A comparison of two colorimetric assays, based upon Lowry and Bradford techniques, to estimate total protein in soil extracts

Hydrogel immobilized bacteria@MOFs composite towards Bisphenol A degradation and the interconnection mechanism elucidation

Bisphenol A (BPA) degradation efficiency by bacteria or by metal-organic-frameworks (MOFs) catalyzed persulfate (PMS) oxidation have been studied intensively. However, their synergistic effect on BPA degradation was less reported. In this study, we combined previously synthesized CNT-hemin/Mn-MOF with an BPA degrading bacteria SQ-2 to form a composite (SQ-2@MOFs). CNT-hemin/Mn-MOF in the composite catalyzed little PMS to promote the degradation efficiency of SQ-2 on BPA. Results indicated SQ-2@MOFs significantly accelerated BPA degradation rate than SQ-2 alone. Furthermore, SQ-2@MOFs composite was successfully immobilized in hydrogel to achieve better degradation performance. Immobilized SQ-2@MOFs could almost completely degrade 1-20 mg/L BPA within 24 h and completely degrade 5 mg/L BPA at pH 4-8. Besides, degradation byproducts also reduced by immobilized SQ-2@MOFs, which promoted the cleaner biodegradation of BPA. Metabolomics and multiple chemical characterization results revealed the interconnection mechanism between CNT-hemin/Mn-MOFs, SQ-2 and hydrogel. CNT-hemin/Mn-MOF helped SQ-2 degrade BPA into more biodegradable products, promoted electron transfer, and augmented BPA degradation ability of SQ-2 itself. SQ-2 enabled the surface electronegativity of SQ-2@MOFs more suitable for BPA contact. Meanwhile, SQ-2 avoided the loss of Fe and Mn of CNT-hemin/Mn-MOF. Hydrogel augmented the above synergistic effect. This study provided new perspective for the development of biodegradation materials through interdisciplinary integration.

Phenolic and Antioxidant Characterization of Fruit By-Products for Their Nutraceuticals and Dietary Supplements Valorization under a Circular Bio-Economy Approach

Agri-food by-products, obtained as waste from the food industry, negatively impact the global economy and the environment. In order to valorize waste materials from fruit juices and tomato sauces as upcycled materials rich in health-promoting compounds, they were characterized in terms of polyphenolic and protein content. The results obtained were compared with those collected for their final products. The recovery of polyphenols was performed via ultrasound-assisted extraction (UAE). A high-performance liquid chromatography-diode array detector (HPLC-DAD) method was developed and validated to depict the quali-quantitative polyphenolic profile of both the by-products and the final products. The antioxidant capacity of the resulting extracts was characterized by UV-Vis spectrophotometric assays in terms of total phenolic content (TPC) and total antioxidant status (TAS). Moreover, the protein content was assessed with the Kjeldahl method too. The results highlighted a significant quantity of polyphenols remaining in peach, apricot, and apple by-products, which were able to exert an antioxidant activity (in the range of 4.95 ± 5.69 × 10-1 to 7.06 ± 7.96 × 10-1 mmol Trolox 100 g-1 of dry weight (DW) sample). Conversely, the tomato by-products were highly rich in proteins (11.0 ± 2.00 to 14.4 ± 2.60 g of proteins 100 g-1 DW). The results proved that all by-products may potentially be sustainable ingredients with nutritional and functional value in a circular bio-economy prospect.

Critical steps in an environmental metaproteomics workflow

Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.

The efficient capture of polysaccharides in Tetradesmus obliquus of indole-3-acetic acid coupling sludge extraction

Polysaccharide is an important biomass of algae. The sludge extract is rich in organic substances, which can be used by algae for biomass growth and high-value biomass synthesis, but its organic toxicity has an inhibitory effect on algae. To overcome inhibition and improve polysaccharide enrichment, Tetradesmus obliquus was cultured with sludge extract with different indole-3-acetic acid (IAA) concentrations. Within 30 days of the culture cycle, T. obliquus showed in good condition at the IAA dosage content of 10-6 M, the maximum cell density and dry weight were respectively (106.78 ± 2.20) × 106 cell/mL and 2.941 ± 0.067 g/L while the contents of chlorophyll-a, chlorophyll-b, and carotenoid were 1.79, 1.91 and 2.80 times that of the blank group, respectively. The highest polysaccharide accumulation was obtained under this culture condition, reaching 533.15 ± 21.11 mg/L on the 30th day, which was 2.49 times that in the blank group. By FT-IR and NMR analysis, it was found that the polysaccharides of T. obliquus were sulfated polysaccharide with glucose and rhamnose as the main monosaccharides. Proteomic showed that the up-regulation of A0A383WL26 and A0A383WLM8 enhanced the light trapping ability, and A0A383WMJ2 enhanced the accumulation of NADPH. The up-regulation of A0A383WHD5 and A0A383WAY6 indicated that IAA culture could repair the damage caused by sludge toxicity, thus promoting the accumulation of biomass. The above findings provided new insights into the mechanism of sludge toxicity removal of T. obliquus and the enhancement of the polysaccharide accumulation effect under different concentrations of IAA.

Proteomics reveals toxin tolerance and polysaccharide accumulation in Chlorococcum humicola under high CO2 concentration

Algae have great application prospects in excess sludge reclamation and recovery of high-value biomass. Chlorococcum humicola was cultivated in this research, using sludge extract (mixed with SE medium) with additions of 10%, 20%, and 30% CO2 (v/v). Results showed that under 20% CO2, the dry weight and polysaccharide yield reached 1.389 ± 0.070 g/L and 313.49 ± 10.77 mg/L, respectively. 10% and 20% CO2 promoted the production of cellular antioxidant molecules to resist the toxic stress and the toxicity of 20% CO2 group decreased from 62.16 ± 3.11% to 33.02 ± 3.76%. 10% and 20% CO2 accelerated the electron transfer, enhanced carbon assimilation, and promoted the photosynthetic efficiency, while 30% CO2 led to photosystem damage and disorder of antioxidant system. Proteomic analysis showed that 20% CO2 mainly affected energy metabolism and the oxidative stress level on the early stage (10 d), while affected photosynthesis and organic substance metabolism on the stable stage (30 d). The up-regulation of PSII photosynthetic protein subunit 8 (PsbA, PsbO), A0A383W1S5 and A0A383VRI4 promoted the efficiency of PSII and chlorophyll synthesis, and the up-regulation of A0A383WH74 and A0A2Z4THB7 led to the accumulation of polysaccharides. The up-regulation of A0A383VDH1, A0A383VX37 and A0A383VA86 promoted respiration. Collectively, this work discloses the regulatory mechanism of high-concentration CO2 on Chlorococcum humicola to overcome toxicity and accumulate polysaccharides.

