Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments

In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).

Enhancement of integrated nano-sensor performance comprised of electrospun PANI/carbonaceous material fibers for phenolic detection in aqueous solutions

The detection of trace levels of organic residue in water samples is a key health issue. This manuscript describes the fabrication of integrated nano-sensors composed of electrospun microfibers consisting of a nanocomposite of carbonaceous materials (CNMs) containing polyaniline (PANI) and polycaprolactone (PCL) for phenolic detection in aqueous solutions. The morphology of the resulting microfiber composite was characterized by scanning electron microscopy. It revealed elongated fibers with a highly interconnected web-like pattern in the presence of reduced graphene oxide (rGO). Shorter microfibers were observed in the composite filled with multi-walled carbon nanotubes (MWCNTs), whereas large agglomerates were formed upon the incorporation of single-walled CNTs (SWCNTs) and graphene 300 (G300). Comparative analysis showed that the PANI/CNM sensors exhibited the best electrochemical properties, in particular in the presence of rGO and MWCNTs, where greater electrical conductivity was achieved, i.e., 4.33 × 10-3 and 7.22 × 10-4 S/cm, respectively, as compared to the PANI-PCL sensor (3.79 × 10-4 S/cm). All the PANI/CNM sensors exhibited high sensitivity. Notably, PANI/rGO was found to have a detection limit of 8.34 × 10-3 µM for aminophenol. All the sensors exhibited good selectivity in the presence of interference to detecting phenolic compounds in aqueous solutions, thus confirming their value for industrial applications.

Influence of grain size, organic carbon and organic matter residue content on the sorption of per- and polyfluoroalkyl substances in aqueous film forming foam contaminated soils - Implications for remediation using soil washing

A soil that was historically contaminated with Aqueous Film Forming Foam (AFFF) was dry sieved into size fractions representative of those produced during soil washing. Batch sorption tests were then conducted to investigate the effect of soil parameters on in situ per- and polyfluoroalkyl substances (PFAS) sorption of these different size fractions: < 0.063 mm, 0.063 to 0.5 mm, 0.5 to 2 mm, 2 to 4 mm, 4 to 8 mm, and soil organic matter residues (SOMR). PFOS (513 ng/g), 6:2 FTS (132 ng/g) and PFHxS (58 ng/g) were the most dominant PFAS in the AFFF contaminated soil. Non-spiked, in situ K_d values for 19 PFAS ranged from 0.2 to 138 L/Kg (log K_d -0.8 to 2.14) for the bulk soil and were dependant on the head group and perfluorinated chain length (spanning C₄ to C₁₃). The K_d values increased with decreasing grain size and increasing organic carbon content (OC), which were correlated to each other. For example, the PFOS K_d value for silt and clay (< 0.063 mm, 17.1 L/Kg, log K_d 1.23) were approximately 30 times higher compared to the gravel fraction (4 to 8 mm, 0.6 L/Kg, log K_d -0.25). The highest PFOS K_d value (116.6 L/Kg, log K_d 2.07) was found for the SOMR fraction, which had the highest OC content. K_oc values for PFOS ranged from 6.9 L/Kg (log K_oc 0.84) for the gravel fraction to 1906 L/Kg (log K_oc 3.28) for the silt and clay, indicating that the mineral composition of the different size fractions also influenced sorption. The results here emphasize the need to separate coarse-grained fractions and fine-grained fractions, and in particular the SOMR, to optimize the soil washing process. Higher K_d values for the smaller size fractions indicate that coarser soils are better suited for soil washing.

