Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology

Aptamer-based biosensors for the detection of neonicotinoid insecticides in environmental samples: A systematic review

Neonicotinoids, sometimes abbreviated as neonics, represent a class of neuro-active insecticides with chemical similarities to nicotine. Neonicotinoids are the most widely adopted group of insecticides globally since their discovery in the late 1980s. Their physiochemical properties surpass those of previously established insecticides, contributing to their popularity in various sectors such as agriculture and wood treatment. The environmental impact of neonicotinoids, often overlooked, underscores the urgency to develop tools for their detection and understanding of their behavior. Conventional methods for pesticide detection have limitations. Chromatographic techniques are sensitive but expensive, generate waste, and require complex sample preparation. Bioassays lack specificity and accuracy, making them suitable as preliminary tests in conjunction with instrumental methods. Aptamer-based biosensor is recognized as an advantageous tool for neonicotinoids detection due to its rapid response, user-friendly nature, cost-effectiveness, and suitability for on-site detection. This comprehensive review represents the inaugural in-depth analysis of advancements in aptamer-based biosensors targeting neonicotinoids such as imidacloprid, thiamethoxam, clothianidin, acetamiprid, thiacloprid, nitenpyram, and dinotefuran. Additionally, the review offers valuable insights into the critical challenges requiring prompt attention for the successful transition from research to practical field applications.

In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer

Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.

More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities

Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members. The production of certain metabolites that can be tied to a specific microbe-microbe interaction might subsequently influence the physicochemical parameters of the habitat, stimulate a change in the trophic network of the community or create new micro-habitats through the formation of biofilms, similar to the production of antimicrobial substances which might negatively affect only one microorganism but cause a ripple effect on the abundance of other community members. Here, we argue that combining established as well as innovative laboratory and computational methods is needed to predict novel interactions and assess their secondary effects. Such efforts will enable future microbiome studies to expand our knowledge on the dynamics of complex microbial communities.

Nisin and Organic Acid Salts Improved the Microbial Quality, Extended the Shelf Life, and Maintained the Sensory Attributes of Semidry Beef Luncheon Marketed at Adverse (35-40 °C) Ambient Summer Temperatures

Semidry beef luncheon may undergo deteriorative changes during storage at ambient temperatures in tropical and subtropical regions including Egypt. This study was conducted in a meat plant in Egypt with the aim of overcoming the economic losses from the returns of spoiled unsold beef luncheon displayed in grocery stores at adverse summer temperatures of 37 °C or more. Ten approaches were applied using different preservatives, comprising sodium nitrite, nisin, potassium sorbate, and organic acid salts (a combination of sodium lactate, sodium acetate, and sodium diacetate). In addition, the product was cooked at different temperatures and was stored for 21 days at 37 °C, during which time the shelf life, microbial quality, pH, and sensory attributes were investigated. By Day 21 of storage, the luncheon contained 50 mg/kg sodium nitrite, 25 mg/kg nisin, and 1000 mg/kg organic acid salts and, when cooked at a final core temperature of 92 °C, exhibited reductions in aerobic plate count, anaerobic plate count, lactic acid bacterial count, and mold and yeast counts by 4.32, 3.54, 3.47, and 1.89 log10 CFU/g, respectively, when compared with the control. The sensory attributes and pH were also maintained in the final products of such treatment, with no product return and the avoidance of economic loss. This study presents a novel approach for solving the major problem of the deteriorative changes that occur in semidry luncheon sausage and similar meat products which require rejection with a huge economic loss, especially in tropical and semitropical areas of the world that have similar problems of high climatic temperatures and a low availability of energy or technological resources.

Comparison of Various Reducing Agents for Methane Production by Methanothermobacter marburgensis

Biological methanation is driven by anaerobic methanogenic archaea, cultivated in different media, which consist of multiple macro and micro nutrients. In addition, a reducing agent is needed to lower the oxidation-reduction potential (ORP) and enable the growth of oxygen-sensitive organisms. Until now, sodium sulfide (Na2S) has been used mainly for this purpose based on earlier published articles at the beginning of anaerobic microbiology research. In a continuation of earlier investigations, in this study, the usage of alternative reducing agents like sodium dithionite (Na2S2O4) and L-Cysteine-HCl shows that similar results can be obtained with fewer environmental and hazardous impacts. Therefore, a newly developed comparison method was used for the cultivation of Methanothermobacter marburgensis. The median methane evolution rate (MER) for the alternatives was similar compared to Na2S at different concentrations (0.5, 0.25 and 0.1 g/L). However, the use of 0.25 g/L Na2S2O4 or 0.1 g/L L-Cys-HCl led to stable MER values over consecutive batches compared to Na2S. It was also shown that a lower concentration of reducing agent leads to a higher MER. In conclusion, Na2S2O4 or L-Cys-HCl can be used as a non-corrosive and non-toxic reducing agent for ex situ biological methanation. Economically, Na2S2O4 is cheaper, which is particularly interesting for scale-up purposes.

