perlite and vermiculite were selected due to their high specific surface area and superior water-holding capacity, which result in the retention of nutrients and biomass and higher methane elimination capacity. While perlite showed high biomass holding capacity and methane transport, vermiculite supported a high growth of methanotrophs. LC-4 immobilized on perlite and vermiculite as the bio-carrier showed maximum methane elimination capacity (MEC) of 291.3 g m-2 day-1 and 155.5 g m-2 day-1, respectively. The low bed height of only 0.13 m and a short start-up period of 2-4 days are promising for use as alternate daily cover in a landfill. The recovered biomass had 12% (w/w) fatty acid methyl ester (FAME), with a high fraction of (∼85%) of C14-C18 saturated and monounsaturated fatty acids, suitable for biodiesel production. The combination of perlite and vermiculite increased MEC and FAME content levels. The current study demonstrated a new bio-augmented system designed with a pure methanotroph for methane elimination with a short start-up time and the valorization of the assimilated methane.

Growing in Saltwater: Biotechnological Potential of Novel Methylotuvimicrobium- and Methylomarinum-like Methanotrophic Bacteria

Methanotrophic bacteria that possess a unique ability of using methane as a sole source of carbon and energy have attracted considerable attention as potential producers of a single-cell protein. So far, this biotechnology implied using freshwater methanotrophs, although many regions of the world have limited freshwater resources. This study aimed at searching for novel methanotrophs capable of fast growth in saltwater comparable in composition with seawater. A methane-oxidizing microbial consortium containing Methylomarinum- and Methylotuvimicrobium-like methanotrophs was enriched from sediment from the river Chernavka (water pH 7.5, total salt content 30 g L-1), a tributary river of the hypersaline Lake Elton, southern Russia. This microbial consortium, designated Ch1, demonstrated stable growth on natural gas in a bioreactor in media with a total salt content of 23 to 35.9 g L-1 at a dilution rate of 0.19-0.21 h-1. The highest biomass yield of 5.8 g cell dry weight (CDW)/L with a protein content of 63% was obtained during continuous cultivation of the consortium Ch1 in a medium with a total salt content of 29 g L-1. Isolation attempts resulted in obtaining a pure culture of methanotrophic bacteria, strain Ch1-1. The 16S rRNA gene sequence of strain Ch1-1 displayed 97.09-97.24% similarity to the corresponding gene fragments of characterized representatives of Methylomarinum vadi, methanotrophs isolated from marine habitats. The genome of strain Ch1-1 was 4.8 Mb in size and encoded 3 rRNA operons, and about 4400 proteins. The genome contained the gene cluster coding for ectoine biosynthesis, which explains the ability of strain Ch1-1 to tolerate high salt concentration.

From anaerobic digestion to single cell protein synthesis: A promising route beyond biogas utilization

The accumulation of a large amount of organic solid waste and the lack of sufficient protein supply worldwide are two major challenges caused by rapid population growth. Anaerobic digestion is the main force of organic waste treatment, and the high-value utilization of its products (biogas and digestate) has been widely concerned. These products can be used as nutrients and energy sources for microorganisms such as microalgae, yeast, methane-oxidizing bacteria(MOB), and hydrogen-oxidizing bacteria(HOB) to produce single cell protein(SCP), which contributes to the achievement of sustainable development goals. This new model of energy conversion can construct a bioeconomic cycle from waste to nutritional products, which treats waste without additional carbon emissions and can harvest high-value biomass. Techno-economic analysis shows that the SCP from biogas and digestate has higher profit than biogas electricity generation, and its production cost is lower than the SCP using special raw materials as the substrate. In this review, the case of SCP-rich microorganisms using anaerobic digestion products for growth was investigated. Some of the challenges faced by the process and the latest developments were analyzed, and their potential economic and environmental value was verified.