Soil moisture dynamics regulates the release rates and lability of copper in contaminated paddy soils

The climate changes have caused more extreme precipitation and drought events in the field and have exacerbated the severity of wet-dry events in soils, which will inevitably lead to severe fluctuations in soil moisture content. Soil moisture content has been recognized to influence the distribution of heavy metals, but how temporal changes of soil moisture dynamics affect the release rates and lability of heavy metals is still poorly understood, which precludes accurate prediction of environmental behavior and environmental risk of heavy metals in the field. In this study, we combined experimental and modeling approaches to quantify copper release rates and labile copper fractions in two paddy soils from southern China under different moisture conditions. Our kinetic data and models showed that the release rates and lability of copper were highly associated with the soil moisture contents, in which, surprisingly, high soil moisture contents effectively reduced the release rates of copper even with little changes in the reactive portions of copper in soils. A suite of comprehensive characterization on soil solid and solution components along the incubation suggested that soil microbes may regulate soil copper lability through forming microbially derived organic matter that sequestered copper and by increasing soil particle aggregation for protecting copper from release. This study highlights the importance of incorporating soil moisture dynamics into future environmental models. The experimental and modeling approaches in this study have provided basis for further developing predictive models applicable to paddy soils with varying soil moisture under the impact of climate change.

Extraction of Proteins from Soil

Soil metaproteomics could explore the proteins involved in life activities and their abundance in the soils to overcome the difficulty in pure cultures of soil microorganisms and the limitations of proteomics of pure cultures. However, the complexity and heterogeneity of soil composition, the low abundance of soil proteins, and the presence of massive interfering substances (including humic compounds) generally lead to an extremely low extraction efficiency of soil proteins. Therefore, the efficient extraction of soil proteins is a prerequisite and bottleneck problem in soil metaproteomics. In this chapter, a soil protein extraction method suitable for most types of soils with low cost and enabling simple operation (about 150 μg protein can be extracted from 5.0 g soil) is described. The quantity and purity of the extracted soil proteins could meet the requirements for further analysis using routine mass spectrometry-based proteomics.

Research progress and prospect of glomalin-related soil protein in the remediation of slightly contaminated soil

Soil pollution caused by organic pollutants and potentially toxic elements poses a serious threat to sustainable agricultural development, global food security and human health. Therefore, strategies for reducing soil pollution are urgently required. Arbuscular mycorrhizal fungi (AMF)-assisted phytoremediation is widely recognized for its ability to remediate slightly-contaminated soil. Glomalin-related soil protein (GRSP) production by AMF is considered a vital mechanism of AMF-assisted phytoremediation. GRSP is widespread in soils and may contribute to the remediation of slightly contaminated soils. GRSP facilitates stabilization of pollutants in soils by interacting with pollutants owing to its abundant functional groups, recalcitrance, and long turnover time. It also enhances soil bioremediation and phytoremediation by stimulating soil microbial activity, improving soil structure, and providing nutrients for plants. However, research on GRSP is still in its early stages, and studies on contaminated soil remediation are limited. The effectiveness of GRSP in situ remediation remains to be proved. This review summarizes current knowledge regarding the GRSP distribution and its contribution to the remediation of slightly contaminated soils. Additionally, we present strategies to increase the GRSP content in contaminated soils, as well as prospects for future studies on the use of GRSP in contaminated soil remediation. This study focuses on recent developments that aim to improve awareness of the role of GRSP in soil remediation and relevant future directions.

Elucidated potential of immobilized Janibacter sp. for saline wastewater phenol removal

Phenolic compounds are commonly found in industrial effluents and can be hazardous to organisms even at low concentrations. Over the years, researchers have demonstrated that bioremediation is a cost-effective and environmentally friendly alternative to physicochemical approaches used to remove phenol. The aim of this study was to investigate the removal of phenol from saline wastewaters by a halotolerant strain of the genus Janibacter. For this purpose, bacterial cells were immobilized on different supports, from which mica and zeolite were ultimately chosen due to their higher removal efficiency. The wet weight of immobilized cells per 1 g of mica and zeolite was 0.51 and 0.48 g, respectively. Free cells consumed 100 mg/L of phenol in 88 h, while immobilized cells used it in 40 h. Immobilized cells revealed a higher thermostability and could operate over a wider pH range and salinity. Unlike free cells, immobilized cells could remove 700 mg/L of phenol and could be reused for at least nine cycles. Interestingly the phenol removal efficiency of zeolite-immobilized cells remained unchanged after 4 months of storage at 4 and - 20 °C, which could be of great advantage for industrial applications. Complete destruction of phenol was observed through the meta pathway comprising phenol hydroxylase and catechol 2,3-dioxygenase enzymes. KEY POINTS: • Mica- and zeolite-immobilized cells were able to consume high concentrations of phenol. • Cells immobilized on mica and zeolite had considerable operational and storage stability. • Immobilized cells could be a good candidate for phenol removal in saline environments.

Alternative methods for RuBisCO extraction from sugar beet waste: A comparative approach of ultrasound and high voltage electrical discharge

Ultrasound (US) and high voltage electric discharge (HVED) with water as a green solvent represent promising novel non-thermal techniques for protein extraction from sugar beet (Beta vulgaris subsp. vulgaris var. altissima) leaves. Compared to HVED, US proved to be a better alternative method for total soluble protein extraction with the aim of obtaining high yield of ribulose-1,5-bisphosphate carboxylase-oxygenase enzyme (RuBisCO). Regardless of the solvent temperature, the highest protein yields were observed at 100% amplitude and 9 min treatment time (84.60 ± 3.98 mg/gd.m. with cold and 96.75 ± 4.30 mg/gd.m. with room temperature deionized water). US treatments at 75% amplitude and 9 min treatment time showed the highest abundance of RuBisCO obtained by immunoblotting assay. The highest protein yields recorded among HVED-treated samples were observed at a voltage of 20 kV and a treatment time of 3 min, disregarding the used gas (33.33 ± 1.06 mg/gd.m. with argon and 34.89 ± 1.59 mg/gd.m. with nitrogen as injected gas), while the highest abundance of the RuBisCO among HVED-treated samples was noticed at 25 kV voltage and 3 min treatment time. By optimizing the US and HVED parameters, it is possible to affect the solubility and improve the isolation of RuBisCO, which could then be purified and implemented into new or already existing functional products.

A Simple Biochemical Method for the Detection of Proteins as Biomarkers of Life on Martian Soil Simulants and the Impact of UV Radiation

The search for life on other planets relies on the detection of biosignatures of life. Many macromolecules have been suggested as potential targets, among which are proteins that are considered vital components of life due to their essential roles in forming cellular structures, facilitating cellular communication and signaling, and catalyzing metabolic reactions. In this context, accurate quantification of protein signatures in soil would be advantageous, and while several proposed methods exist, which are limited by their sensitivity and specificity, their applicability needs further testing and validation. To this aim, we optimized a Bradford-based assay with high sensitivity and reproducibility and a simple protocol to quantify protein extracted from a Martian soil simulant. Methods for protein spiking, extraction, and recovery were optimized, using protein standards and bacterial proteins as representative models. The proposed method achieved high sensitivity and reproducibility. Taking into account that life remains could exist on the surface of Mars, which is subjected to UV radiation, a simulation of UV exposure was performed on a spiked soil simulant. UV radiation degraded the protein spike, thus highlighting the importance of searching for the remaining signal from degraded proteins. Finally, the applicability of the method was explored in relation to the storage of the reagent which was stable even up to 12 months, thus making its application possible for future planetary exploration missions.