Real-time monitoring of biomass during Escherichia coli high-cell-density cultivations by in-line photon density wave spectroscopy

An efficient monitoring and control strategy is the basis for a reliable production process. Conventional optical density (OD) measurements involve superpositions of light absorption and scattering, and the results are only given in arbitrary units. In contrast, photon density wave (PDW) spectroscopy is a dilution-free method that allows independent quantification of both effects with defined units. For the first time, PDW spectroscopy was evaluated as a novel optical process analytical technology tool for real-time monitoring of biomass formation in Escherichia coli high-cell-density fed-batch cultivations. Inline PDW measurements were compared to a commercially available inline turbidity probe and with offline measurements of OD and cell dry weight (CDW). An accurate correlation of the reduced PDW scattering coefficient µs ' with CDW was observed in the range of 5-69 g L-1 (R2  = 0.98). The growth rates calculated based on µs ' were comparable to the rates determined with all reference methods. Furthermore, quantification of the reduced PDW scattering coefficient µs ' as a function of the absorption coefficient µa allowed direct detection of unintended process trends caused by overfeeding and subsequent acetate accumulation. Inline PDW spectroscopy can contribute to more robust bioprocess monitoring and consequently improved process performance.

The overshadowed role of electron ionization-mass spectrometry in analytical biotechnology

Target and untargeted analysis of several compounds are crucial methods in important areas such as omics sciences. Gas chromatography coupled to mass spectrometry (GC-MS) is widely used for volatile and thermally stable compounds. In this case, the electron ionization technique (EI) is preferable as it produces highly fragmented and reproducible spectra comparable to spectral libraries. However, only a fraction of target compounds is analyzable by GC without chemical derivatization. Therefore, liquid chromatography (LC) coupled with MS is the most used technique. Contrary to EI, electrospray ionization does not produce reproducible spectra. That is why researchers have been working on interfaces between LC and EI-MS to bridge the gap between those techniques. This short review will discuss advancements, applications, and perspectives on biotechnological analysis.

Application of KHSO5 for remediation of soils polluted by organochlorides: A comprehensive study on the treatment's efficacy, environmental implications, and phytotoxicity

Soil pollution caused by complex organochloride mixtures has been increasing in many parts of the world in recent years; as a result, countless numbers of people are exposed to dangerous pollutions; hence, the treatment of organochlorides-polluted soils is gaining considerable attention. In this study, the potential of unactivated peroxymonosulfate (KHSO₅) in remediating soil co-contaminated with trichlorophenol, para-dichlorobenzene, and para-chloro-meta-cresol was investigated. In addition, the treatment's collateral effect on critical soil properties was explored. The result revealed that treating 10 g of soil with 20 mL of 5 mM KHSO₅ for 60 min could oxidize 70.49% of the total pollutants. The pH of the soil was decreased following the treatment. The significant decrease, (p < 0.05), in the soil organic matter following the remediation has affected cation exchange capacity, and available nitrogen. It was also observed that the treatment reduced the β-glucosidase, urease, invertase, and cellulase activities significantly, (p < 0.05). The treatment, on the other hand, brought negligible effects on available phosphorus, available potassium, and particle size distribution. The phytotoxicity tests, which included seed germination and root elongation and soil respiration tests revealed that the treatment did not leach toxins into the treated soil. The treatment method was found to be relatively ecofriendly and cost effective.

PHAs production by facultative anaerobic bacteria Bacillus cereus FM5 through submerged and solid-state fermentation under anoxic condition

PHAs (polyhydroxyalkanoates) are the bio-polyester synthesized by different aerobic and anaerobic bacteria as energy storage granule. However, its synthesis by anaerobes or facultative anaerobes is an imperative part of their physiology via assimilating broad range of substrates than aerobes. Thus, three Gram positive facultative anaerobic PHAs producers viz., Enterococcus sp. FM3, Actinomyces sp. CM4 and Bacillus sp. FM5 were selected. Among them, Bacillus sp. FM5 showed higher cell biomass production in MSM (mineral salt medium) comprised of glucose & peptone as carbon & nitrogen source at pH 9, temperature 37 °C, inoculum 10% and incubation period 72 h. Under optimized condition, Bacillus sp. FM5 produced 0.89 and 1.5 g l^-1 of PHAs through submerged and solid-state fermentation in anoxic condition. In-silico analysis confirmed the facultative anaerobic PHAs producing bacteria as Bacillus cereus FM5. IR spectra of PHAs illustrated a strong absorption peak at 1718.50 cm^-1 representing carbonyl ester (C=O) functional group of PHB (polyhydroxybutyrate), belonging to the family PHAs. It is the first report demonstrating PHAs production by Bacillus cereus FM5 in anoxic condition through different bioprocess technology, which may pave the way in the arena of further biopolymer research.