Biosensing systems for the detection and quantification of methane gas

Climate change due to the continuous increase in the release of green-house gasses associated with anthropogenic activity has made a significant impact on the sustainability of life on our planet. Methane (CH4) is a green-house gas whose concentrations in the atmosphere are on the rise. CH4 measurement is important for both the environment and the safety at the industrial and household level. Methanotrophs are distinguished for their unique characteristic of using CH4 as the sole source of carbon and energy, due to the presence of the methane monooxygenases that oxidize CH4 under ambient temperature conditions. This has attracted interest in the use of methanotrophs in biotechnological applications as well as in the development of biosensing systems for CH4 quantification and monitoring. Biosensing systems using methanotrophs rely on the use of whole microbial cells that oxidize CH4 in presence of O2, so that the CH4 concentration is determined in an indirect manner by measuring the decrease of O2 level in the system. Although several biological properties of methanotrophic microorganisms still need to be characterized, different studies have demonstrated the feasibility of the use of methanotrophs in CH4 measurement. This review summarizes the contributions in methane biosensing systems and presents a prospective of the valid use of methanotrophs in this field. KEY POINTS: • Methanotroph environmental relevance in methane oxidation • Methanotroph biotechnological application in the field of biosensing • Methane monooxygenase as a feasible biorecognition element in biosensors.

MOF-based catalysts: insights into the chemical transformation of greenhouse and toxic gases

Metal-organic framework (MOF)-based catalysts are outstanding alternative materials for the chemical transformation of greenhouse and toxic gases into high-add-value products. MOF catalysts exhibit remarkable properties to host different active sites. The combination of catalytic properties of MOFs is mentioned in order to understand their application. Furthermore, the main catalytic reactions, which involve the chemical transformation of CH4, CO2, NOx, fluorinated gases, O3, CO, VOCs, and H2S, are highlighted. The main active centers and reaction conditions for these reactions are presented and discussed to understand the reaction mechanisms. Interestingly, implementing MOF materials as catalysts for toxic gas-phase reactions is a great opportunity to provide new alternatives to enhance the air quality of our planet.

Methanotrophic oxidation of organic micropollutants and nitrogen upcycling in a hybrid membrane biofilm reactor (hMBfR) for simultaneous O2 and CH4 supply

Pharmaceuticals and other organic micropollutants (OMPs) present in wastewater effluents are of growing concern, as they threaten environmental and human health. Conventional biological treatments lead to limited removal of OMPs. Methanotrophic bacteria can degrade a variety of OMPs. By employing a novel bubble-free hybrid membrane biofilm bioreactor (hMBfR), we grew methanotrophic bacteria at three CH4 loading rates. Biomass productivity and CH4 loading showed a linear correlation, with a maximum productivity of 372 mg-VSS·L-1·d-1, with corresponding biomass concentration of 1117.6 ± 56.4 mg-VSS·L-1. Furthermore, the biodegradation of sulfamethoxazole and 1H-benzotriazole positively correlated with CH4 oxidation rates, with highest biodegradation kinetic constants of 3.58 L·g-1·d-1 and 5.42 L·g-1·d-1, respectively. Additionally, the hMBfR recovered nutrients as microbial proteins, with an average content 39% DW. The biofilm community was dominated by Methylomonas, while the bulk was dominated by aerobic heterotrophic bacteria. The hMBfR removed OMPs, allowing for safer water reuse while valorising CH4 and nutrients.

From methane to value-added bioproducts: microbial metabolism, enzymes, and metabolic engineering

Methane is abundant in nature, and excessive emissions will cause the greenhouse effect. Methane is also an ideal carbon and energy feedstock for biosynthesis. In the review, the microorganisms, metabolism, and enzymes for methane utilization, and the advances of conversion to value-added bioproducts were summarized. First, the physiological characteristics, classification, and methane oxidation process of methanotrophs were introduced. The metabolic pathways for methane utilization and key intermediate metabolites of native and synthetic methanotrophs were summarized. Second, the enzymatic properties, crystal structures, and catalytic mechanisms of methane-oxidizing and metabolizing enzymes in methanotrophs were described. Third, challenges and prospects in metabolic pathways and enzymatic catalysis for methane utilization and conversion to value-added bioproducts were discussed. Finally, metabolic engineering of microorganisms for methane biooxidation and bioproducts synthesis based on different pathways were summarized. Understanding the metabolism and challenges of microbial methane utilization will provide insights into possible strategies for efficient methane-based synthesis.

