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Soils function under highly variable weather conditions which can be challenging to capture in models and metrics. A previous metric of soil resilience used an empirical model to characterize a key soil function (substrate induced respiration) and how this changed over repeated stress cycles. Here, we apply this laboratory and modelling approach to soils from a plot experiment in which cover crops (single species monocultures and 4-species polycultures) were grown over the summer in between autumn sown cash crops in a cereal rotation to compare their resilience. Open Top Chambers (OTCs) were also used to warm the soil surface of part of each plot to mimic climate change impact. Soil samples were collected from these experimental plots after harvesting the cereal crop and we assessed barley grass powder substrate induced soil respiration (a measure of soil microbial function) after 0, 1, 2, 4, and 8 wet/dry cycles imposed in the laboratory. In contrast to previous studies, the initial drying and rewetting stress did not markedly decrease or alter the substrate induced respiration profiles, suggesting that the soil was highly resilient to this stress. Warming slightly reduced soil microbial function after 8 repeated wet/dry cycles, relative to microbial function after 0 wet/dry cycles. However, cover crops, and particularly the 4-species cover crop polyculture, increased soil microbial function significantly after 8 repeated wet/dry cycles, relative to microbial function after 0 wet/dry cycles. The modelling approach suggested high resilience of this soil function in all plots, but did not detect any differences in the resilience of soil carbon functioning for soils from the different plots, but it was unclear whether this was due to lack of sensitivity of the approach. This further emphasizes the challenges in quantifying the ‘resilience’ of soil functioning as it is highly dependent on context.

A field experiment was carried out to investigate the impact of two improved tillage systems (conventional tillage combined with the incorporation of solid anaerobic digestate, no-tillage) on the prokaryotic community composition in two tree orchard (olive, citrus) soils with contrasting texture, carbonate content, and pH, located in Southern Italy. Soil samples were taken over a 5-month period to assess immediate (2 days) vs short-term (7 and 18 weeks) responses. Phylogenetic diversity and compositional shifts of both total and metabolically active soil prokaryotic communities were assessed by next-generation sequencing of 16S rRNA gene templates from soil-extracted DNA/RNA. In both digestate-treated soils, copiotrophic α-Proteobacteria and oligotrophic Acidobacteria, Gemmatimonadetes, and Verrucomicrobia showed an immediate (2 days) but short-lived (7 weeks) shift in their relative abundance similar in persistence but not in magnitude; whereas selective soil type-dependent responses were observed for Actinobacteria, Chloroflexi, Firmicutes, and Planctomycetes. The autochthonous soil microbiota demonstrated resilience to the addition of the anaerobic digestate, which was dominated by Firmicutes, Bacteroidetes, Deinococcus-Thermus, and Euryarchaeota (Methanomicrobia). Likewise, a temporary increase in the relative abundances of copiotrophic taxa (Firmicutes, Bacteroidetes, Thaumarchaeota) was observed under conventional tillage, especially in the sandy loam (citrus) soil. Conversely, no-tillage favored the establishment of oligotrophic Chloroflexi and Verrucomicrobia in both soils. The active and the total prokaryotic communities differed from each other only in physically disturbed soils. Soil management induced compositional shifts in the predominant microbial copiotrophic/oligotrophic community balance, whose persistence was linked to the tillage system, while magnitude depended on soil type.

Soil contamination by SARS-CoV-2 is highly probable because soil can collect several transporters of the virus, such as fallout aerosols, wastewaters, relatively purified sludges, and organic residues. However, the fate and status of SARS-CoV-2 in soil and the possible risks for human health through contaminated food are unknown. Therefore, this perspective paper discusses the challenges of determining the SARS-CoV-2 in soil and the mechanisms concerning its adsorption, movement, and infectivity in soil, considering what has already been reported by perspective papers published up to May 2021. These issues are discussed, drawing attention to the soil virus bibliography and considering the chemical structure of the virus. The mechanistic understanding of the status and behavior of SARS-CoV-2 in soil requires setting up an accurate determination method. In addition, future researches should provide insights into i) plant uptake and movement inside the plant, ii) virus adsorption and desorption in soil with the relative infectivity, and iii) its effects on soil functions. Models should simulate spatial localization of virus in the soil matrix.

Arbuscular mycorrhizal fungi (AMF) have gained remarkable importance, having been proved to alleviate drought stress-induced damage in wheat due to their ability to ameliorate plant water use efficiency and antioxidant enzyme activity. However, despite the current relevance of the topic, the molecular and physiological processes at the base of this symbiosis never consider the single cultivar affinity to mycorrhization as an influencing factor for the metabolic response in the AMF-colonized plant. In the present study, the mycorrhizal affinity of two durum wheat species (T. turgidum subsp. durum (Desf.)) varieties, Iride and Ramirez, were investigated. Successively, an untargeted metabolomics approach has been used to study the fungal contribution to mitigating water deficit in both varieties. Iride and Ramirez exhibited a high and low level of mycorrhizal symbiosis, respectively; resulting in a more remarkable alteration of metabolic pathways in the most colonised variety under water deficit conditions. However, the analysis highlighted the contribution of AMF to mitigating water deficiency in both varieties, resulting in the up- and down-regulation of many amino acids, alkaloids, phenylpropanoids, lipids, and hormones.