Regulatory mechanism of high-concentration CO2 on polysaccharide accumulation in Tetradesmus obliquus cultured in sludge extract

Microalgae such as Tetradesmus obliquus have great potential in immobilizing high-concentration CO₂ and removing highly toxic organic matters, which could be produced from coal chemical industry and coal chemical wastewater biological treatment process. In this study, Tetradesmus obliquus was cultured in sludge extract and high-concentration CO₂ was added. The maximum cell density and dry weight were respectively (111.46 ± 4.87) × 10⁶ cell/mL and 3.365 ± 0.168 g/L under 30% CO₂. Tetradesmus obliquus accumulated the most polysaccharides (629.60 ± 31.48 mg/L) on the 30th day under 30% CO₂. The results of proteomic showed that the upregulation of A0A2Z4THB7 and A0A383VAT1 promoted polysaccharide accumulation. Polysaccharide was mainly formed at the stable phase instead of the log-growth phase due to the abiotic stress caused by high TOC at the log-growth phase. Collectively, this study revealed the regulatory mechanism of high-concentration CO₂ on the toxicity removal and accumulation of polysaccharides in Tetradesmus obliquus.

Synthesis of magnetically recyclable porous cross-linked aggregates of Tramates versicolor MTCC 138 laccase for the efficient removal of pentachlorophenol from aqueous solution

The primary objective of this study is to synthesize the magnetically separable highly active porous immobilized laccase for the removal of pentachlorophenol (PCP) in an aqueous solution. Magnetic porous cross-linked enzyme aggregates (Mp-CLEAs) of laccase were synthesized using 1% starch solution with 5 mM glutaraldehyde followed by 10 h of cross-linking time with an activity recovery of 90.85 ± 0.2%. The biocatalytic efficiency of magnetic porous CLEAs (Mp-CLEAs) was 2-fold higher than that of magnetic CLEAs. The synthesized Mp-CLEAs were mechanically stable with enhanced catalytic efficiency, and reusability thus overcoming the mass transfer limitations and enzyme loss. At 40 °C, the thermal stability of the magnetic porous immobilized laccase was improved, with a 602 min half-life compared to 207 min half-life for the free enzyme. Using 40 U/mL of laccase for the removal of 100 ppm of PCP, M-CLEAs, and Mp-CLEAs removed 60.44% and 65.53% of PCP, respectively. Furthermore, to enhance PCP removal, a laccase-aided system was harnessed by optimizing various surfactants and mediators. Of these, 0.1 mM of rhamnolipid and 2,3 dimethoxy phenol had the highest PCP removal rates of 95.12% and 99.41%, respectively, for Mp-CLEAs. This study demonstrates the efficacy of the laccase-surfactant-mediator system for the removal of PCP from the aqueous solution, which can also be proposed for real-time application.

Enhanced production of amylase, pyruvate and phenolic compounds from glucose by light-driven Aspergillus niger-CuS nanobiohybrids

BACKGROUND

The demand for value-added compounds such as amylase, pyruvate and phenolic compounds produced by biological methods has prompted the rapid development of advanced technologies for their enhanced production. Nanobiohybrids (NBs) make use of both the microbial properties of whole-cell microorganisms and the light-harvesting efficiency of semiconductors. Photosynthetic NBs were constructed that link the biosynthetic pathways of Aspergillus niger with CuS nanoparticles.

RESULTS

In this work, NB formation was confirmed by negative values of the interaction energy, i.e., 2.31 × 10⁸ to -5.52 × 10⁸ kJ mol^-1 for CuS-Che NBs, whereas for CuS-Bio NBs the values were -2.31 × 10⁸ to -4.62 × 10⁸ kJ mol^-1 for CuS-Bio NBs with spherical nanoparticle interaction. For CuS-Bio NBs with nanorod interaction, it ranged from -2.3 × 10⁷ to -3.47 × 10⁷ kJ mol^-1 . Further, the morphological changes observed by scanning electron microscopy showed the presence of the elements Cu and S in the energy-dispersive X-ray spectra and the presence of CuS bonds in Fourier transform infrared spectroscopy indicate NB formation. In addition, the quenching effect in photoluminescence studies confirmed NB formation. Production yields of amylase, phenolic compounds and pyruvate amounted to 11.2 μmol L^-1, 52.5 μmol L^-1 and 28 nmol μL^-1, respectively, in A. niger-CuS Bio NBs on the third day of incubation in the bioreactor. Moreover, A niger cells-CuS Bio NBs had amino acids and lipid yields of 6.2 mg mL^-1 and 26.5 mg L^-1, respectively. Furthermore, probable mechanisms for the enhanced production of amylase, pyruvate and phenolic compounds are proposed.

CONCLUSION

Aspergillus niger-CuS NBs were used for the production of the amylase enzyme and value-added compounds such as pyruvate and phenolic compounds. Aspergillus niger-CuS Bio NBs showed a greater efficiency compared to A. niger-CuS Che NBs as the biologically produced CuS nanoparticles had a higher compatibility with A. niger cells. © 2022 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).

Effects of different concentrations of CO2 on Scenedesmus obliquus to overcome sludge extract toxicity and accumulate biomass

Large amounts of toxic excess sludge as well as high concentrations of carbon dioxide can be produced in coal-gasification industry. Microalgae has huge potential in the use of nutrients, the removal of toxic organic matter in excess sludge and CO₂ fixation. At the same time, the cultivation of the microalgae and the accumulation of high-quality biomass are also the key problems of concern. In this study, the growth and biomass synthesis of Scenedesmus obliquus cultured in sludge extract under 0%-15% (v/v) CO₂ were investigated. Results indicated that the highest microalgae biomass yield of 1.609 ± 0.012 g/L can be achieved under 15% CO₂ on the 30th day. The maximal photochemical efficiency of PSⅡ (Fv/Fm) decreased in the first 12 h and then increased with the culture time, and the decline amplitude decreased with the increase of the CO₂ concentration, indicating that CO₂ slowed down the toxic inhibition of sludge extract to Scenedesmus obliquus, which was expressed as the down-regulation of p53 signaling pathway and protein A0A383WFI7. Proteomic analysis showed that under high-concentration CO₂, the protein interaction network with the protein of photosystem II assembly (A0A383VSL5) as the core protein regulated the growth of Scenedesmus obliquus in terms of energy metabolism and material transportation. On the 4th day, Methyltransf_11 domain-containing protein (A0A383VH03) was up-regulated and promoted lipid synthesis, leading to the accumulation of lipids in Scenedesmus obliquus in the early stage and the increase of polysaccharides in the later stage. Collectively, this study revealed the regulation mechanism of CO₂ on toxicity removal and carbon distribution of Scenedesmus obliquus.

