Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities.

Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we explored how applying organic residue, vinasse, as fertilizer in its natural state (V) versus its concentrated form (CV) impacts soil microbiota. We conducted two field experiments, evaluating soil prokaryotic and fungal communities over 24 and 45 days with vinasse (V or CV) plus N fertilizer. We used 16S rRNA gene and ITS amplicon sequencing. Inorganic N had no significant impact on bacterial and fungal diversity compared to the control. However, the varying concentrations of organic C and nutrients in vinasse significantly influenced the soil microbiome structure, with smaller effects observed for V compared to CV. Prokaryotic and fungal communities were not correlated (co-inertia: RV coefficient = 0.1517, p = 0.9708). Vinasse did not change the total bacterial but increased the total fungal abundance. A higher C input enhanced the prokaryotic but reduced the fungal diversity. Our findings highlight vinasse's role as an abiotic filter shaping soil microbial communities, with distinct effects on prokaryotic and fungal communities. Vinasse primarily selects fast-growing microorganisms, shedding light on the intricate dynamics between organic residues, nutrient concentrations, and soil microbes.

The impact of farming on prehistoric culinary practices throughout Northern Europe.

To investigate changes in culinary practices associated with the arrival of farming, we analysed the organic residues of over 1,000 pottery vessels from hunter-gatherer-fisher and early agricultural sites across Northern Europe from the Lower Rhine Basin to the Northeastern Baltic. Here, pottery was widely used by hunter-gatherer-fishers prior to the introduction of domesticated animals and plants. Overall, there was surprising continuity in the way that hunter-gatherer-fishers and farmers used pottery. Both aquatic products and wild plants remained prevalent, a pattern repeated consistently across the study area. We argue that the rapid adaptation of farming communities to exploit coastal and lagoonal resources facilitated their northerly expansion, and in some cases, hunting, gathering, and fishing became the most dominant subsistence strategy. Nevertheless, dairy products frequently appear in pottery associated with the earliest farming groups often mixed with wild plants and fish. Interestingly, we also find compelling evidence of dairy products in hunter-gatherer-fisher Ertebølle pottery, which predates the arrival of domesticated animals. We propose that Ertebølle hunter-gatherer-fishers frequently acquired dairy products through exchange with adjacent farming communities prior to the transition. The continuity observed in pottery use across the transition to farming contrasts with the analysis of human remains which shows substantial demographic change through ancient DNA and, in some cases, a reduction in marine consumption through stable isotope analysis. We postulate that farmers acquired the knowledge and skills they needed to succeed from local hunter-gatherer-fishers but without substantial admixture.

Parallel worlds and mixed economies: multi-proxy analysis reveals complex subsistence systems at the dawn of early farming in the northeast Baltic.

The transition from foraging to farming was a key turning point in ancient socio-economies. Yet, the complexities and regional variations of this transformation are still poorly understood. This multi-proxy study provides a new understanding of the introduction and spread of early farming, challenging the notions of hierarchical economies. The most extensive biological and biomolecular dietary overview, combining zooarchaeological, archaeobotanical, dietary stable isotope and pottery lipid residue analyses is presented, to unravel the nature and extent of early farming in the 3rd millennium cal BCE in the northeast Baltic. Farming was introduced by incoming Corded Ware cultural groups (CWC), but some dietary segregation existed within these communities, with some having more access to domesticates, others incorporating more wild resources into their diet. The CWC groups coexisted in parallel with local hunter-fisher-gatherers (HFG) without any indication of the adoption of domesticates. There was no transition from foraging to farming in the 3rd millennium cal BCE in the NE Baltic. Instead, we see a complex system of parallel worlds with local HFGs continuing forager lifeways, and incoming farmers practising mixed economies, with the continuation of these subsistence strategies for at least a millennium after the first encounter with domesticated animals.

Compound-specific carbon isotope analysis of short-chain fatty acids from Pine tissues: characterizing paleo-fire residues and plant exudates.