Thermotolerant methanotrophs belonging to the Methylocaldum genus dominate the methanotroph communities in biogas slurry and cattle dung: A culture-based study from India

Biogas reactors run on various types of waste, with cattle dung and agricultural wastes being the primary sources in India. As biogas contains 50-60% methane, there is a possibility that the reactors harbour methanotrophs or methane-oxidizing bacteria. We set up serial endpoint dilution enrichments for the cultivation of methanotrophs using slurry from a small biogas reactor and cattle dung samples and obtained cultures of Methylocaldum gracile, a thermotolerant methanotroph. The study was expanded by sampling reactors of another small reactor of 20 L capacity and two 1000 L reactors. Dung samples were obtained from two Indian cattle breeds (Tharparkar and Gir). Pulverized rice straw used for feeding the biogas was also used for experiments. All the enrichment bottles were incubated at 39 °C, the reactors' in-situ temperature, and the rumen gut temperature. Our study isolated four pure cultures most related to Methylocaldum gracile VKM-14L^T, two strains from cattle dung samples, and two from reactors. The study also resulted in the cultivation of four additional cultures of Methylocaldum gracile and Methylocaldum tepidum, which were non-axenic and identified by pmoA gene sequencing. Pure cultures Methylocaldum gracile RS-9 and CDP-2 were studied for optimum temperature and oxygen. Both the strains were thermotolerant and grew in the temperature range of 25-45 °C with the optimum between 37 and 45 °C. The cultures could grow with minimal oxygen (0.5%-1%) in the headspace, with growth up to 10% oxygen. To summarize, we report the cultivation and isolation of methanotrophs from biogas slurries and cattle dung samples. Methylocaldum was the dominant methanotroph cultured, probably due to its thermotolerant nature and the ability to grow under variable oxygen conditions. The present study also expands the existing knowledge about habitats known for the genus Methylocaldum. An analysis of the isolated cultures would help us design strategies for methane mitigation from ruminants.

Microbial protein production from sulfide-rich biogas through an enrichment of methane- and sulfur-oxidizing bacteria

This study evaluated the possibility of combining methane oxidizing bacteria (MOB) with sulfur oxidizing bacteria (SOB) to enable the utilization of sulfide-rich biogas for microbial protein production. For this purpose, a MOB-SOB mixed-culture enriched by feeding both methane and sulfide was benchmarked against an enrichment of solely MOB. Different CH₄:O₂ ratios, starting pH values, sulfide levels and nitrogen sources were tested and evaluated for the two enrichments. The MOB-SOB culture gave promising results in terms of both biomass yield (up to 0.07±0.01 g VSS/g CH₄-COD) and protein content (up to 73±5% of VSS) at 1500 ppm of equivalent H₂S. The latter enrichment was able to grow also under acidic pH (5.8-7.0), but as inhibited outside the optimal CH₄:O₂ ratio of 2:3. The obtained results show the capability of MOB-SOB mixed-cultures to directly upcycle sulfide-rich biogas into microbial protein potentially suited for feed, food or biobased product applications.

Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications

Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH₄ ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH₄ , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH₄ monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.

Dietary inclusion of methanotrophic microbial cell-derived protein in the early post-weaning period sustains growth performance and intestinal health of weaner piglets

The global demand for sustainably produced protein feeds for animal production is increasing. Methanotrophic bacteria grow on methane and convert it into microbial cell protein (MCP) that has been shown to have high nutritive value for growing pigs. The present aimed to investigate how increasing amounts of MCP in diets fed during the first 15 days after weaning affect the growth performance of piglets from weaning until day 43 postweaning. Furthermore, the effect of MCP on intestinal morphology and histopathology was assessed on day 15 after weaning. During seven consecutive weeks, approximately 480 piglets were recruited for the experiment per batch. The piglets were divided into four groups and housed in eight double pens with 60 piglets per pen. The piglets were fed one of four experimental diets with 0, 3, 6, or 10% of MCP included at the expense of fishmeal and subsequently potato protein for the first 15 days postweaning. Thereafter, all pigs were fed commercial weaner diets in two phases (days 16-30 and days 31-43) until day 43 postweaning. All diets were without medicinal zinc. Feed intake and growth were registered on double pen level during all three phases. On day 15 after weaning, 10 piglets per treatment were randomly selected, autopsied, and sampled for intestinal morphology and histopathology. Daily gain during the first 15 days postweaning tended (P = 0.09) to be affected by the inclusion of MCP in the weaning diet being lowest in the group fed 10% MCP. Treatment did not affect daily feed intake; however, Feed Conversion Ratio (FCR) was significantly affected (P = 0.003) showing the highest FCR in piglets fed 10% MCP. Growth performance was not affected by the experimental treatment during the following phases. In the small intestine, villous height tended (P = 0.09) to show a quadratic response to level of MCP in the diet with the longest villi observed after feeding 6% MCP. Dietary treatment did not affect crypt depth. The villous height to crypt depth (VC) ratio showed a quadratic response to increased dietary inclusion of MCP (P = 0.02) with piglets fed 6% MCP having the highest VC ratio. In conclusion, this study demonstrated that MCP could constitute 6% of diets as-fed (22% of total CP), at the expense of fishmeal and potato protein, for newly weaned piglets without negative effects on growth rates and FCR. The inclusion of MCP in diets for newly weaned piglets could be part of improving the sustainability of pig production.