Comparative study of methods for detecting extraterrestrial life in exploration mission of Mars and the solar system

The detection and analysis of extraterrestrial life are important issues of space science. Mars is among the most important planets to explore for extraterrestrial life, owing both to its physical properties and to its ancient and present environments as revealed by previous exploration missions. In this paper, we present a comparative study of methods for detecting extraterrestrial life and life-related substances. To this end, we have classified and summarized the characteristics targeted for the detection of extraterrestrial life in solar system exploration mission and the methods used to evaluate them. A summary table is presented. We conclude that at this moment (i) there is no realistic single detection method capable of concluding the discovery of extraterrestrial life, (ii) no single method has an advantage over the others in all respects, and (iii) there is no single method capable of distinguishing extraterrestrial life from terrestrial life. Therefore, a combination of complementary methods is essential. We emphasize the importance of endeavoring to detect extraterrestrial life without overlooking possible alien life forms, even at the cost of tolerating false positives. Summaries of both the targets and the detection methods should be updated continuously, and comparative studies of both should be pursued. Although this study assumes Mars to be a model site for the primary environment for life searches, both the targets and detection methods described herein will also be useful for searching for extraterrestrial life in any celestial environment and for the initial inspection of returned samples.

Bacterial diversity evolution process based on physicochemical characteristics of sludge treating hydroquinone during acclimation

Hydroquinone is one of the main pollutants in coal-gasification wastewater, which is biologically toxic and difficult to remove. The aerobic biodegradation rate, organic toxicity, and microbial community structure at different acclimation stages of degradation of hydroquinone by activated sludge were investigated. In each acclimation cycle, the removal of hydroquinone reached 100% after 5 days, indicating that high-concentration hydroquinone in the activated sludge could be completely biodegraded. When the microbial flora was inhibited by the influent hydroquinone, the enzyme system experienced stress conditions and led to the secretion of secondary metabolites, extracellular protein of 5-10 kDa mainly contributing to the sludge organic toxicity. Microbial diversity analysis showed that with the increase of the concentration of hydroquinone, β-Proteus bacteria such as Azoarcus and Dechloromonas gradually accumulated, which improved the removal of hydroquinone with aerobic activated sludge in the sequencing batch reactor (SBR) system. As the inhibition degree exceeded the appropriate tolerance range of microorganisms, bacteria would secrete much more secondary metabolites, and the organic toxicity of sludge would reach a relatively high level.

Metagenomics uncovers the effect of nitrogen-doped graphene on anammox consortia and microbial function

The effect of 50 mg/L nitrogen-doped graphene (N-G) on anammox microbial guild was studied by metagenomics in this paper. The continuous experiment results showed the average NRE improved by 17.57% with N-G addition. The metagenomic analysis revealed N-G significantly increased the relative abundance of dominant AnAOB (Candidatus Kuenenia) from 18.10% to 28.30%. And the FISH assay further manifested N-G promoted the growth of AnAOB biomass. Meanwhile, metagenomics indicated that N-G enriched the abundance of genes (Hzs, Hdh, NosZ, NorB, NirK, NirS and NrfA) involved in nitrogen metabolism to varying degrees. Furthermore, N-G not only improved the microbial functionality in terms of "Metabolism", but markedly upregulated the abundance of c-di-GMP synthesized genes and genes related to quinolone signal molecule, which contributed to more EPS content and better sludge settleability. In brief, this study provided a novel perspective for anammox biomass enrichment, which may be valuable for practical engineering applications of anammox.

Mechanistic insight into the removal of aqueous Cd using an immobilized ZIF-8 and microflora cooperative composite

Biotechnology and metal-organic-frameworks (MOFs) materials have been investigated intensively for the removal of heavy metal from wastewater. However, the cooperative effect of bacteria and MOFs on heavy metal adsorption was less reported. Considering this, this study has screened out microflora with cadmium (Cd) adsorption ability. Furthermore, it was combined with zeolitic imidazolate framework-8 (ZIF-8) to form a ZIF-8 and microflora complex (ZMC). Moreover, ZMC was further immobilized to improve its Cd adsorption effect and reusability. Results revealed that the immobilized ZMC exhibited 99.91% and 78.83% Cd adsorption rate for 20 mg L^-1 and 300 mg L^-1 Cd, respectively. Meanwhile, the immobilized ZMC maintained a relatively stable adsorption effect under varied external pH. The reaction mechanism was summarized as covalent binding accompanied with a small amount of electrostatic attraction. Microflora could enhance the surface electronegativity of ZIF-8. ZIF-8 could strengthen the response of antioxidant activity of microflora and augmented the affinity of microflora secretions for Cd. This proposed method may provide a new insight for the removal of heavy metal contaminants in water.

Protocol for bioelectrochemical enrichment, cultivation, and characterization of extreme electroactive microorganisms

Electroactive microorganisms (EAMs) are a group of microbes that can access solid extracellular electron donors or acceptors via extracellular electron transfer processes. EAMs are useful in developing various microbial electrochemical technologies. This protocol describes the use of bioelectrochemical systems (BESs) to enrich EAMs at the cathode from an extreme haloalkaline habitat. It also provides information for a detailed characterization of enriched cathodic biofilms via various cross-disciplinary techniques, including electrochemical, analytical, microscopic, and gene sequencing techniques.

For complete details on the use and execution of this protocol, please refer to Chaudhary et al. (2021).

•

Detailed protocol for the electrochemical enrichment of extreme microorganisms

•

Useful for cultivating different microbes at cathode of bioelectrochemical systems

•

Protocols for characterizing electrotrophic biofilm and metabolic products provided

•

These include electrochemical, analytical, microscopic, and gene sequencing techniques

Distinct granulation pathways of aerobic granular sludge under poly aluminum chloride enhancement

Aerobic granular sludge (AGS), a novel strategy for nutrient removal which exhibits compact structure, good settleability, and resilience against high organic load, has been considered as a highly potential wastewater treatment technology. However, the long start-up period for granulation prevented its widespread development. In this study, the distinct pathways of PAC-enhanced AGS granulation were systematically investigated. Four identical sequencing batch reactors (SBR) with different PAC dosages (with 0, 50, 100, 400 mg/L effective Al³⁺ respectively) were applied. It was observed that the presence of PAC accelerated granules formation, promoted mechanical strength as well as denitrification rate of granules, and thus notably enhanced removal efficacies of COD, NH₄⁺-N, NO₂^- and NO₃^-. According to the dissolved oxygen (DO) distribution inside the sludge and the denitrification rate (SDNR) measurements, distinguishing structures of granules under different PAC addition were discovered. Comparatively, AGS under low PAC addition (i.e., 50 mg/L) resulted in the largest granule size, the biggest anaerobic zone and the highest denitrification rate. Presumably, for the system with the low PAC addition (50 mg/L), appropriate aluminum ions (Al³⁺) neutralized part of the negative charge on the microorganism surface, thereby promoting cells aggregation. In contrast, a high dosage of PAC (400 mg/L) induced excessive Al³⁺ absorbed on the cell surface after neutralization, which increased the repulsive force between microorganisms, leading to more cavities and channels existed inside the granules. Therefore, granules under low PAC dosage (i.e., 50 mg/L) presented large anaerobic zone and high denitrification rate, thus favored the best internal structure and nutrients removal efficiencies.