Different types of plant tissues and resin can account for the wax lipids found in sedimentary contexts and archaeological samples. Consequently, there is increasing research to characterize the fatty acid carbon isotope ratios of different plant anatomical parts and their plant exudates (resin). With the aim to explore isotopic differences between plant tissues, state of the fine organic matter, effect of thermal degradation, and to identify plant residues we measured the δ13C values of short-chain fatty acids (δ13C16:0 and δ13C18:0) in: i) dead and fresh (collected and immediately dried) pine needles and branches (Pinus canariensis) and pine resin from laboratory-controlled heating experiments and ii) sediment and charred pine tissue samples from a wild pine forest fire. Our results are compared to previously published experimental open-air fire experiments and pine-fuelled archaeological combustion features. We found that for both fatty acid types, there are differences in δ13C signatures among anatomical parts and initial moisture content. These data allow us to characterize the isotopic signature of pine tissue and the effect of degradation on isotopic biomarkers, as well as to estimate combustion temperatures in pine-fuelled anthropogenic fires. Supplementary Information: The online version contains supplementary material available at 10.1007/s12520-023-01815-3.

Potential reuse of domestic organic residues as soil organic amendment in the current waste management system in Australia, China, and The Netherlands.

Soil organic carbon (SOC) is essential for most soil functions. Changes in land use from natural land to cropland disrupt long-established SOC balances and reduce SOC levels. The intensive use of chemical fertilisers in modern agriculture accelerates the rate of SOC depletion. Domestic organic residues (DOR) are a valuable source of SOC replenishment with high carbon content. However, there is still a lack of knowledge and data regarding whether and to what extent DOR can contribute to replenishing SOC. This paper aims to unpack the potential of DOR as a SOC source. Total SOC demand and annual SOC loss are defined and calculated. The carbon flow within different DOR management systems is investigated in three countries (China, Australia, and The Netherlands). The results show that the total SOC demand is too large to be fulfilled by DOR in a short time. However, DOR still has a high potential as a source of SOC as it can mitigate the annual SOC loss by up to 100%. Achieving this 100% mitigation requires a shift to more circular management of DOR, in particular, more composting, and direct land application instead of landfilling and incineration (Australia and China), or a higher rate of source separation of DOR (The Netherlands). These findings form the basis for future research on DOR recycling as a SOC source.

Integrated life cycle assessment of biotreatment and agricultural use of domestic organic residues: Environmental benefits, trade-offs, and impacts on soil application.

Extensive agricultural activities have been shown to degrade soils, promoting research into improving soil quality. One such method is to increase the amount of organic matter in the soil, and domestic organic residues (DOR) are commonly used for this purpose. The environmental impact of DOR-derived products, from production to agricultural application, remains unclear in current research. With the aim to have a more comprehensive understanding of the challenges and opportunities in DOR management and reuse, this study extended the boundaries of Life Cycle Assessment (LCA) to include the transport, treatment, and application of treated DOR on a national level while also quantifying soil carbon sequestration that has been less addressed in relevant LCA studies. This study focuses on The Netherlands, where incineration predominates, as a representative case to explore the benefits and trade-offs of moving towards more biotreatment for DOR. Two main biotreatments were considered, composting and anaerobic digestion. The results indicate that biotreatment of kitchen and yard residues generally has higher environmental impacts than incineration, including increased global warming and fine particulate matter formation. However, biotreatment of sewage sludge has lower environmental impacts than incineration. Substitution of nitrogen and phosphorus fertilisers with compost reduces mineral and fossil resource scarcity. In fossil-based energy systems like The Netherlands, replacing incineration with anaerobic digestion yields the highest benefit for fossil resource scarcity (61.93 %) due to energy recovery from biogas and the predominant use of fossil resources in the Dutch energy system. These findings indicate that replacing incineration with biotreatment of DOR may not benefit all impact categories in LCA. The environmental performance of substituted products can significantly influence the environmental benefits of increased biotreatment. Future studies or implementation of increased biotreatment should consider trade-offs and local context.

Detection of dairy products from multiple taxa in Late Neolithic pottery from Poland: an integrated biomolecular approach.

The detection of dairy processing is pivotal to our understanding of ancient subsistence strategies. This culinary process is linked to key arguments surrounding the evolution of lactase persistence in prehistory. Despite extensive evidence indicating the presence of dairy products in ceramics in the European Neolithic, questions remain about the nature and extent of milk (and lactose) processing and consumption. In order to investigate past patterns of dairy processing, here we analyse ancient proteins identified from Late Neolithic Funnel Beaker ceramics, scrutinizing the principle that curd and whey proteins partition during the production of dairy foods from milk. Our results indicate the presence of casein-rich dairy products in these vessels suggesting the creation of curd-enriched products from raw milk. Moreover, this analysis reveals the use of multiple species for their dairy products in the Late Neolithic, adding to a growing body of evidence for the period. Alongside palaeoproteomic analysis, we applied well-established lipid residue analysis. Differential interpretations between these two approaches show that palaeoproteomics is especially useful where the effects from isotope mixing may underestimate the frequency of dairy products in archaeological ceramics, highlighting the potential utility of a multi-stranded approach to understand life histories of vessel use.