Molecular evidence for new foodways in the early colonial Caribbean: organic residue analysis at Isla de Mona, Puerto Rico

Ceramic objects account for over 90% of the cultural material recovered from archaeological sites in the Caribbean. However, little research has been conducted on molecular evidence for past food production from these same vessels. Forty ceramic sherds from Isla de Mona have been analysed by GC-MS and GC-C-IRMS in order to address questions surrounding foodways in the Greater Antilles prior to and post European arrival. We evaluate evidence for dietary changes to illuminate aspects of cultural exchange between Indigenous populations and the first generations of Spanish colonists. Here, we show that plant residues are found in a variety of pottery forms, with some evidence for non-ruminant and ruminant fats. The dearth of marine biomarkers is curious given the volume of fish bones found in archaeological contexts on Isla de Mona and may offer evidence for spit-roasting, pit-roasting, or the use of a 'barbacoa' to cook fish on the island. The ubiquity of plant residues in a variety of pottery forms may relate to the large-scale cultivation and export of cassava (Manihot esculenta) from the island. A Spanish olive jar revealed evidence of wine residues, which may constitute the earliest detection of wine residues in pottery found in the Americas.

Supplementary information

The online version contains supplementary material available at 10.1007/s12520-023-01771-y.

Ecotoxicological effects of untreated pig manure from diets with or without growth-promoting supplements on Eisenia andrei in subtropical soils

This study aimed to evaluate the effects of untreated pig manure from diets incorporating growth-promoting supplements (antibiotics and Zn oxide) on the survival and reproduction of Eisenia andrei earthworms. The tested manures were obtained from four different groups of pigs fed with four different diets: CS, a diet based on corn and soymeal; TR, a diet based on corn, soymeal, and ground wheat (15%); CSa, a diet based on corn and soymeal + 100 ppm of doxycycline + 50 ppm of colistin + 2500 ppm of Zn oxide; and TRa, a diet based on corn, soymeal, and ground wheat (15%) + 100 ppm of doxycycline + 50 ppm of colistin + 2500 ppm of Zn oxide. The study used two soils representative of the Southern region of Brazil (Oxisol and Entisol). In general, there were no significant differences between the different manures tested in each soil. However, there were differences in the toxicity manure on E. andrei between the soils, and the magnitude of this effect was dependent on the applied dose. In Oxisol, LC₅₀ values were higher than 80 m³ ha^-1, and EC₅₀ varied from 9 to 27 m³ ha^-1. In Entisol, the LC₅₀ values were below the lowest dose tested (< 25 m³ ha^-1), and EC₅₀ remained around 5 m³ ha^-1. It may be possible that the effects observed were attributed to an excess of nitrogen, copper, and zinc, promoted by the addition of the untreated manure and how these factors interacted with soil type.

Effects of temperature and soil fauna on the reduction and leaching of deoxynivalenol and zearalenone from Fusarium graminearum-infected maize stubbles

A microcosm study was conducted at two different temperatures under laboratory conditions to investigate the regulatory capacity and the interactive performance of two soil fauna species (Aporrectodea caliginosa, earthworms, and Proisotoma minuta, collembolans) on the reduction of Fusarium toxins in contaminated maize stubbles. Single and mixed species treatments were exposed to artificially infected maize stubbles highly contaminated with the mycotoxins deoxynivalenol (DON) (10,462 µg kg⁻¹) and zearalenone (ZEN) (2,780 µg kg⁻¹) at 17 °C and 25 °C for time periods of 3 and 6 weeks. Immediately after the respective end of incubation, the microcosms were heavily watered to determine the leaching potential of DON and ZEN from contaminated maize stubbles. Maize residues, soil, and eluted water (percolate) samples were analysed for mycotoxin content using liquid chromatography coupled to mass spectrometry. The biomass of introduced earthworms and number of collembolans were monitored to get information about their adaptability to the experimental conditions. While the decline of ZEN was temperature-dependent, but not influenced by faunal activities, a reduction of DON due to faunal impact was observed by trend. In the leaching experiment, 67–82% of the DON content in the residual maize stubbles leached from the plant material by irrigation and was detected in the soil (1.9–3.4 µg kg⁻¹) and in the percolate (12–295 µg L⁻¹). In the case of ZEN, 27–50% of the mycotoxin leached from the residual maize stubbles due to watering but was only occasionally detected in traces in the soil and not found in the percolate. The results clearly reveal a leaching potential of both DON and ZEN, respectively, but a mobilisation with water was only observed for DON. Temperature confirmed to be a key factor, affecting the fate of the mycotoxins in the soil by driving the interaction between different soil fauna members as well as functional and trophic levels within the soil food web.