Effects of reducing, stabilizing, and antibiotic agents on "Candidatus Kuenenia stuttgartiensis"

Anaerobic ammon ium oxidizing (anammox) bacteria oxidize ammonium and reduce nitrite, producing N₂, and could play a major role in energy-optimized wastewater treatment. However, sensitivity to various environmental conditions and slow growth currently hinder their wide application. Here, we attempted to determine online the effect of environmental stresses on anammox bacteria by using an overnight batch activity test with whole cells, in which anammox activity was calculated by quantifying N₂ production via headspace-pressure monitoring. A planktonic mixed culture dominated by "Candidatus Kuenenia stuttgartiensis" strain CSTR1 was cultivated in a 30-L semi-continuous stirring tank reactor. In overnight resting-cell anammox activity tests, oxygen caused strong inhibition of anammox activity, which was reversed by sodium sulfite (30 µM). The tested antibiotics sulfamethoxazole, kanamycin, and ciprofloxacin elicited their effect on a dose-dependent manner; however, strain CSTR1 was highly resistant to sulfamethoxazole. Anammox activity was improved by activated carbon and Fe₂O₃. Protein expression analysis from resting cells after anammox activity stimulation revealed that NapC/NirT family cytochrome c (KsCSTR_12840), hydrazine synthase, hydrazine dehydrogenase, hydroxylamine oxidase, and nitrate:nitrite oxidoreductase were upregulated, while a putative hydroxylamine oxidoreductase HAO (KsCSTR_49490) was downregulated. These findings contribute to the growing knowledge on anammox bacteria physiology, eventually leading to the control of anammox bacteria growth and activity in real-world application. KEY POINTS: • Sulfite additions can reverse oxygen inhibition of the anammox process • Anammox activity was improved by activated carbon and ferric oxide • Sulfamethoxazole marginally affected anammox activity.

Analysis of biomass productivity and physiology of Nitrososphaera viennensis grown in continuous culture

Microbial ammonia oxidation is the first and usually rate limiting step in nitrification and is therefore an important step in the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) play an important role in nitrification. Here, we report a comprehensive analysis of biomass productivity and the physiological response of Nitrososphaera viennensis to different ammonium and carbon dioxide (CO₂) concentrations aiming to understand the interplay between ammonia oxidation and CO₂ fixation of N. viennensis. The experiments were performed in closed batch in serum bottles as well as in batch, fed-batch, and continuous culture in bioreactors. A reduced specific growth rate (μ) of N. viennensis was observed in batch systems in bioreactors. By increasing CO₂ gassing μ could be increased to rates comparable to that of closed batch systems. Furthermore, at a high dilution rate (D) in continuous culture (≥ 0.7 of μ_max) the biomass to ammonium yield (Y_(X/NH3)) increased up to 81.7% compared to batch cultures. In continuous culture, biofilm formation at higher D prevented the determination of D _crit. Due to changes in Y_(X/NH3) and due to biofilm, nitrite concentration becomes an unreliable proxy for the cell number in continuous cultures at D towards μ_max. Furthermore, the obscure nature of the archaeal ammonia oxidation prevents an interpretation in the context of Monod kinetics and thus the determination of K _S. Our findings indicate that the physiological response of N. viennensis might be regulated with different enzymatic make-ups, according to the ammonium catalysis rate. We reveal novel insights into the physiology of N. viennensis that are important for biomass production and the biomass yield of AOA. Moreover, our study has implications to the field of archaea biology and microbial ecology by showing that bioprocess technology and quantitative analysis can be applied to decipher environmental factors affecting the physiology and productivity of AOA.

Sensors and Techniques for On-Line Determination of Cell Viability in Bioprocess Monitoring

In recent years, the bioprocessing industry has experienced significant growth and is increasingly emerging as an important economic sector. Here, efficient process management and constant control of cellular growth are essential. Good product quality and yield can only be guaranteed with high cell density and high viability. Whereas the on-line measurement of physical and chemical process parameters has been common practice for many years, the on-line determination of viability remains a challenge and few commercial on-line measurement methods have been developed to date for determining viability in industrial bioprocesses. Thus, numerous studies have recently been conducted to develop sensors for on-line viability estimation, especially in the field of optical spectroscopic sensors, which will be the focus of this review. Spectroscopic sensors are versatile, on-line and mostly non-invasive. Especially in combination with bioinformatic data analysis, they offer great potential for industrial application. Known as soft sensors, they usually enable simultaneous estimation of multiple biological variables besides viability to be obtained from the same set of measurement data. However, the majority of the presented sensors are still in the research stage, and only a few are already commercially available.