Cuisine in transition? Organic residue analysis of domestic containers from 9th-14th century Sicily.

From the 9th to 14th centuries AD, Sicily experienced a series of rapid and quite radical changes in political regime, but the impact of these regime changes on the lives of the people that experienced them remains largely elusive within the historical narrative. We use a multi-faceted lipid residue approach to give direct chemical evidence of the use of 248 everyday domestic ceramic containers from Islamic and post-Islamic contexts in western Sicily to aid our understanding of daily habits throughout this period of political change. A range of commodities was successfully identified, including animal fats, vegetable products, fruit products (potentially including wine) and plant resins. The study highlights the complexity of residues in early medieval Mediterranean society as, in many cases, mixtures of commodities were observed reflecting sequential cooking events and/or the complex mixtures reflective of medieval recipes. However, overall, there were no clear changes in the composition of the residues following the imposition of Norman control over the island and through subsequent periods, despite some differences between urban centres and rural sites. Thus, lending to the idea that post-Islamic populations largely flourished and benefited from the agricultural systems, resources and recipes left by their predecessors.

Synergistic enhancement of the phytostabilization of a semiarid mine tailing by a combination of organic amendment and native microorganisms (Funneliformis mosseae and Bacillus cereus).

The goal of this work was to evaluate the effects of fermented sugar beet residue and inoculation with a native arbuscular mycorrhizal (AM) fungus, Funneliformis mosseae (Nicol. and Gerd.) Gerd. and Trappe, or a native bacterium, Bacillus cereus Frankland & Frankland, alone or in combination, on the establishment of Lygeum spartum L. seedlings grown in a mine tailing under semiarid conditions. We conducted a field study to analyse root and shoot dry biomass, shoot nutrient contents, mycorrhization, plant nitrate reductase (NR) and acid phosphomonoesterase activities, soil enzyme activities and aggregate stability. Ten months after field transplanting, it was found that the three experimental factors had interacted synergistically with regard to shoot and root biomass, with increases of about 410% and 370%, respectively relative to plants in the untreated soil. The treatment combining all three factors increased the root content of all heavy metals, and the levels of nitrogen (N), phosphorus, potassium and NR activity in shoot tissues, whereas it decreased root acid phosphomonoesterase activity. Soil dehydrogenase, protease and ß-glucosidase activities, total N content and aggregate stability were increased by the combined treatment. In conclusion, the combination of the organic amendment, the native AM fungus and the native bacterium can be regarded as a suitable tool for phytostabilization with L. spartum due to its ability to enhance the tolerance of plants to heavy metals, improve the plant nutritional status and increase the soil microbial function related to the C cycling.

Incineration disposal of organic waste bio-residue via a deep dewatering process using refuse incineration bottom ash: moisture transfer and low calorific value improvement.

Bio-residue is a by-product from organic waste anaerobic digestion process with high moisture, high organic matter, low calorific value and poor biological stability, and may be incinerated after deep dewatering. The moisture existence forms of bio-residue were clarified firstly, finding that adsorbed water, capillary water and bound water occupied 75.61%, 23.81% and 0.58%, respectively. Furthermore, refuse incineration bottom ash was used as a typical deep dewatering reagent, when compared with calcium oxide (CaO), refuse incineration fly ash and iron powder-potassium persulfate (Fe(0)-K2S2O8). Results showed that the addition of bottom ash powder could decrease the bio-residue's moisture from 80.0% to 37.9% at the optimal dosage of 2.0%, and corresponding low calorific value reached 10.5 MJ/kg at the 10th d. It was suggested that ZnCl2 and ZnSO4 present in bottom ash powder could react with moisture in bio-residue, forming hydrates of inorganic salt and breaking the polyacrylamide colloid, and lead to the release of adsorbed water in the bio-residue.

Gas chromatography-mass spectrometric determination of organic acids by ion pair liquid extraction followed by in-situ butylation from aqua feed samples.