Microbial meat: A sustainable vegan protein source produced from agri-waste to feed the world

In the modern world, animal and plant protein may not meet the sustainability criteria due to their high need for arable land and potable water consumption, among other practices. Considering the growing population and food shortage, finding alternative protein sources for human consumption is an urgent issue that needs to be solved, especially in developing countries. In this context, microbial bioconversion of valuable materials in nutritious microbial cells represent a sustainable alternative to the food chain. Microbial protein, also known as single-cell protein (SCP), consist of algae biomass, fungi or bacteria that are currently used as food source for both humans and animals. Besides contributing as a sustainable source of protein to feed the world, producing SCP, is important to reduce waste disposal problems and production costs meeting the sustainable development goals. However, for microbial protein as feed or food to become an important and sustainable alternative, addressing the challenges of raising awareness and achieving wider public regulatory acceptance is real and must be addressed with care and convenience. In this work, we critically reviewed the potential technologies for microbial protein production, its benefits, safety, and limitations associated with its uses, and perspectives for broader large-scale implementation. We argue that the information documented in this manuscript will assist in developing microbial meat as a major protein source for the vegan world.

Embracing a low-carbon future by the production and marketing of C1 gas protein

Food scarcity and environmental deterioration are two major problems that human populations currently face. Fortunately, the disruptive innovation of raw food materials has been stimulated by the rapid evolution of biomanufacturing. Therefore, it is expected that the new trends in technology will not only alter the natural resource-dependent food production systems and the traditional way of life but also reduce and assimilate the greenhouse gases released into the atmosphere. This review article summarizes the metabolic pathways associated with C1 gas conversion and the production of single-cell protein for animal feed. Moreover, the protein function, worldwide authorization, market access, and methods to overcome challenges in C1 gas assimilation microbial cell factory construction are also provided. With widespread attention and increasing policy support, the production of C1 gas protein will bring more opportunities and make tremendous contributions to our sustainable future.

Gas to protein: Microbial single cell protein is an alternative to fishmeal in aquaculture

Methanotrophic bacteria represent an appealing opportunity to convert methane, a potent greenhouse gas, into a highly nutritious animal feed ingredient, single-cell protein (SCP). SCP has a comparable or superior nutritional profile that to most conventional protein sources and can be produced within a lower environmental footprint. The present study investigated the effect of replacing fishmeal (FM) with methanotrophic SCP in diets for barramundi (Lates calcarifer), a carnivorous fish with a high demand for dietary protein and energy. Dietary inclusion levels of 0 %, 10 %, 20 % and 30 % SCP (representing 0, 25, 50 and 75 % FM replacement) were tested, with and without additives. Triplicate groups of juvenile barramundi were fed the diets over 31 days. The inclusion of SCP significantly improved weight gain and feed conversion efficiency (FCE). Dietary SCP inclusion supported good gut health, with decreasing trends of hepatosomatic index, improved plasma biochemistry, and no adverse histopathological changes. Barramundi fed the SCP diets showed an intact intestinal barrier and a significant improvement in villi and lamina propria area when fed the additive supplemented SCP diets. This study demonstrates that this SCP is highly palatable to barramundi (even without dietary additives) and can replace up to 75 % FM with significant improvements in growth and FCE.