Assessing Microbial Monitoring Methods for Challenging Environmental Strains and Cultures

This paper focuses on the comparison of microbial biomass increase (cell culture growth) using field-relevant testing methods and moving away from colony counts. Challenges exist in exploring the antimicrobial growth of fastidious strains, poorly culturable bacteria and bacterial communities of environmental interest. Thus, various approaches have been explored to follow bacterial growth that can be efficient surrogates for classical optical density or colony-forming unit measurements. Here, six species grown in pure culture were monitored using optical density, ATP assays, DNA concentrations and 16S rRNA qPCR. Each of these methods have different advantages and disadvantages concerning the measurement of growth and activity in complex field samples. The species used as model systems for monitoring were: Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica. All four techniques were found to successfully measure and detect cell biomass/activity differences, though the shape and accuracy of each technique varied between species. DNA concentrations were found to correlate the best with the other three assays (ATP, DNA concentrations and 16S rRNA-targeted qPCR) and provide the advantages of rapid extraction, consistency between replicates and the potential for downstream analysis. DNA concentrations were determined to be the best universal monitoring method for complex environmental samples.

Influence of cerium oxide nanoparticles on dairy effluent nitrate and phosphate bioremediation

This study investigated, for the first time, the role of cerium oxide nanoparticles (CeO₂ NPs) on dairy effluent nitrate and phosphate bioremediation using different inoculum sources. Two inoculum sources (wastewater and sludge) were obtained from the dairy wastewater treatment plant unit. A culture was prepared to be tested in the treatment of nitrate and phosphate effluent, and the role of CeO₂ NPs was checked to be completely efficient after 5 days of incubation. The reduction efficiency of nitrate using sludge as inoculum source was improved up to 89.01% and 68.12% for phosphate compared to control. In the case of using wastewater as an inoculum source, the nitrate reduction was improved up to 83.30% and 87.75% for phosphate compared to control. The bacterial richness showed a significant variance (higher richness) between control and other samples. The optimal concentration of CeO₂ NPs for inoculum richness and nitrate and phosphate reduction was (sludge: 1 × 10^-10 ppm) and (wastewater: 1 × 10^-12 ppm). The results revealed that CeO₂ NPs could enhance the microbial growth of different inoculum sources that have a key role in dairy effluent nitrate and phosphate bioremediation.

The Historical Development of Cultivation Techniques for Methanogens and Other Strict Anaerobes and Their Application in Modern Microbiology

The cultivation and investigation of strictly anaerobic microorganisms belong to the fields of anaerobic microbial physiology, microbiology, and biotechnology. Anaerobic cultivation methods differ from classic microbiological techniques in several aspects. The requirement for special instruments, which are designed to prevent the contact of the specimen with air/molecular oxygen by different means of manipulation, makes this field more challenging for general research compared to working with aerobic microorganisms. Anaerobic microbiological methods are required for many purposes, such as for the isolation and characterization of new species and their physiological examination, as well as for anaerobic biotechnological applications or medical indications. This review presents the historical development of methods for the cultivation of strictly anaerobic microorganisms focusing on methanogenic archaea, anaerobic cultivation methods that are still widely used today, novel methods for anaerobic cultivation, and almost forgotten, but still relevant, techniques.

Low-Cost Clamp-On Photometers (ClampOD) and Tube Photometers (TubeOD) for Online Cell Density Determination

Optical density (OD) measurement is the gold standard to estimate microbial cell density in aqueous systems. Recording microbial growth curves is essential to assess substrate utilization, gauge sensitivity to inhibitors or toxins, or determine the perfect sampling point. Manual sampling for cuvette-photometer-based measurements can cause disturbances and impact growth, especially for strictly anaerobic or thermophilic microbes. For slow growing microbes, manual sampling can cause data gaps that complicate analysis. Online OD measurement systems provide a solution, but are often expensive and ill-suited for applications such as monitoring microbial growth in custom or larger anaerobic vessels. Furthermore, growth measurements of thermophilic cultures are limited by the heat sensitivity of complex electronics. Here, we present two simple, low-cost, self-assembled photometers—a “TubeOD” for online measurement of anaerobic and thermophilic cultures in Hungate tubes and a “ClampOD” that can be attached to virtually any transparent growth vessel. Both OD-meters can be calibrated in minutes. We detail the manufacturing and calibration procedure and demonstrate continuous acquisition of high quality cell density data of a variety of microbes, including strict anaerobes, a thermophile, and gas-utilizing strains in various glassware. When calibrated and operated within their detection limits (ca. 0.3–90% of the photosensor voltage range), these self-build OD-meters can be used for continuous measurement of microbial growth in a variety of applications, thereby, simplifying and enhancing everyday lab operations.