Glycoproteins of arbuscular mycorrhiza for soil carbon sequestration: Review of mechanisms and controls

Glycoproteins, e.g., glomalin related soil proteins (GRSP), are sticky organic substances produced by arbuscular mycorrhizal fungi (AMF). This review summarizes the information on i) the biochemical nature, physical state and origin of GRSP, ii) GRSP decomposition and residence time in soil, iii) GRSP functions, in particular the physical, chemical, and biochemical roles for soil aggregation and carbon (C) sequestration, and finally iv) how land use and agricultural management affect GRSP production and subsequently, organic C sequestration. GRSP augment soil quality by increasing water holding capacity, nutrient storage and availability, microbial and enzymatic activities, and microbial production of extracellular polysaccharides. After release into the soil, GRSP become prone to microbial decomposition due to stabilization with organic matter and sesquioxides, and thereby increasing the residence time between 6 and 42 years. Temperate soils contain 2-15 mg GRSP g^-1, whereas arid and semiarid grasslands amount for 0.87-1.7 mg g^-1, and GRSP are lower in desert soils. GRSP content is highest in acidic soils as compared to neutral and calcareous soils. Conservation tillage, organic fertilizers and AMF inhabiting crops (e.g. maize, sorghum, soybean, and wheat) increase GRSP production and transform C into stable forms, thereby sustaining soil health and reducing CO₂ emissions. Crop rotations with non-mycorrhizal species (e.g. rapeseed) and fallow soils reduce AMF growth and consequently, the GRSP production. The GRSP production increases under nutrient and water deficiency, soil warming and elevated CO₂. In the context of global climate change, increased C sequestration through GRSP induced aggregate formation and organic matter stabilization prolong the mean residence time of soil C. Protecting soils against degradation under intensive land use, stable aggregate formation, and prolonging the residence time of C calls for strategies that maximize GRSP production and functions based on reduced tillage, AMF-relevant crop rotations and organic farming.

Improving the color and functional properties of seabuckthorn seed protein with phytase treatment combined with alkaline solubilization and isoelectric precipitation

BACKGROUND

Reducing anti-nutritional factors like phytates in seed protein products requires an ongoing effort. This study was the first to investigate the phytic acid content in seabuckthorn seed protein (SSP) and its reduction by an exogenous phytase during protein isolation from seabuckthorn seed meal through the common alkaline solubilization-isoelectric precipitation process.

RESULTS

The additional phytase treatment could reduce the content of phytic acid from 22.46 to 13.27 g kg^-1 , leading to SSP products with lighter color (lower ΔE^* ), higher protein solubility, higher in vitro digestibility, but lower phenolic antioxidant content (including flavonoids and procyanidins) and some beneficial ions like Ca, Fe, Mg, and Zn. The Fourier transform infrared (FTIR) results indicated that the secondary structure of protein changed under the treatment with phytase. Correlation analysis showed that L* was significantly negatively correlated with TP, TPC and TF (P < 0.001), while a* and b* were significantly positively correlated with them (P < 0.001).

CONCLUSIONS

There may be a trade-off between protein functionalities and other health-promoting components when a phytase treatment is included in SSP isolation. © 2021 Society of Chemical Industry.

Polyphenolic-protein-polysaccharide conjugates from Spica of Prunella vulgaris: Chemical profile and anti-herpes simplex virus activities

Previous studies showed that the water extract (PVW) from Spica of Prunella vulgaris Linn. (Labiatae) exerts anti-herpes simplex virus (HSV) activity. Evaluation the antiviral activity of the graded ethanol precipitations indicated that 30% ethanol precipitate (PVE30) was the active principle of water extract (PVW). Further activity-oriented separation of PVE30 through salting-out method revealed that the anti-HSV activity of P. vulgaris glycoconjugates (PVG) was more potent than PVE30 and PVW, 2-fold and 4-fold, respectively. UPLC-QTOF-MS/MS, FT-IR and NMR techniques identified PVG as a type of polyphenolic-protein-polysaccharides (PPPs) with an average molecular weight of 41.69 kDa. PVG was composed of dibenzylbutyrolactone lignan units, and rich in galacturonic acid, xylose, rhamnose, rhamnose, arabinose, glucose monosaccharide units, glutamic acid and aspartic acid. Further in vitro antiviral testing confirmed that PVG substantially and stably inhibited acyclovir (ACV) resistant HSV strains; its inhibitory action was even better than the positive control ACV. Overall, our findings support PVG as a potential drug resource for anti-HSV therapy.

A critical review of 25 years of glomalin research: a better mechanical understanding and robust quantification techniques are required

Arbuscular mycorrhizal fungi (AMF) are important contributors to both plant and soil health. Twenty-five years ago, researchers discovered 'glomalin', a soil component potentially produced by AMF, which was unconventionally extracted from soil and bound by a monoclonal antibody raised against Rhizophagus irregularis spores. 'Glomalin' can resist boiling, strong acids and bases, and protease treatment. Researchers proposed that 'glomalin' is a 60 kDa heat shock protein produced by AMF, while others suggested that it is a mixture of soil organic materials that are not unique to AMF. Despite disagreements on the nature of 'glomalin', it has been consistently associated with a long list of plant and soil health benefits, including soil aggregation, soil carbon storage and enhancing growth under abiotic stress. The benefits attributed to 'glomalin' have caused much excitement in the plant and soil health community; however, the mechanism(s) for these benefits have yet to be established. This review provides insights into the current understanding of the identity of 'glomalin', 'glomalin' quantification, and the associated benefits of 'glomalin'. We invite the community to think more critically about how glomalin-associated benefits are generated. We suggest a series of experiments to test hypotheses regarding the nature of 'glomalin' and associated health benefits.

Chromametric and spectroscopic determinations of natural organic matter in water and caffeine/phosphoric acid-containing soft drink using grape (V. vinifera) extract

Natural anthocyanin dyes are safe for human and the environment due to their biocompatibility and rapid biodegradability. In this paper, an aqueous anthocyanin extract from grapes was used as a colouring reagent for the determination of humic acid (a cancer-promoting agent) in water and caffeine/phosphoric acid-containing caramelized soft drink. Three techniques, viz: chromametry, ultraviolet-visible spectrophotometry (UV-Vis) and Fourier transform infrared spectroscopy (FTIR) were employed for comparative quantifications. The results showed that the chromametry technique exhibited better sensing performance than the spectroscopic techniques in terms of the limit of detection (LOD) and % recovery. However, both chromametry and UV-Vis techniques agreed that the presence of HA could easily be detected in the soft drink at a spiked concentration of 6.4 ppm where less interference occurred.

Bacillus subtilis CtpxS2-1 induces systemic resistance against anthracnose in Andean lupin by lipopeptide production

OBJECTIVE

To evaluate the role of the biocontrol agent Bacillus subtilis CtpxS2-1 in inducing lupin systemic resistance against anthracnose caused by Colletotrichum acutatum by lipopeptide production.