Killing two birds with one stone: chemical and biological upcycling of polyethylene terephthalate plastics into food

Most polyethylene terephthalate (PET) plastic waste is landfilled or pollutes the environment. Additionally, global food production must increase to support the growing population. This article explores the feasibility of using microorganisms in an industrial system that upcycles PET into edible microbial protein powder to solve both problems simultaneously. Many microorganisms can utilize plastics as feedstock, and the resultant microbial biomass contains fats, nutrients, and proteins similar to those found in human diets. While microbial degradation of PET is promising, biological PET depolymerization is too slow to resolve the global plastic crisis and projected food shortages. Evidence reviewed here suggests that by coupling chemical depolymerization and biological degradation of PET, and using cooperative microbial communities, microbes can efficiently convert PET waste into food.

Cre/lox-Mediated CRISPRi Library Reveals Core Genome of a Type I Methanotroph Methylotuvimicrobium buryatense 5GB1C

Methanotrophs play key roles in global methane cycling and are promising platforms for methane bioconversion. However, major gaps existing in fundamental knowledge undermines understanding of these methane-consuming microorganisms. To associate genes with a phenotype at the genome-wide level, we developed a Cre/lox-mediated method for constructing a large-scale CRISPRi library in a model methanotroph Methylotuvimicrobium buryatense 5GB1C. The efficiency of this Cre mediated integration method was up to a level of 10⁵ CFU/μg DNA. Targeting 4,100 predicted protein-coding genes, our CRISPRi pooled screening uncovered 788 core genes for the growth of strain 5GB1C using methane. The core genes are highly consistent with the gene knockout results, indicating the reliability of the CRISPRi screen. Insights from the core genes include that annotated isozymes generally exist in metabolic pathways and many core genes are hypothetical genes. This work not only provides functional genomic data for both fundamental research and metabolic engineering of methanotrophs, but also offers a method for CRISPRi library construction. IMPORTANCE Due to their key role in methane cycling and their industrial potential, methanotrophs have drawn increasing attention. Genome-wide experimental approaches for gene-phenotype mapping accelerate our understanding and engineering of a bacterium. However, these approaches are still unavailable in methanotrophs. This work has two significant implications. First, the core genes identified here provide functional genetic basics for complete reconstruction of the metabolic network and afford more clues for knowledge gaps. Second, the Cre-mediated knock-in method developed in this work enables large-scale DNA library construction in methanotrophs; the CRISPRi library can be used to screen the genes associated with special culture conditions.

Graphene as Thinnest Coating on Copper Electrodes in Microbial Methanol Fuel Cells

Dehydrogenation of methanol (CH₃OH) into direct current (DC) in fuel cells can be a potential energy conversion technology. However, their development is currently hampered by the high cost of electrocatalysts based on platinum and palladium, slow kinetics, the formation of carbon monoxide intermediates, and the requirement for high temperatures. Here, we report the use of graphene layers (GL) for generating DC electricity from microbially driven methanol dehydrogenation on underlying copper (Cu) surfaces. Genetically tractable Rhodobacter sphaeroides 2.4.1 (Rsp), a nonarchetypical methylotroph, was used for dehydrogenating methanol at the GL-Cu surfaces. We use electrochemical methods, microscopy, and spectroscopy methods to assess the effects of GL on methanol dehydrogenation by Rsp cells. The GL-Cu offers a 5-fold higher power density and 4-fold higher current density compared to bare Cu. The GL lowers charge transfer resistance to methanol dehydrogenation by 4 orders of magnitude by mitigating issues related to pitting corrosion of underlying Cu surfaces. The presented approach for catalyst-free methanol dehydrogenation on copper electrodes can improve the overall sustainability of fuel cell technologies.

Fungi as a Source of Edible Proteins and Animal Feed

It is expected that the world population will reach 9 billion by 2050. Thus, meat, dairy or plant-based protein sources will fail to meet global demand. New solutions must be offered to find innovative and alternative protein sources. As a natural gift, edible wild mushrooms growing in the wet and shadow places and can be picked by hand have been used as a food. From searching mushrooms in the forests and producing single cell proteins (SCP) in small scales to mega production, academia, United Nations Organizations, industries, political makers and others, play significant roles. Fermented traditional foods have also been reinvestigated. For example, kefir, miso, and tempeh, are an excellent source for fungal isolates for protein production. Fungi have unique criteria of consuming various inexpensive wastes as sources of carbon and energy for producing biomass, protein concentrate or amino acids with a minimal requirement of other environmental resources (e.g., light and water). Fungal fermented foods and SCP are consumed either intentionally or unintentionally in our daily meals and have many applications in food and feed industries. This review addresses fungi as an alternative source of edible proteins and animal feed, focusing mainly on SCP, edible mushrooms, fungal fermented foods, and the safety of their consumption.