Variation of soil microbial carbon use efficiency (CUE) and its Influence mechanism in the context of global environmental change: a review

Soil microbial carbon utilization efficiency (CUE) is the efficiency with which microorganisms convert absorbed carbon (C) into their own biomass C, also referred to as microorganism growth efficiency. Soil microbial CUE is a critical physiological and ecological parameter in the ecosystem’s C cycle, influencing the processes of C retention, turnover, soil mineralization, and greenhouse gas emission. Understanding the variation of soil microbial CUE and its influence mechanism in the context of global environmental change is critical for a better understanding of the ecosystem’s C cycle process and its response to global changes. In this review, the definition of CUE and its measurement methods are reviewed, and the research progress of soil microbial CUE variation and influencing factors is primarily reviewed and analyzed. Soil microbial CUE is usually expressed as the ratio of microbial growth and absorption, which is divided into methods based on the microbial growth rate, microbial biomass, substrate absorption rate, and substrate concentration change, and varies from 0.2 to 0.8. Thermodynamics, ecological environmental factors, substrate nutrient quality and availability, stoichiometric balance, and microbial community composition all influence this variation. In the future, soil microbial CUE research should focus on quantitative analysis of trace metabolic components, analysis of the regulation mechanism of biological-environmental interactions, and optimization of the carbon cycle model of microorganisms’ dynamic physiological response process.

Challenges and opportunities for the production of lactic acid bacteria inoculants aimed for ensiling processes

The use of bacterial inoculants for ensiling based on lactic acid bacteria (LAB) to obtain conserved forages has become an alternative for the improvement of milk and meat productivity in cattle, specifically by optimizing the nutritional and microbial quality of animal feed. LAB inoculant production involves microbial and technological aspects such as biomass obtention, the use of cocultures, the inclusion of probiotics, the production of antimicrobial peptides, operational methods used in bioreactors, and the formulation of the end product to be commercialized to farmers. This review explores the technical aspects of the manufacture of bacterial inoculants, from the main features desired in LAB for ensiling purposes to the alternatives of the bioprocess involved.

Phytochemicals and in vitro anti-apoptotic properties of ethanol and hot water extracts of Cassava (Manihot esculenta Crantz) peel biogas slurry following anaerobic degradation

Background

Wastes emanating from cassava (Manihot Esculenta Crantz) processing in African countries significantly contribute to environmental pollution, besides, such toxic wastes contribute to greenhouse gas emission. Although cassava peel has been successfully used as a raw material in mushroom cultivation, feedstock for livestock, biogas production but the bio-transformed products recovered from the anaerobic digestion of cassava wastes, especially the peels have often been overlooked. Therefore, this research aimed at quantifying the secondary metabolites in the slurry recovered from ethanol and hot water extraction of cassava peel subjected to biogas production, in vitro, for anti-apoptotic properties.

Methods

Fresh cassava peels were allowed to ferment anaerobically to produce three states of matter; gas, solid, and liquid/slurry. The slurry was extracted using 95 % ethanol and 100 oC hot water to obtain crude extracts, which were then subjected to anti-apoptotic screening using the mitochondrial swelling assay. The qualitative phytochemical analysis of the crude extracts was done using standard methods. Further characterization of the crude extracts was done by FTIR for the chemical elucidation of the functional groups present.

Results

The qualitative phytoconstituents revealed that the slurry extracts are naturally enriched with alkaloids, steroids, flavonoids, and saponins. The infrared spectrum of the crude extracts revealed the presence of hydroxyl, alkane, carboxyl groups in the ethanol extract, and hydroxyl, alkene, amide, carbonyl groups in the hot water extract. In the presence and absence of exogenous Ca2+, both extracts of the slurry induced liver mitochondrial permeability transition pore opening albeit at low amplitude swelling as the mean absorbance was less than one (at 540 nm).

Conclusions

Based on these results obtained, the crude extracts of cassava peel biogas slurry have been proven to possess bioactive compounds that could induce liver mitochondrial permeability transition pore opening, in vitro.

System dynamics kinetic model for predicting biogas production in anaerobic condition: Preliminary assessment

INTRODUCTION

This preliminary assessment of a grey-box model, was predicated on system dynamics principles and developed using Vensim® DSS software. The purpose is to predict biogas production under anaerobic conditions for energy utilization at the design stage.

OBJECTIVE

To describe the process of a developed system dynamics model to predict biogas production under anaerobic conditions.

METHODS

This method involves two-stage kinetics of the biogas production process in anaerobic conditions using the first-order and Gompertz functions. The model is depicted in two parts: causal loop diagram and stock-flow diagram. The causal loop diagram describes the anaerobic digestion process a substrate undergoes for the production of biogas, while stock-flow diagram depicts basic building blocks of the dynamic behavior of an anaerobic digestion process. Primary data is from a laboratory-scale experiment of biogas production using vegetal wastes, while the secondary one is from the literature on studies using similar substrates.

RESULTS

Primary and secondary data are used to validate and stimulate the developed model. The kinetic model shows the substrate being reduced exponentially with increasing time; consumption of substrate and production of methane and carbon dioxide follows exponential growth and decay pattern, with carbon dioxide production starting early compared to methane, and was produced at a rate faster due to the strong and resilient characteristics of fermentative microorganisms.