Continuous pretreatment, hydrolysis, and fermentation of organic residues for the production of biochemicals

Agricultural residues pose a valuable resource. Through microbial fermentations, a variety of products can be obtained, ranging from fuels to platform chemicals. Depending on the nature of the organic residue, pretreatment and hydrolysis are needed prior to fermentation in order to release fermentable sugars. Continuous set-ups are common for the production of methane or ethanol from lignocellulosic biomass, however, this does not apply for the fermentative generation of biochemicals, an approach that conserves chemical functionality present in biomass. Certainly, continuous set-ups could beneficially contribute to bioeconomy by providing techniques allowing the production of biochemicals in a sustainable and efficient way. This review summarizes research conducted on the continuous pretreatment, hydrolysis, and fermentation of lignocellulosic biomass, and particularly towards the production of the biobased molecules: Succinic and lactic acid.

Phosphorus sorption and availability in an andosol after a decade of organic or mineral fertilizer applications: Importance of pH and organic carbon modifications in soil as compared to phosphorus accumulation

The effect of organic fertilizers on soil phosphorus (P) availability is usually mainly associated with the rate and forms of P applied, while they also alter the soil physical-chemical properties, able to change P availability. We aimed to highlight the impact of pH and organic C modifications in soil on the inorganic P (Pi) sorption capacity and availability as compared to the effect of P accumulation after mineral or organic fertilizers. We conducted a 10-years-old field experiment on an andosol and compared fields that had been amended with mineral or organic (dairy slurry and manure compost) fertilizers against a non-fertilized control. Water and Olsen extractions and Pi sorption experiments were realized on soils sampled after 6 and 10 years of trial. We also realized an artificial and ex situ alkalization of the control soil to isolate the effect of pH on Pi sorption capacity. Organic fertilizer application increased total P, pH, and organic C in soil. Pi-Olsen increased mainly with soil total P (r² adj = 0.79), while Pi-water increased jointly with soil total P and pH (r² adj = 0.85). The Pi sorption capacity decreased with organic fertilizer application. Artificial and ex situ alkalization of the control soil showed that Pi sorption capacity decreased with increasing pH. Our study demonstrated that, beyond the P fertilization rate, the increase in organic C content and even more so in pH induced by a decade of organic fertilizer applications in soil decreased the Pi sorption capacity and consequently increased Pi-water in soil.

Ionic speciation and risks associated with agricultural use of industrial biosolid applied in Inceptisol

The evaluation of the chemical leaching potential from soils amended with biosolid is of extreme importance for environmental safety of agricultural use of these residues. The objective of this study was to evaluate the polluting potential and possible risks associated with the agricultural use of biosolids generated by the polyethylene terephthalate (PET) fiber and resin industry through ionic speciation and analysis of the activity of chemical species present in the leached solution from Inceptisol treated with rates 0, 6, 12, 18, 24, 48, 96, and 144 Mg ha^-1 on dry basis. The experiment was conducted in a lysimeter and the treatments with three replications were distributed at random. Chemical leaching was made by application of CaC1₂ 0.01 mol L^-1 solutions in a volume fourfold higher than the water retention capacity of the soil, divided into five leaching events: 210, 245, 280, 315, and 350 days of incubation. Chemical species concentrations in collected leachates were used for ionic speciation by geochemical software Visual MINTEQA2 version 4.0. Impact factor of chemical species was calculated as the ratio between maximum concentration in the leach solution in the treated soil and control. Dissolved organic carbon had strong influence on Pb⁺² and Cu⁺² leaching, but these elements in free or complexed forms presented low activities in solution. Leaching of NO₃^-, Zn⁺², and Na⁺ represents the main environmental risk of agricultural use of this residue. However, these risks can be minimized if technical criteria and critical limits for the agronomic use of biosolids were observed.