Objective: The present study assessed physico-chemical, techno-functional, thermal and textural characteristics of propolis samples (n = 30) collected from four Northern zones of India. Methods: The propolis samples were analyzed according to the Association of Official Analytical Chemists (AOAC) official protocols for their ash, moisture, and protein content. Soxtech, Fiber tech, Hunter LAB Colorimeter, TA.XT2i Texture Analyzer, Thermo gravimetric Analyzer, Discovery DSC 25 have been used to assess the crude fat, fibre content, colour, texture and thermal properties, respectively. Results and conclusions: Physico-chemical properties of propolis differed significantly (p

Environmental DNA is made-up of intracellular (iDNA) and extracellular (eDNA) pools. In soils, eDNA can be present up to 40% and could distort the assessment of living microorganisms. Distribution of microbial community is inconsistent among different size-aggregates, and the persistence and turnover of eDNA are thus uneven. Uneven persistence and distribution of eDNA could lead to heterogeneity in community analysis biases that arise due to eDNA sequences at micro-scale distribution. Here, we investigated the diversity and structure of eDNA and iDNA bacterial communities in bulk soil and different size-aggregates. Significant differences were observed between eDNA and iDNA bacterial diversity and composition. Changes in community composition are more important than the amount of eDNA to assess the biases caused by eDNA in community analysis. Furthermore, variations were also observed in aggregates-levels for eDNA and iDNA community which indicates that colonization pattern of iDNA community and protection of eDNA through absorbance on particle surface within soil-matrix is heterogeneous. Our work provides empirical evidence that eDNA presence could mask the detection of aggregates-level spatial dynamics in soil microbial community and have potential to qualitatively baffle observed live effects of given treatment by adequately muting the actual response dynamics of the soil microbiome.

The combined action of physical protection and chemical stabilisation is the main factor regulating the persistence of soil organic matter (SOM). In particular, physical protection refers to the compartmentalization of SOM and microbial biomass within aggregates. Thus, we have investigated the role of (macro-, meso- and micro-) soil aggregates in the protection of SOM and extracellular and intracellular DNA (eDNA vs iDNA) from oxidative stress by treating aggregates with Low Temperature Ashing (LTA) for different durations (0, 5, 24 and 48 h). DNA (exDNA vs iDNA) was sequentially extracted from the different aggregate size classes, and qualitatively (agarose gel electrophoresis) and quantitatively (fluorimetry; spectrophotometry) analysed, discriminating between double stranded (ds) and single stranded (ss) DNA. In addition, comparative PCR-DGGE (exDNA vs iDNA) was performed to assess the bacterial, fungal and archaeal communities of the different aggregate size classes. The use of LTA enabled to determine the amount of physically protected DNA in different aggregate sizes, evidencing the potential involvement of both exDNA and iDNA in the formation of the aggregates. Our results also provided insights into the important role of soil aggregates in protecting the genetic information of the autochthonous soil microbiota. The PCoA of bacterial, archaeal and fungal DGGE patterns displayed contrasting results. While fungal and archaeal fingerprinting patterns revealed direct relationships with aggregate sizes and LTA treatment, the bacterial community was not affected by these factors. This suggests a selective action of the size of aggregates on the dominant soil microbial community members. Our findings indicate that aggregates provide a protective habitat for the soil microbial community against environmental stress conditions, such as oxidative stress. Further, the specific protection of the soil microbiota (bacteria vs archaea vs fungi) is directly correlated to the size distribution of the microbial community and the aggregate size classes.

The World Health Organization (WHO) states that in developing nations, there are three million cases of agrochemical poisoning. The prolonged intensive and indiscriminate use of agrochemicals adversely affected the soil biodiversity, agricultural sustainability, and food safety, bringing in long-term harmful effects on nutritional security, human and animal health. Most of the agrochemicals negatively affect soil microbial functions and biochemical processes. The alteration in diversity and composition of the beneficial microbial community can be unfavorable to plant growth and development either by reducing nutrient availability or by increasing disease incidence. Currently, there is a need for qualitative, innovative, and demand-driven research in soil science, especially in developing countries for facilitating of high-quality eco-friendly research by creating a conducive and trustworthy work atmosphere, thereby rewarding productivity and merits. Hence, we reviewed (1) the impact of various agrochemicals on the soil microbial diversity and environment; (2) the importance of smallholder farmers for sustainable crop protection and enhancement solutions, and (3) management strategies that serve the scientific community, policymakers, and land managers in integrating soil enhancement and sustainability practices in smallholder farming households. The current review provides an improved understanding of agricultural soil management for food and nutritional security.