RESULTS

First, growth inhibition and thin layer chromatography-bioautography analysis confirmed that CtpxS2-1 cultures and their lipopeptide extracts, specifically fengycin, have strong antifungal activity against C. acutatum. Subsequent microscopic examination of these fungal inhibition zones showed mycelial pathogen deformations. PCR amplification of CtpxS2-1 confirmed the presence of genes encoding fengycins E and C, bacillomycin C, iturin A, and surfactins B and C. Based on this evidence, the effect of CtpxS2-1 and its lipopeptides on the induction of the lupin defence- and growth-related genes PR-1, PR-4, SOD-2, PIN-1 and PIN-3 was evaluated by RT-qPCR. In seedlings from roots treated with CtxpS2-1, a significant increase in the expression of these genes was induced. Efficacy assays showed that CtpxS2-1 treatment completely controlled anthracnose incidence (0.0%) compared with the untreated control. Furthermore, root and shoot growth in treated seedlings with CtpxS2-1 significantly increased due to disease control, as did the synthesis of the defence enzymes catalase, peroxidase and superoxide dismutase.

CONCLUSION

B. subtilis CtpxS2-1 is a key factor enhancing Andean lupin health by producing lipopeptides that damage C. acutatum cellular structures and inhibit their growth, as well as by inducing the expression of defence-related genes of lupin plants involved in systemic acquired resistance (SAR) against anthracnose.

Dual chemotherapy with benznidazole at suboptimal dose plus curcumin nanoparticles mitigates Trypanosoma cruzi-elicited chronic cardiomyopathy

Curcumin (Cur) is a natural polyphenolic flavonoid isolated from the rhizomes of Curcuma longa. Its anti-inflammatory and cardioprotective properties are increasingly considered to have beneficial effects on the progression of cardiomyopathy associated with Chagas disease, caused by Trypanosoma cruzi. However, the Cur therapeutic limitation is its bioavailability and new Cur nanomedicine formulations are developed to overcome this obstacle. In this research, we provide evidence showing that oral therapy with a suboptimal dose of the standard parasiticidal drug benznidazole (BZ) in combination with Cur-loaded nanoparticles is capable of reducing myocardial parasite load, cardiac hypertrophy, inflammation and fibrosis in mice with long-term infection by T. cruzi. Treatment with BZ plus Cur was highly effective in downregulating myocardial expression of proinflammatory cytokines/chemokines (IL-1β, TNF-α, IL-6, CCL5), and the level/activity of matrix metalloproteinases (MMP-2, MMP-9) and inducible enzymes (cyclooxygenase, nitric oxide synthase) implicated in leukocyte recruitment and cardiac remodeling. Oral administration of a Cur-based nanoformulation displays potential as a complementary strategy to the conventional BZ chemotherapy in the treatment of chronic Chagas heart disease.

Persistent Activities of Extracellular Enzymes Adsorbed to Soil Minerals

Adsorption of extracellular enzymes to soil minerals is assumed to protect them against degradation, while modifying their activities at the same time. However, the persistence of the activity of adsorbed enzymes remains poorly understood. Therefore, we studied the persistence of cellulase and α-amylase activities after adsorption to soil amended with various amounts (+1, +5, and +10 wt.%) of three typical soil minerals, montmorillonite, kaolinite, and goethite. Soil without mineral addition (pure soil), pure minerals, and pure dissolved enzymes were used as references. Soil mineral–enzyme complexes were prepared and then incubated for 100 days; temporal changes in enzyme activities were analyzed after 0, 0.1, 1, 10, and 100 days. The specific enzyme activities (activities normalized to protein content) and their persistence (activities relative to activities at day 0) were compared to enzyme activities in solution and after sorption to the control soil. Amylase adsorption to pure minerals increased in the following order: montmorillonite > kaolinite > goethite. That of cellulase increased in the following order: goethite > montmorillonite > kaolinite. Adsorption of enzymes to soils did not increase in the same order of magnitude as the addition of reactive binding sites. Based on inverse relationships between the amount of enzyme adsorbed and the specific enzyme activity and their persistency, we showed that a limited availability of sorption sites is important for high specific activity and persistence of the enzymes. This is probably the consequence of less and weaker bonds, as compared to a high availability of sorption sites, resulting in a smaller impact on the active sites of the enzyme. Hence, we suppose that the soil mineral phase supports microorganisms in less-sorptive environments by saving energy on enzyme production, since small enzyme release could already result in sufficient activities to degrade respective target carbon substrates.

Probing the structure-holding interactions in cheeses by dissociating agents - A review and an experimental evaluation with emmental cheese

Interactions holding protein structure in cheese has been a subject of considerable investigation, with conclusions varying among studies. We present a review on this topic, covering fresh curds, ripened cheeses, and processed cheeses. We discuss the usual chemicals and conditions used to probe different types of interactions. Furthermore, we did our own study with solutions of urea, SDS, EDTA, NaCl, and NaOH, at different concentrations and combinations, for Emmental cheese. To quantify solubilized protein, we developed a modification of a spectrometric-based method that can be conveniently employed to quantify total protein in cheese, with statistically similar results to those obtained by the Kjeldahl method. Our results point out that caseins in the Emmental cheese are held together by a set of hydrophobic interactions, hydrogen bonds, and other electrostatic ones, including ionic bonds. Hydrogen bonds seem to have an important role, comparable to hydrophobic interactions, a conclusion not commonly reported for cheese structures.

Biochemical and economical effect of application biostimulants containing seaweed extracts and amino acids as an element of agroecological management of bean cultivation

The implementation of agronomic activities, based on the use of biostimulants, is an important element of agroecological practices. Therefore, comprehensive research was carried on the use of biostimulants. A field experiment was performed in 2016-2018 with common bean of Mexican Black cultivar. In particular growing seasons, bean plants were treated with Kelpak SL (seaweed extracts) and Terra Sorb Complex (free amino acids) in the form of single and double spraying with two solutions concentrations. According to the obtained data, application of biostimulants increased the yield of bean. Better results were observed after the use of Kelpak SL. The application of preparations influenced nutritional and nutraceutical quality of bean seeds. Terra Sorb Complex caused the highest increase in proteins level. In the light of achieved data, biostimulants in similar level decreased the starch accumulation. The most promising results, in the context of nutraceutical value of bean, were obtained in the case of increasing level of fiber. A positive impact of biostimulants on the seeds antioxidant potential was noted, expressed by the increased synthesis of phenolics, flavonoid, anthocyanins and antioxidant activities. Results of this study, directly indicate economic benefits from the use of biostimulants, which are extremely important to the farmers.