Manure pellet, woodchip and their biochars differently affect wheat yield and carbon dioxide emission from bulk and rhizosphere soils

Application of biochars produced by pyrolyzing organic residues to cropland has been proposed to be an effective approach to better use of organic residues, decrease soil greenhouse gas emission and increase soil fertility. However, the effect of biochar application on processes occurring in the bulk soil vs that in the rhizosphere is poorly understood. This study investigated the effects of manure pellet and woodchip biochars, as compared to that of unpyrolyzed (raw) manure pellet and woodchip, on plant grain yield, and soil respiration in the bulk and rhizosphere soils in a greenhouse experiment using the rhizobox technique. The raw manure pellet and woodchip and their biochars were applied to the soil at the rate of 57 t ha^-1 and spring wheat (Triticum aestivum L. var. GP168) was grown in the rhizosphere compartment of the rhizobox. Soil amendment with raw manure pellet and its biochar significantly increased plant grain yield by 36.3 and 16.1%, as compared to the control (without amendment), while raw woodchip and its biochar applications significantly decreased plant grain yield. Manure pellet and woodchip biochars significantly reduced soil respiration from the rhizosphere by 24.6 and 29.7%, respectively, relative to the control, but not that from the bulk soil (P > 0.05). Relativized cumulative CO₂ emission was significantly reduced by both manure pellet and woodchip biochars from rhizosphere and bulk soils. Dissolved organic carbon and nitrogen were increased (P < 0.01) in all soil amendment treatments in both bulk and rhizosphere soils, but microbial biomass carbon and nitrogen in the rhizosphere soil were reduced by manure pellet biochar application. We conclude that biochars produced from organic residues have differential impacts on processes in bulk and rhizosphere soils, and thus measurements based on bulk soil alone may result in erroneous conclusions about the effect of biochars on soil CO₂ emission.

Utilization of organic residues using heterotrophic microalgae and insects

Various organic residues occur globally in the form of straw, wood, green biomass, food waste, feces, manure etc. Other utilization strategies apart from anaerobic digestion, composting and incineration are needed to make use of the whole potential of organic residues as sources of various value added compounds. This review compares the cultivation of heterotrophic microalgae and insects using organic residues as nutrient sources and illuminates their potential with regard to biomass production, productivity and yield, and utilization strategies of produced biomasses. Furthermore, cultivation processes as well as advantages and disadvantages of utilization processes are identified and discussed. It was shown that both heterotrophic algae and insects are able to reduce a sufficient amount of organic residues by converting it into biomass. The biomass composition of both organisms is similar which allows similar utilization strategies in food and feed, chemicals and materials productions. Even though insect is the more complex organism, biomass production can be carried out using simple equipment without sterilization and hydrolysis of organic residues. Contrarily, heterotrophic microalgae require a pretreatment of organic residues in form of sterilization and in most cases hydrolysis. Interestingly, the volumetric productivity of insect biomass exceeds the productivity of algal biomass. Despite legal restrictions, it is expected that microalgae and insects will find application as alternative food and feed sources in the future.

Enzymatic dynamics into the Eisenia fetida (Savigny, 1826) gut during vermicomposting of coffee husk and market waste in a tropical environment

Epigeic worms modify microbial communities through their digestive processes, thereby influencing the decomposition of organic matter in vermicomposting systems. Nevertheless, the enzyme dynamics within the gut of tropically adapted earthworms is unknown, and the enzymes involved have not been simultaneously studied. The activities of 19 hydrolytic enzymes within three different sections of the intestine of Eisenia fetida were determined over a fasting period and at 24 h and 30, 60, and 90 days of vermicomposting, and data were evaluated by multivariate analyses. There were found positive correlations between the maximal activity of glycosyl hydrolases and one esterase with the anterior intestine (coincident with the reduction of hemicellulose in the substrate) and the activity of the protease α-chymotrypsin with posterior intestine. The results suggest that activities of enzymes change in a coordinated manner within each gut section, probably influenced by selective microbial enzyme enrichment and by the availability of nutrients throughout vermicomposting.