DISCUSSION

Comparing data from empirical and model simulation shows some close relationship, though not too perfectly. Both results reflect signs of inhibitions occurring within the substrates in the digester under anaerobic conditions explaining the low methane yield or instability.

Polyaza functionalized graphene oxide nanomaterial based sensor for Escherichia coli detection in water matrices

Water quality is widely discussed owing to its significance in public health due to the inability to access clean water. Waterborne diseases account for the presence of pathogens like Escherichia coli (E. coli) in drinking water in the environmental community. Owing to the rapid increase of such bacterial microorganisms, a cost-effective sensor setup has been developed. Herein, we demonstrate the amine-functionalized graphene oxide (fGO) based 2D nanomaterial used to graft E. coli on its surface. The comparative analysis of the deposition of nanosheets on the glass substrate and PDMS was executed. The impedance variations of GO-based nanosensor at various concentrations of E. coli were performed and their potential difference was recorded. It was observed that the impedance changes inversely with the bacterial concentrations and was fed to the Arduino microcontroller. The experimental setup was standardized for the range of 0.01 Hz to 100 kHz. The obtained analog data was programmed with a microcontroller and the bacterial concentration in colony-forming units was displayed. The real-time analysis showsthe low-level detection of E. coli in aquatic environments. Experiments were conducted using the developed nanosensor to test the efficiency in complex water matrices and whose behavior changes with various physical, chemical, and environmental factors.

Design and engineering of artificial microbial consortia for biohydrogen production

In natural microbial ecosystems the metabolic diversity of the organisms enables interaction among the community members and allows them to engage in syntrophic interactions. With regard to biotechnology, artificial microbial consortium engineering is used to improve productivities and yields of bioprocesses. However, to achieve supreme productivity or efficiency at industrial scale, defined ecosystems must be physiologically well-selected to meet eco-biotechnological demands. Here, we present an artificial microbial consortia design and engineering pipeline for developing dark fermentative biohydrogen production processes. The proposed pipeline might be considered as a blue-print for enhancing other bioprocesses that fundamentally face metabolic restrictions or kinetic limitations.

Microbial Removal of Pb(II) Using an Upflow Anaerobic Sludge Blanket (UASB) Reactor

The main objective of this study was to achieve the continuous biorecovery and bioreduction of Pb(II) using an industrially obtained consortia as a biocatalyst. An upflow anaerobic sludge blanket reactor was used in the treatment process. The bioremediation technique that was applied made use of a yeast extract as the microbial substrate and Pb(NO3)2 as the source of Pb(II). The UASB reactor exhibited removal efficiencies of between 90 and 100% for the inlet Pb concentrations from 80 to 2000 ppm and a maximum removal rate of 1948.4 mg/(L·d) was measured. XRD and XPS analyses of the precipitate revealed the presence of Pb0, PbO, PbS and PbSO4. Supporting experimental work carried out included growth measurements, pH, oxidation–reduction potentials and nitrate levels.

Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories

Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH₄) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH₄ production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH₄ cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyr^α444 Gly^α445 Tyr^α446 in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH₄ production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.

Intestinal Microbiota and Perspectives of the Use of Meta-Analysis for Comparison of Ulcerative Colitis Studies

Meta-analysis is a statistical process summarizing comparable data from a number of scientific papers. The use of meta-analysis in microbiology allows decision-making that has an impact on public health policy. It can happen that the primary researches come to different conclusions, although these are targeted with the same research question. It is, therefore, inevitable to have the means to systematically evaluate information and compare research results. Ulcerative colitis together with Crohn's disease are among the two main inflammatory bowel diseases. This chronic disease of the gastrointestinal tract, with an as yet unclear etiology, is presented by an uncontrolled inflammatory immune response in genetically predisposed individuals to as yet undefined environmental factors in interaction with the intestinal microbiota itself. In patients with ulcerative colitis (UC), changes in the composition and relative abundance of microorganisms could be observed. Sulfate-reducing bacteria (SRB), which commonly occur in the large intestine as part of the commensal microbiota of animals and humans involved in the pathogenesis of the disease, have been shown to occur. SRB are anaerobic organisms affecting short-chain fatty acid metabolism. This work outlines the perspectives of the use of meta-analysis for UC and changes in the representation of intestinal organisms in these patients.

Exploring microbial consortia from various environments for plastic degradation

Many complex natural and synthetic compounds are degraded by microbial assemblages rather than single strains, due to usually limited metabolic capacities of single organisms. It can therefore be assumed that plastics can be more efficiently degraded by microbial consortia, although this field has not been as widely explored as plastic degradation by individual strains. In this chapter, we present some of the current studies on this topic and methods to enrich and cultivate plastic-degrading microbial consortia from aquatic and terrestrial ecosystems, including substrate preparation and biodegradation assessment. We focus on both conventional and biodegradable plastics as potential growth substrates. Cultivation methods for both aerobic and anaerobic microorganisms are presented.