Cell-Free Protein Synthesis of Particulate Methane Monooxygenase into Nanodiscs

Particulate methane monooxygenase (pMMO) is a multi-subunit membrane metalloenzyme used by methanotrophic bacteria to convert methane to methanol. A major hurdle to studying pMMO is the lack of a recombinant expression system, precluding investigation of individual residues by mutagenesis and hampering a complete understanding of its mechanism. Here, we developed an Escherichia coli lysate-based cell-free protein synthesis (CFPS) system that can be used to express pMMO in vitro in the presence of nanodiscs. We used a SUMO fusion construct to generate the native PmoB subunit and showed that the SUMO protease (Ulp1) cleaves the protein in the reaction mixture. Using an affinity tag to isolate the complete pMMO complex, we demonstrated that the complex forms without the need for exogenous translocon machinery or chaperones, confirmed by negative stain electron microscopy. This work demonstrates the potential for using CFPS to express multi-subunit membrane-bound metalloenzymes directly into lipid bilayers.

Enhanced production of ectoine from methane using metabolically engineered Methylomicrobium alcaliphilum 20Z

Background

Ectoine (1,3,4,5-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) is an attractive compatible solute because of its wide industrial applications. Previous studies on the microbial production of ectoine have focused on sugar fermentation. Alternatively, methane can be used as an inexpensive and abundant resource for ectoine production by using the halophilic methanotroph, Methylomicrobium alcaliphilum 20Z. However, there are some limitations, including the low production of ectoine from methane and the limited tools for the genetic manipulation of methanotrophs to facilitate their use as industrial strains.

Results

We constructed M. alcaliphilum 20ZDP with a high conjugation efficiency and stability of the episomal plasmid by the removal of its native plasmid. To improve the ectoine production in M. alcaliphilum 20Z from methane, the ectD (encoding ectoine hydroxylase) and ectR (transcription repressor of the ectABC-ask operon) were deleted to reduce the formation of by-products (such as hydroxyectoine) and induce ectoine production. When the double mutant was batch cultured with methane, ectoine production was enhanced 1.6-fold compared to that obtained with M. alcaliphilum 20ZDP (45.58 mg/L vs. 27.26 mg/L) without growth inhibition. Notably, a maximum titer of 142.32 mg/L was reached by the use of an optimized medium for ectoine production containing 6% NaCl and 0.05 μM of tungsten without hydroxyectoine production. This result demonstrates the highest ectoine production from methane to date.

Conclusions

Ectoine production was significantly enhanced by the disruption of the ectD and ectR genes in M. alcaliphilum 20Z under optimized conditions favoring ectoine accumulation. We demonstrated effective genetic engineering in a methanotrophic bacterium, with enhanced production of ectoine from methane as the sole carbon source. This study suggests a potentially transformational path to commercial sugar-based ectoine production.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02104-2.

Impact of recovered phosphorus supply on methanotrophic cultivation and microbial protein production

Microbial protein is a promising dietary supplement alternative to traditional sources, being methane oxidising bacteria (MOB) an attractive option to produce it. Though current production processes rely on fossil resources, there is an increasing trend of using recovered residual nutrient streams, with most research focusing on nitrogen and methane, paying little attention to phosphorus. Struvite and precipitated calcium phosphate (PCP) were evaluated as potential residual P sources for microbial protein production after dissolved them with strong acids. MOB growth was studied in batch experiments. Yields ranged from 0.21 to 0.29 g CDW g CH₄^-1. Crude protein contents above 50% of dried weight were achieved, and neither the P nor the N source affected the amino acid profile significantly. The highest protein content (75%) was observed when using struvite as nutrient source, but also yielded cadmium and lead accumulation above limits set in legislation.