A rapid and sensitive analytical method was developed to quantitatively determine organic acids (OAs) from fish feed samples extracted by ion-pair (IP) solvent extraction, followed by in-situ butylation and gas chromatography-mass spectrometric (GC-MS) analysis. The extraction of OAs was carried out with acetonitrile containing 10 mM tetrabutylammonium hydroxide (TBAH), and the analytes were derivatized to their butyl esters in the injection port of the GC-MS system. The developed method was validated in the range of 1-5000 ng/g, with recoveries ranging from 93-117%. The limit of detection (LOD) and limit of quantification (LOQ) of the method was 1-5 ng/g and 2-10 ng/g, respectively, yielding good linearity (R2 > 0.9990) and precision with a relative standard deviation less than 10%. The proposed method was successfully applied to analyze OAs in sinking and floating fish feed samples. The analyzed samples showed the presence of benzoic, succinic, fumaric, glutaric, adipic, and phthalic acids in sinking feed samples; and benzoic, succinic, adipic, phthalic acids in floating feed samples, respectively.

Contribution of the carbonized rice husk added to the substrate in the production of vegetable seedlings

The carbonized rice husk (CRH) is an agro-industrial residue with great potential for use in mixtures with other substrates for the production of vegetable seedlings. Thus, the purpose of this study was to evaluate the effect of the addition of CRH to the commercial substrate for the production of greenhouse seedlings. The evaluated vegetables were lettuce, broccoli and mustard, cultivated in polystyrene foam (Styrofoam®) trays. Five treatments were evaluated: 100% of the commercial substrate (CS); 25% of CRH + 75% of CS; 50% of CRH + 50% of CS; 75% CRH + 25% CS; and 100% CRH, in a completely randomized design with twelve replicates. The substrates were evaluated for their physical and chemical characteristics. The morphometric evaluations were: number of leaves per plant, plant height, shoot fresh matter yield, root length, and shoot and root dry matter yield. The data were submitted to regression analysis, and the homogeneity of the variance between the experiments was confirmed by the Cochran test. With the addition of CRH to the substrate, there was an increase in total porosity and P content and a reduction in density, water holding capacity, cation exchange capacity, electrical conductivity, and N, K, S, Ca and Mg contents. The carbonized rice husk added to the commercial substrate is a viable alternative for the production of lettuce, broccoli and mustard seedlings. The quality of the vegetable seedlings was higher when there was a 25% CRH + 75% CS mixture.

Feeding Babies at the Beginnings of Urbanization in Central Europe.

Small ceramic vessels with spouts, from which liquid can be poured, became popular during the Late Bronze and Early Iron Ages in Central Europe (c. 1200-600 BC). Such feeding vessels represent a functional type and are highly variable in size, shape and decoration. Found both on settlements and within graves, their association with child burials suggest they might have been used to feed babies and small children. Combined lipid and isotope analysis was performed on 24 of these feeding vessels, with seven delivering interpretable results. Feeding vessels associated with child burials tend to deliver a ruminant milk signal, whereas other vessels were used to process ruminant and non-ruminant adipose fats. Here, we highlight the potential significance of feeding vessels as indicators of changing childcare practices during times of population increase, settlement nucleation and mobility, possibly involving out-sourcing the feeding of babies and small children to persons other than the mother.

Bee products in the prehistoric southern levant: evidence from the lipid organic record.

Beehive products have a rich global history. In the wider Levantine region, bees had a significant role in Egypt and Mesopotamia, and intensive beekeeping was noted in Israel during the Biblical period when apiaries were first identified. This study investigates the origins of this extensive beekeeping through organic residue analysis of pottery from prehistoric sites in the southern Levant. The results suggest that beehive products from likely wild bees were used during the Chalcolithic period as a vessel surface treatment and/or as part of the diet. These functions are reinforced by comparison to the wider archaeological record. While the true frequency of beeswax use may be debated, alternatives to beehive products were seemingly preferred as wild resources contrasted with the socio-economic system centred on domesticated resources, controlled production and standardization. Bee products only became an important part of the economic canon in the southern Levant several millennia later.

Investigating the formation and diagnostic value of ω-(o-alkylphenyl)alkanoic acids in ancient pottery.