A newly isolated Bacillus amyloliquefaciens SRB04 for the synthesis of selenium nanoparticles with potential antibacterial properties

The aim of this study was to isolate and characterize marine bacterial strains capable of converting selenite to elemental selenium with the formation of Se nanoparticles (SeNPs). For the first time, a novel marine strain belonging to Bacillus amyloliquefaciens (GenBank accession no. MK392020) was isolated from the coast of the Caspian Sea and characterized based on its ability for transformation of selenite to SeNPs under aerobic conditions. The preliminary formation of SeNPs was confirmed via color changes and the products characterized by UV-Vis spectroscopy. The field-emission scanning electron microscopy (FESEM) together with energy-dispersive X-ray (EDX) analysis showed the presence of the spherical SeNPs on both the surface of the bacterial biomass and in the supernatant solution. Dynamic light scattering (DLS) analysis showed the SeNPs to have an average particle size (Z-average) around 45.4-68.3 nm. The X-ray diffraction (XRD) studies substantiated the amorphous nature of the biosynthesized SeNPs. Fourier-transform infrared spectroscopic (FTIR) studies of the SeNPs indicated typical proteinaceous and lipid-related bands as capping agents on the SeNPs. Different effective parameters corresponding the yield of SeNPs by B. amyloliquefaciens strain SRB04 were optimized under resting cell strategy. Results showed that the optimal process conditions for SeNP production were 2 mM of selenite oxyanion, 20 g/L of cell biomass, and 60 h reaction time. The synthesized SeNPs had a remarkable antibacterial activity on Staphylococcus aureus compared with chloramphenicol as a broad-spectrum antibiotic.

Porphyromonas spp. have an extensive host range in ill and healthy individuals and an unexpected environmental distribution: A systematic review and meta-analysis

Studies on the anaerobic bacteria Porphyromonas, mainly focused on P. gingivalis, have revealed new bacterial structures, metabolic pathways, and physiologic functionalities. Porphyromonas are mainly described as being associated with mammals and involved in chronic oral infections and secondary pathologies such as cancers or neurodegenerative diseases. In this review, we collected and analyzed information regarding Porphyromonas isolation sites and associated conditions and showed that Porphyromonas are detected in numerous pristine and anthropic environments and that their host range appears wider than previously believed, including aquatic animals, arthropods, and birds, even if their predominant hosts remain humans, pets, and farm animals. Our analyses also revealed their presence in multiple organs and in a substantial proportion of healthy contexts. Overall, the growing numbers of microbiota studies have allowed unprecedented advances in the understanding of Porphyromonas ecology but raise questions regarding their phylogenic assignment. In conclusion, this systematic and meta-analysis provides an overview of current knowledge regarding Porphyromonas ecological distribution and encourages additional research to fill the knowledge gaps to better understand their environmental distribution and inter- and intra-species transmission.

Landfill leachate treatment by a boron-doped diamond-based photo-electro-Fenton system integrated with biological oxidation: A toxicity, genotoxicity and by products assessment

A photo-electro-Fenton (PEF) reactor employing boron-doped diamond (BDD) and soft iron anodes was studied in landfill leachate (LL) treatment. The reactor operation parameters (ROP) H₂O₂ concentration, current intensity and flow rate were investigated in the removal of Abs 254 nm. The PEF process with BDD anode, operating at the best operational conditions, was used as a pre-treatment and enabled biological oxidation (BO). The treatment strategy of PEF followed by BO showed to be the most efficient, reaching reductions of 77.9% chemical oxygen demand (COD), 71.5% total carbon (TC) and 76.3% radiation absorbance in 254 nm (Abs 254 nm), as well as a significant reduction in the genotoxicity (Allium cepa), observed by an increase in the mitotic index (MI) (131.5%) and decrease in the abnormalities (47.8%). The reduction of the toxic potential of LL using the integration of processes was also observed in the gas chromatography-mass spectrometry (GC-MS) byproducts analysis, which indicated the removal of emerging contaminants, such as Bisphenol-A (BPA), N,N-Diethyl-3-methylbenzamide (DEET) and Diisooctyl phthalate (DIOP). Thus, the PEF process integrated with BO presented a considerable efficiency in the removal of contaminants present in LL, becoming an alternative for the minimization of the environmental impacts caused by the discharge of this effluent in the environment.