Top-Down Characterization of an Antimicrobial Sanitizer, Leading From Quenchers of Efficacy to Mode of Action

We developed a top-down strategy to characterize an antimicrobial, oxidizing sanitizer, which has diverse proposed applications including surface-sanitization of fresh foods, and with benefits for water resilience. The strategy involved finding quenchers of antimicrobial activity then antimicrobial mode of action, by identifying key chemical reaction partners starting from complex matrices, narrowing down reactivity to specific organic molecules within cells. The sanitizer electrolyzed-water (EW) retained partial fungicidal activity against the food-spoilage fungus Aspergillus niger at high levels of added soils (30–750 mg mL^–1), commonly associated with harvested produce. Soil with high organic load (98 mg g^–1) gave stronger EW inactivation. Marked inactivation by a complex organics mix (YEPD medium) was linked to its protein-rich components. Addition of pure proteins or amino acids (≤1 mg mL^–1) fully suppressed EW activity. Mechanism was interrogated further with the yeast model, corroborating marked suppression of EW action by the amino acid methionine. Pre-culture with methionine increased resistance to EW, sodium hypochlorite, or chlorine-free ozonated water. Overexpression of methionine sulfoxide reductases (which reduce oxidized methionine) protected against EW. Fluoroprobe-based analyses indicated that methionine and cysteine inactivate free chlorine species in EW. Intracellular methionine oxidation can disturb cellular FeS-clusters and we showed that EW treatment impairs FeS-enzyme activity. The study establishes the value of a top-down approach for multi-level characterization of sanitizer efficacy and action. The results reveal proteins and amino acids as key quenchers of EW activity and, among the amino acids, the importance of methionine oxidation and FeS-cluster damage for antimicrobial mode-of-action.

Soil protein as a potential antimicrobial agent against methicillin -resistant Staphylococcus aureus

Recently, the interest is increasing to find alternatives to replace the usage of antibiotics since their massive and improper usage enhance the antibiotic resistance in human pathogens. In this study, for the first time we showed that the soil proteins have very high antibacterial activity (98% of growth inhibition) against methicillin resistant Staphylococcus aureus (MRSA), one of the most threatening human pathogens. We found that the protein extract (C3) from the forest with past intensive management showed higher antibacterial activity than that of unmanaged forest. The MIC and IC₅₀ were found to be 30 and 15.0 μg protein g^-1 dry soil respectively. C3 was found to kill the bacteria by cell wall disruption and genotoxicity which was confirmed by optical and fluorescent microscopy and comet assay. According to qPCR study, the mecA (the antibiotic resistant gene) expression in MRSA was found to be down-regulated after C3 treatment. In contrast, C3 showed no hemolytic toxicity on human red blood cells which was confirmed by hemolytic assay. According to ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS), 144 proteins were identified in C3 among which the majority belonged to Gram negative bacteria (45.8%). Altogether, our results will help to develop novel, cost-effective, non-toxic and highly efficient antibacterial medicines from natural sources against antibiotic resistant infections.

Anode potential-dependent protection of electroactive biofilms against metal ion shock via regulating extracellular polymeric substances

Extracellular polymeric substances (EPS) have been considered as a barrier for toxic species penetration into the cells, but their function in protecting electroactive biofilms (EABs) had been rarely revealed. In this study, the anode potential was used to regulate the EPS quantity and components in mixed-culture EABs, where their resistance to Ag⁺ shock was assessed. The results showed that the EAB grown at 0 V showed the highest anti-shock capability by the Ag⁺ exposure compared to those grown at -0.2, 0.2, and 0.4 V. The EAB produced at 0 V had both of the highest amounts of loosely bound EPS (LB-EPS; 61.9 mg-EPS/g-VSS) and tightly bound EPS (TB-EPS; 74.8 mg-EPS/g-VSS) than those grown under other potentials, where proteins and humic acid were the predominated components. The abundance of genes associated with EPS biosynthesis were also confirmed to be related with the applied anode potentials, based on the metagenomic analysis. Considering proteins and humic acid in LB-EPS showed positive linearity with the current recovery and viability of the EABs, these two main components might play important roles in reducing the Ag⁺ toxicity. Synchronous fourier transform infrared (FTIR) spectroscopy integrated two-dimensional correlation spectroscopy (2D-COS) analyses further confirmed that the oxygen and nitrogen moieties (i.e. amide, carbonyl CO, phenolic, and C-O-C) in proteins and humic acid of the LB-EPS were response for the binding with the Ag⁺ to prevent the penetration into the cells. The underlying molecular mechanisms of EPS in protecting EABs from the Ag⁺ shock explored in this study can provide implications for developing new methods to construct highly stable EABs.

Effect of oleuropein on oxidative stress, inflammation and apoptosis induced by ischemia-reperfusion injury in rat kidney

AIMS

This study aimed to evaluate the effect of oleuropein (OLE), the main phenolic compound present in olive leaves, on kidney ischemia-reperfusion injury (IRI) and to explore the underlying protective mechanism.

MAIN METHODS

Rat kidneys were subjected to 60 min of bilateral warm ischemia followed by 120 min of reperfusion. OLE was administered orally 48 h, 24 h and 30 min prior to ischemia at doses of 10, 50 and 100 mg/kg body weight. The creatinine, urea, uric acid concentrations and lactate dehydrogenase (LDH) activity in plasma were evaluated. Oxidative stress and inflammation parameters were also assessed. Renal expression of AMP-activated protein kinase (p-AMPK), endothelial nitric oxide synthase (eNOS), mitogen-activated protein kinases (MAPK), inflammatory proteins and apoptotic proteins were evaluated using Western blot.

KEY FINDINGS

Our results showed that OLE at 50 mg/kg reduced kidney IRI as revealed by a significant decrease of plasmatic creatinine, urea, uric acid concentrations and LDH activity. In parallel, OLE up-regulated antioxidant capacities. Moreover, OLE diminished the level of CRP and the expression of cyclooxygenase 2 (COX-2). Finally, OLE enhanced AMPK phosphorylation as well as eNOS expression whereas MAPK, and cleaved caspase-3 implicated in cellular apoptosis were attenuated in the ischemic kidneys.

SIGNIFICANCE

In conclusion, this study shows that OLE could be used as therapeutic agent to reduce IRI through its anti-oxidative, anti-inflammatory and anti-apoptotic properties.

Photobiomodulation alters the viability of HUVECs cells

The aim of the present study was to investigate the influence of low-level red (660 nm) and infrared (780 nm) laser with four different radiance exposures on human umbilical vein endothelial cells (HUVECs) in vitro. HUVECs (1.5 × 10⁴) were incubated in 96-well culture plates. The cells were maintained in M199 medium supplemented with 20% fetal bovine serum, 1% antibiotic (penicillin), 1% anti-mycotic (Fungizone), and 1% endothelial cell growth supplement. After centrifugation, irradiations (660/780 nm, 40 mW, 1, 5, 10, and 20 J/cm², 1 s, 5 s, 10 s, and 20 s, respectively, total energy 0.4 J, 2 J, 4 J, and 8 J, and beam spot size at target 0.04 cm²) were performed at the bottom of Falcon tubes such that the laser beam directly reached the cell without passing through the culture medium. The cells were divided into groups based on radiant exposures. Cell viability and protein concentration were verified after 1, 2, 3, 6, 8, and 10 days. Red laser increased the cell viability and protein concentration in all groups (three-way ANOVA, p < 0.05) beginning on the second day. The greatest peak compared with the control was found when the radiant exposure was 5 J/cm² and 10 J/cm². Infrared laser inhibited cell viability and modulated the protein concentration in the cells, with the highest peak protein concentration found on the second day in the group with radiant exposure of 1 J/cm² and 10 J/cm² (three-way ANOVA, p < 0.05). Red laser increased the viability and concentration of total proteins in HUVECs, whereas infrared laser had an inhibitory effect on cell viability, while maintaining the total protein concentration similar to that found in the control group.