Long-chain ω-(o-alkylphenyl)alkanoic acids (APAAs) derived from the heating of unsaturated fatty acids have been widely used for the identification of aquatic products in archaeological ceramic vessels. To date, little attention has been paid to the diagnostic potential of shorter chain (< C20) APAAs, despite their frequent occurrence. Here, a range of laboratory and field experiments and analyses of archaeological samples were undertaken to investigate whether APAAs could be used to further differentiate different commodities. The results provide new insights about the conditions for the formation of APAAs and enable the proposition of novel criteria to distinguish different natural products.

[Determination of eight organic residues in ion exchange resins by headspace gas chromatography].

An analytical method based on headspace gas chromatography was developed for the determination of eight organic residues in ion exchange resins, methyl isopropyl ketone, methyl butyrate, 3-pentanone, 1,3-diethyl benzene, 1,4-diethyl benzene, dichloroethane, 1,3-dichlorobenzene, and methyl methacrylate. The organic residues in different types of resins were studied to provide a basis for the safe use of ion-exchange resins in food and medicine. The main factors (chromatographic column, equilibrium temperature, equilibrium time, flow rate, etc.) that affect the accuracy and sensitivity of the eight organic residues were investigated during instrument analysis. The extraction solvent and chromatographic conditions for the samples were optimized. According to the extraction efficiencies of methyl benzene, methyl alcohol and dimethyl sulfoxide, 2.0 g of the sample was extracted with dimethyl sulfoxide under ultrasonic conditions at 20 ℃. A DB-23 chromatographic column (60 m×0.32 mm×0.25 µm) and hydrogen flame ionization detector (FID) were selected for the GC method, and good separation and quantitative results were obtained for the eight organic residues. The process and conditions are summarized as follows. The equilibration time of the headspace sampler was 30 min, and the equilibrium temperature was 80 ℃. The temperature of the sampler was 240 ℃, while that of the FID detector was 300 ℃, with nitrogen being used as the carrier gas. The programmed temperature of the column was maintained at 60 ℃ for 16 min, then increased to 200 ℃ at a heating rate of 20 ℃/min, and maintained at this level for 2 min. The flow rate was 1.2 mL/min for detection. The external standard method was utilized for quantitative analysis. Good linear relationships were observed for the eight organic residues, and the correlation coefficients (R2) were all above 0.999 in the mass concentration range of 0.02-200 mg/L. The limits of detection (LODs) were 0.0050-0.0375 ng/g. The average recoveries for the eight organic residues were in the range of 82.3% to 109.2% at three spiked levels, and the relative standard deviation (RSD, n=6) was 1.06% to 4.16%. Eleven types of resin samples were detected by this method, and a certain amount of organic compounds were observed in the resin samples. The methyl methacrylate content in the methacrylate resin XAD761 was 414.4 µg/g, while that in the styrene resin LX-69B was as high as 470.8 µg/g. As opposed to traditional analytical methods, the present method has high sensitivity, good accuracy, and precision, with simple operation without derivatization or the need for acid-base treatment of the sample to reduce contamination. This method can be used to simultaneously detect a variety of organic residues in ion-exchange resins, so that the detection efficiency is significantly improved.

Non-Destructive Detection Pilot Study of Vegetable Organic Residues Using VNIR Hyperspectral Imaging and Deep Learning Techniques.

Contamination is a critical issue that affects food consumption adversely. Therefore, efficient detection and classification of food contaminants are essential to ensure food safety. This study applied a visible and near-infrared (VNIR) hyperspectral imaging technique to detect and classify organic residues on the metallic surfaces of food processing machinery. The experimental analysis was performed by diluting both potato and spinach juices to six different concentration levels using distilled water. The 3D hypercube data were acquired in the range of 400-1000 nm using a line-scan VNIR hyperspectral imaging system. Each diluted residue in the spectral domain was detected and classified using six classification methods, including a 1D convolutional neural network (CNN-1D) and five pre-processing methods. Among them, CNN-1D exhibited the highest classification accuracy, with a 0.99 and 0.98 calibration result and a 0.94 validation result for both spinach and potato residues. Therefore, in comparison with the validation accuracy of the support vector machine classifier (0.9 and 0.92 for spinach and potato, respectively), the CNN-1D technique demonstrated improved performance. Hence, the VNIR hyperspectral imaging technique with deep learning can potentially afford rapid and non-destructive detection and classification of organic residues in food facilities.