Ecotoxicological effects of pig manure on Folsomia candida in subtropical Brazilian soils

The effects of pig manure, from diets incorporating veterinary pharmaceuticals, on survival and reproduction of Folsomia candida were evaluated. Manures derived from the following diets: corn and soymeal (CS); 85% CS diet+15% wheat meal (TR); CS diet+100ppm doxycycline+50ppm colistin+2500ppm Zn oxide (CSa); TR diet+100ppm doxycycline+50ppm colistin+2500ppm Zn oxide (TRa). Manures were tested in two subtropical soils representative of southern (Oxisol and Entisol). Despite the antibiotics no significant differences were found between the four manures within each soil. However, strong differences were found on the toxicity between soils. In Oxisol, LC50 values were around 100m(3)ha(-1), and EC50 values around 80m(3)ha(-1). In Entisol these were much lower, with LC50 values oscillating around 20m(3)ha(-1) and EC50 values between 10-15m(3)ha(-1). The observed toxicity on both soils was attributed to excess of nitrogen, Cu and Zn in the highest doses. The strong difference between soils could be explained by soil properties, namely CEC, organic matter, and clay contents that were lower in Entisol, indicating a poor ability to retain contaminants increasing their availability in soil. Results suggest that the application of these residues should be regulated not only using a volume-based criterion, but should incorporate data on soil properties, complemented by an ecotoxicological assessment.

Biochar amendment before or after composting affects compost quality and N losses, but not P plant uptake

We investigated the use of biochar (10% on a dry weight basis) to improve the composting process and/or the compost quality by adding it to either the feedstock mixture or the mature compost. The addition of biochar to the feedstocks was essayed in a full scale trial using a mixture of green waste and the organic fraction of municipal solid waste. Addition of biochar to mature compost was performed in a medium scale experiment. The use of biochar, even in small amounts, changed the composting process and the properties of the end products. However these effects depended on the time of application. We observed a faster decomposition in the bio-oxidative phase and lower greenhouse gas emissions when biochar was added at the beginning of the composting process, and a reduction in readily available P when biochar was applied during compost storage. Biochar as a means to increase the C content of the compost was only effective during compost storage. The P fertilizer replacement value of the compost with and without biochar was tested in a plant trial with annual ryegrass. While there was a clear effect on readily available P concentrations in the compost, adding biochar to the feedstock or the compost did not affect the P fertilizer replacement value.

A closed loop for municipal organic solid waste by lactic acid fermentation

In order to investigate the feasibility of producing lactic acid from municipal organic solid waste different pH values (4-7) and temperatures (37°C and 55°C) were tested. For the evaluation of fermentation conditions the chemical, physical, and microbial characters were monitored over a period of 7days. Quantitative real time PCR, PCR-DGGE, and next generation sequencing of a 16S rRNA gene library were applied to identify the key players of the lactic acid production and their association. Lactobacillus acidophilus and its closest relatives were found to be efficient lactic acid producers (>300mM) under most suitable fermentation conditions tested in this study: 37°C with either uncontrolled pH or at a pH of 5. These data provide the first step in the realization of the idea "reuse, reduce, and recycle" of municipal organic solid waste.

Identification of oil residues in Roman amphorae (Monte Testaccio, Rome): a comparative FTIR spectroscopic study of archeological and artificially aged samples

The application of Fourier Transform InfraRed (FTIR) spectroscopy to the analysis of oil residues in fragments of archeological amphorae (3rd century A.D.) from Monte Testaccio (Rome, Italy) is reported. In order to check the possibility to reveal the presence of oil residues in archeological pottery using microinvasive and\or not invasive techniques, different approaches have been followed: firstly, FTIR spectroscopy was used to study oil residues extracted from roman amphorae. Secondly, the presence of oil residues was ascertained analyzing microamounts of archeological fragments with the Diffuse Reflectance Infrared Spectroscopy (DRIFT). Finally, the external reflection analysis of the ancient shards was performed without preliminary treatments evidencing the possibility to detect oil traces through the observation of the most intense features of its spectrum. Incidentally, the existence of carboxylate salts of fatty acids was also observed in DRIFT and Reflectance spectra of archeological samples supporting the roman habit of spreading lime over the spoil heaps. The data collected in all steps were always compared with results obtained on purposely made replicas.