New Insights into Modelling Bacterial Growth with Reference to the Fish Pathogen Flavobacterium psychrophilum

Simple Summary

Flavobacteriumpsychrophilum is a cold-water bacterium responsible for cold water disease and rainbow trout fry syndrome which has significant impacts on fish health and, by extension, negative economic impacts on aquaculture operations. Models can be applied to bacterial growth curves yielding parameter estimates describing rates of bacterial growth and the time it takes for a bacterium to reach its exponential phase of growth (lag time). These parameter estimates can be used to establish the relationship between microbial growth and environmental variables such as pH, temperature and effect of anti-microbial treatments. Two novel models are derived and their potential to describe bacterial growth assessed through their ability to mimic the growth of Flavobacteriumpsychrophilum on liquid media. Due to their mechanistic derivation, the proposed models result in flexible and robust growth functions that can be expressed as equations with biologically meaningful parameters. Based upon statistical measures of goodness-of-fit and cross-validation, the purposed models were able to describe satisfactorily the growth of Flavobacteriumpsychrophilum on various media. Furthermore, the proposed models also provide insight into underlying mechanisms that are driving microbial growth and how the current environment affects bacterial rate of growth.

Abstract

Two new models, based upon the principles promulgated by Baranyi and co-workers are presented and resulting growth functions evaluated based upon their ability to mimic bacterial growth of the fish pathogen Flavobacterium psychrophilum. These growth functions make use of a dampening function to suppress potential growth, represented by a logistic, and are derived from rate:state differential equations. Dampening effects are represented by a rectangular hyperbola or a simple exponential, incorporated into a logistic differential equation and solved analytically resulting in two newly derived growth equations, viz. logistic × hyperbola (log × hyp) and logistic × exponential (log × exp). These characteristics result in flexible and robust growth functions that can be expressed as equations with biologically meaningful parameters. The newly derived functions (log × hyp and log × exp), along with the Baranyi (BAR), simple logistic (LOG) and its modified form (MLOG) were evaluated based upon examination of residuals and measures of goodness-of-fit and cross-validation. Using these criteria, log × hyp, log × exp and BAR performed better than, or at least equally well as, LOG and MLOG. In contrast with log × exp and BAR, log × hyp can be easily manipulated mathematically allowing for simple algebraic expressions for time and microbial biomass at inflexion point, in addition to maximum and scaled maximum growth rates.

Whole-cell biocatalysis for hydrogen storage and syngas conversion to formate using a thermophilic acetogen

BACKGROUND

In times of global climate change, the conversion and capturing of inorganic CO₂ have gained increased attention because of its great potential as sustainable feedstock in the production of biofuels and biochemicals. CO₂ is not only the substrate for the production of value-added chemicals in CO₂-based bioprocesses, it can also be directly hydrated to formic acid, a so-called liquid organic hydrogen carrier (LOHC), by chemical and biological catalysts. Recently, a new group of enzymes were discovered in the two acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui which catalyze the direct hydrogenation of CO₂ to formic acid with exceptional high rates, the hydrogen-dependent CO₂ reductases (HDCRs). Since these enzymes are promising biocatalysts for the capturing of CO₂ and the storage of molecular hydrogen in form of formic acid, we designed a whole-cell approach for T. kivui to take advantage of using whole cells from a thermophilic organism as H₂/CO₂ storage platform. Additionally, T. kivui cells were used as microbial cell factories for the production of formic acid from syngas.

RESULTS

This study demonstrates the efficient whole-cell biocatalysis for the conversion of H₂ + CO₂ to formic acid in the presence of bicarbonate by T. kivui. Interestingly, the addition of KHCO₃ not only stimulated formate formation dramatically but it also completely abolished unwanted side product formation (acetate) under these conditions and bicarbonate was shown to inhibit the membrane-bound ATP synthase. Cell suspensions reached specific formate production rates of 234 mmol g_protein ^-1 h^-1 (152 mmol g_CDW ^-1 h^-1), the highest rates ever reported in closed-batch conditions. The volumetric formate production rate was 270 mmol L^-1 h^-1 at 4 mg mL^-1. Additionally, this study is the first demonstration that syngas can be converted exclusively to formate using an acetogenic bacterium and high titers up to 130 mM of formate were reached.

CONCLUSIONS

The thermophilic acetogenic bacterium T. kivui is an efficient biocatalyst which makes this organism a promising candidate for future biotechnological applications in hydrogen storage, CO₂ capturing and syngas conversion to formate.

Non-invasive cell counting of adherent, suspended and encapsulated mammalian cells using optical density

In situ measurement to determine mammalian cell number in a non-invasive, non-destructive and reagent-free manner is needed to enable continuous cell manufacturing. An analytical method is presented for non-invasive cell counting by conducting multiwavelength spectral analysis of mammalian cells achieving a minimal detectable cell count of 62,500 at 295 nm. Light absorbance was insensitive to culture volume, giving an absolute cell count rather than a concentration. The activation state of cells was also considered. The study was extended to quantification within polymeric microcapsules as an advanced substrate for mammalian cell growth in bioreactor formats and resulted in an offset directly correlating with the absorbance maxima of the polymer. These studies provide feasibility for optical density as a simple end point to indirectly quantify mammalian cell number for continuous monitoring of cell cultures.