Chemical evidence for the persistence of wine production and trade in Early Medieval Islamic Sicily.

Although wine was unquestionably one of the most important commodities traded in the Mediterranean during the Roman Empire, less is known about wine commerce after its fall and whether the trade continued in regions under Islamic control. To investigate, here we undertook systematic analysis of grapevine products in archaeological ceramics, encompassing the chemical analysis of 109 transport amphorae from the fifth to the eleventh centuries, as well as numerous control samples. By quantifying tartaric acid in relation to malic acid, we were able to distinguish grapevines from other fruit-based products with a high degree of confidence. Using these quantitative criteria, we show beyond doubt that wine continued to be traded through Sicily during the Islamic period. Wine was supplied locally within Sicily but also exported from Palermo to ports under Christian control. Such direct evidence supports the notion that Sicilian merchants continued to capitalize on profitable Mediterranean trade networks during the Islamic period, including the trade in products prohibited by the Islamic hadiths, and that the relationship between wine and the rise of Islam was far from straightforward.

Nutrient composition of diverse organic residues and their long-term effects on available nutrients in a tropical sandy soil.

Intensive use of sandy soils for agriculture leads to significant land degradation. The application of locally available organic residues can improve soil fertility, particularly in the context of organic farming practices. This research examined nutrient concentrations in locally available organic residues with different biochemical compositions/qualities and investigated the effects of long-term application of these residues on available nutrients, such as P, K, Ca, Mg, Fe, Mn, and Zn, as well as on total organic carbon (TOC) accumulation in tropical sandy soil. A field experiment was conducted in Northeast Thailand, where four local organic residues, groundnut stover (GN), tamarind leaf litter (TM), dipterocarp leaf litter (DP), and rice straw (RS), had been applied annually for 22 years. These organic residues were acidic (pH 3.7-5.8). The macronutrients N, P, and K were present at elevated levels in the high-quality organic residue GN, whereas medium-quality TM and low-quality RS and DP were dominated by the macronutrients Ca and Mg and the micronutrients Fe, Mn, and Zn. The incorporation of organic residues, particularly TM, resulted in the accumulation of TOC. Furthermore, long-term incorporation of TM increased soil pH, whereas incorporation of GN, DP, and RS did not. The higher increase in the soil pH of TM soil is likely because TM contains higher levels of ash alkalinity compared to other residues. The application of medium-quality TM increased the soil available P, Ca, and Mg, whereas low-quality organic residue RS and DP applications increased the concentrations of soil micronutrients (e.g., Mn and Zn). However, long-term applications of local organic residues did not increase available K in the sandy soil.

Reductive soil disinfestation incorporated with organic residue combination significantly improves soil microbial activity and functional diversity than sole residue incorporation.

Reductive soil disinfestation (RSD) is an effective agricultural practice to eliminate soil-borne pathogens that heavily relies on the organic substrate used. However, the influences of combined application of organic residues on disinfestation efficiency, soil microbiomes, and their associated functional characteristics are still not well-characterized. In this work, four treatments, i.e., untreated soil (CK), RSD with 15 t ha-1 sugarcane bagasse (SB), bean dregs (BD), and their combinations (1:1, SB+BD), were conducted to investigate their influence on disinfestation efficiency, microbial functional diversity, community diversity, and composition using Biolog analysis, real-time PCR, and high-throughput sequencing. The SB+BD treatment had synergetic effects on soil microbial activity, metabolic activity, and functional diversity with similar efficacy in pathogen elimination and soil salinization alleviation, as compared to the SB and BD treatments. Moreover, the SB+BD treatment distinctly altered the structure and composition of bacterial and fungal communities, especially enriched the core microbiomes associated with soil general functions such as organic decomposition and nitrate removal. The SB+BD treatment also strengthened the soil specific functions including disease suppression through the regulation of unique microbiomes. In addition, the microbial richness, diversity, and evenness were significantly higher in the SB+BD-treated soil as compared to the SB- and BD-treated soils. Taken together, RSD incorporated with organic residue combination not only efficiently restore the degraded soils, but also considerably improve soil functions, which may benefit to the health for the future plant generations. KEY POINTS: • Organic residue combination effectively declines pathogen density. • Organic residue combination improves soil microbial activity and functional diversity. • The enriched core microbiome is responsible for soil general functions. • The induced unique microbiome is important for soil specific functions.