Soil organic carbon, extracellular polymeric substances (EPS), and soil structural stability as affected by previous and current land-use

While soil microbial ecology, soil organic carbon (SOC) and soil physical quality are widely understood to be interrelated - the underlying drivers of emergent properties, from land management to biochemistry, are hotly debated. Biological binding agents, microbial exudates, or 'extracellular polymeric substances' (EPS) in soil are now receiving increased attention due to several of the existing methodological challenges having been overcome. We applied a recently developed approach to quantify soil EPS, as extracellular protein and extracellular polysaccharide, on the well-characterised soils of the Highfield Experiment, Rothamsted Research, UK. Our aim was to investigate the links between agricultural land use, SOC, transient binding agents known as EPS, and their impacts on soil physical quality (given by mean weight diameter of water stable aggregates; MWD). We compared the legacy effects from long-term previous land-uses (unfertilised grassland, fertilised arable, and fallow) which were established > 50 years prior to investigation, crossed with the same current land-uses established for a duration of only 2.5 years prior to sampling. Continuously fallow and grassland soils represented the poorest and greatest states of structural integrity, respectively. Total SOC and N were found to be affected by both previous and current land-uses, while extractable EPS and MWD were driven primarily by the current land-use. Land-use change between these two extremes (fallow → grass; grass → fallow) resulted in smaller SOC differences (64% increase or 37% loss) compared to MWD (125% increase or 78% loss). SOC concentration correlated well to MWD (adjusted R 2 = 0.72) but the greater SOC content from previous grassland was not found to contribute directly to the current stability (p < 0.05). Our work thus supports the view that certain distinct components of SOC, rather than the total pool, have disproportionately important effects on a soil's structural stability. EPS-protein was more closely related to aggregate stability than EPS-polysaccharide (p values of 0.002 and 0.027, respectively), and ranking soils with the 5 greatest concentrations of EPS-protein to their corresponding orders of stability (MWD) resulted in a perfect match. We confirmed that both EPS-protein and EPS-polysaccharide were transient fractions: supporting the founding models for aggregate formation. We suggest that management of transient binding agents such as EPS -as opposed to simply increasing the total SOC content- may be a more feasible strategy to improve soil structural integrity and help achieve environmental objectives.

Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide-producing bacteria during soil formation

Polymeric substances produced by microbes play a key role for the development of soil aggregates. Here, we investigated the dynamics of bacterial families contributing to the formation of exopolysaccharides and lipopolysaccharides, major constituents of polymeric substances, at a managed land reclamation site of a post-mining area. We collected soil samples from the initial and the agricultural management phase and expected a peak in the abundance of bacteria capable for exopolysaccharide and lipopolysaccharide production at the points of the biggest disturbances. We used shotgun metagenomic sequencing in combination with measurements of exopolysaccharide concentrations. Our results underline the importance of exopolysaccharide and lipopolysaccharide-producing bacteria after nutrient input combined with structural disturbance events, caused here by the initial planting of alfalfa and the introduction of a tillage regime together with organic fertilization in the agricultural management phase. Moreover, the changes in management caused a shift in the exopolysaccharide/lipopolysaccharide-producing community. The initial phase was dominated by typical colonizers of oligotrophic environments, specifically nitrogen fixers (Rhizobiaceae, Comamonadaceae, Hyphomicrobiaceae), while bacteria common in agricultural soils, such as Sphingomonadaceae, Oxalobacteraceae and Nitrospiraceae, prevailed in the agricultural management phase.

Flavonoids interference in common protein assays: Effect of position and degree of hydroxyl substitution

Flavonoids interfere with colorimetric protein assays in a concentration- and structure-dependent manner. Degree (≥3) and position (C₃) of -OH substitution was associated with intensified interference (p < 0.05). Significant overestimation of protein (~3-5 folds) could occur at higher flavonoid concentrations (>5 μM) and is particularly evident at lower protein concentrations (25-250 μg/ml). Since, healthy human urinary protein (<200 μg/ml) and flavonoids urinary excretion (0.5-2 μg/ml) levels fall in this range, overestimation of protein concentration with flavonoids consumption in diet, including natural supplements, remains relevant issue for diagnostic and research labs. Protein precipitation by acetone to remove interfering flavonoid successfully resolves the problem.

Towards Sustainable Agriculture—Agronomic and Economic Effects of Biostimulant Use in Common Bean Cultivation

Today, one of the greatest challenges faced by the agriculture industry is the development of sustainable and environmentally-friendly systems to meet nutritional demands of the continuously growing global population. A number of research studies have recently been undertaken with the aim to indicate types of parameters used in plant production that would be able to improve plant growth as well as the effectiveness and quality of yield, and to help plants cope with environmental stress. The aim of this study was to verify a hypothesis that the implementation of a sustainable agricultural technology, based on the use of synthetic biostimulants, will allow not only increasing crop yield and quality but also improving the cost-effectiveness of common bean cultivation. The field experiment was conducted in three growing seasons (2016–2018). In the growing season, the plants were treated with Atonik and Tytanit biostimulants in the form of single or double spraying. We determinated biometric traits, seed yield, seed number, and 1000-seed weight. Further analyses included contents of nutraceutical potential. The economic effect of using biostimulants was also calculated. The results of our experiment allowed verifying a hypothesis that the implementation of a sustainable agricultural technology based on the use of synthetic preparations was an effective method to increase plant productivity and, consequently, economic profits to farmers.

Proteomic method to extract, concentrate, digest and enrich peptides from fossils with coloured (humic) substances for mass spectrometry analyses

Humic substances are breakdown products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content and remove humics, producing clean samples easily analysed by mass spectrometry (MS). This method includes: (i) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; (ii) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; (iii) centrifugal stage tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (approx. 800-1000 years) dark with humic content, generating colourless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.

Disruption of flavin homeostasis in isolated rat liver mitochondria

It has been shown that spontaneous release of non-covalent flavins (from flavoenzymes) begins after isolation of mitochondria from rat liver, which is hydrolyzed to riboflavin. This process is stopped by 1 mM EDTA in the incubation medium. In the presence of NADH, deflavinization of flavoproteins leads to formation of superoxide by at least of three processes. The first of these occurs in complex I as a result of the spontaneous release of FMN from the active center. This process is inhibited by adenosine and guanosine phosphates, as well as NAD, but amplified by nicotinamide. The second process is associated with enzymatic hydrolysis of FAD and FMN to riboflavin; it is blocked by EDTA, AMP, NA, NAD. The third process is associated with non-enzymatic hydrolysis of FAD by iron ions in matrix; it is blocked by EDTA and AMP.

A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures

The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.