The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded form (eDNAss). The present paper is the first to investigate the quantitative relevance of eDNAss in the total soil eDNA pool, discriminating between its linear (eDNAssl) and circular (eDNAssc) forms and the respective weakly (wa) and tightly (ta) adsorbed fractions. The results showed the prevalence of eDNAss and its linear form in both the total soil eDNA pool and its wa and ta fractions. Both of the eDNAss fractions (linear and circular) were characterized by small fragments.

Study of the microbial expression profile in the rhizosphere of two contrasting maize lines, differing in the Nitrogen Use efficiency (NUE). The Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in rhizoboxes allowing precise sampling of rhizosphere and bulk soils. We conducted metatranscriptomic of rhizosphere and bulk soil by m-RNA sequencing. High activity of bacteria was observed compared to archaea and fungi in both rhizosphere and bulk soils of both maize lines. Proteobacteria and Actinobacteria were involved in all processes, while significant shifts occurred in the expression of Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria, Cyanobacteria, archaea and fungi, indicating their possible role in specific processes occurring in rhizosphere of two maize lines. Maize plants with different NUE induced changes in microbial processes, especially in N cycling, with high NUE maize favouring ammonification and nitrification processes and low NUE maize inducing expression of genes encoding for denitrifying process, likely favoured by longer N residence time in the rhizosphere. Overall our results showed that maize lines with different NUE shaped not only microbial communities but also conditioned the microbial functions and the N cycle in their rhizosphere. While the plant NUE is genetically determined and an inherent plant physiological trait, it also stimulates changes in the microbial community composition and gene expression in the rhizosphere, favouring microbial processes that mineralize and oxidize N in the high NUE maize. These results can improve our understanding on plant-microbe interaction in the rhizosphere of crop plants with potential applications for improving the management practices of the agro-ecosystems.

A majority of biochemical reactions are often catalysed by different types of enzymes. Adsorption of the enzyme is an imperative phenomenon, which protects it from physical or chemical degradation resulting in enzyme reserve in soil. This article summarizes some of the key results from previous studies and provides information about how enzymes are adsorbed on the surface of the soil solid phase and how different factors affect enzymatic activity in soil. Many studies have been done separately on the soil enzymatic activity and adsorption of enzymes on solid surfaces. However, only a few studies discuss enzyme adsorption on soil perspective; hence, we attempted to facilitate the process of enzyme adsorption specifically on soil surfaces. This review is remarkably unmatched, as we have thoroughly reviewed the relevant publications related to protein adsorption and enzymatic activity. Also, the article focuses on two important aspects, adsorption of enzymes and factors limiting the activity of adsorbed enzyme, together in one paper. The first part of this review comprehensively lays emphasis on different interactions between enzymes and the soil solid phase and the kinetics of enzyme adsorption. In the second part, we encircle various factors affecting the enzymatic activity of the adsorbed enzyme in soil.

Cellulose is the most abundant polysaccharide in the dead plant biomass, and its degradation is an important part of global carbon cycle. β-Glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. Genetic potential and expression of β-glucosidase genes were studied in the topsoil of a Picea abies forest in two contrasting seasons. These seasons were the summer, representing the peak of plant photosynthetic activity, and late winter, after an extended period with no photosynthate input. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families GH1 and GH3 amplified from DNA and RNA and amplicon pools were analyzed. Transcript pool were largely corresponded to gene pools, although some abundant transcripts were not found in the gene pool. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and Basidiomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria Acidobacteria and Deinococcus-Thermus. This indicates that a diverse microbial community utilized cellobiose. Seasonality influenced both genetic diversity of β-glucosidase genes and their expression. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in forest soils. Even β-glucosidase genes showing low abundance in DNA may be functionally important as revealed by their high expression especially in basidiomycota. The functional diversity in the studied ecosystem clearly exhibited a seasonal pattern.

In the last decades, many studies were addressed to focus the interplay between plant and microbial community into the soil and especially in the small soil zone in contact to plant root, called rhizosphere, which can be considered as a hotspot for interactions and therefore is a major target for improving nutrient use efficiency in crops. In this regard, unraveling the microbial activities that can be used to improve nutrient use efficiency may be the major challenge considering a sustainable agricultural contest. However, although using different approaches (metabolomics and transcriptomic) it has made it possible to characterize many interaction mechanisms, more remains largely unknown. Here, we summarize and discuss the abiotic and biotic factors that may manage plant-microbe interactions in the rhizosphere as well as in those parts of the soil furthest from the root, focusing on root architecture and nitrate as well.

It is essential to investigate to which extent and how specifically soil&ndash, plant&ndash, microbe interactions can be conditioned by different agricultural practices. Legumes such as Vicia faba is one of the essential functional group in intercropping and crop rotations due to its higher N fixing capacity. Hence, it is important to study the living microbial community of this legume. Further, it is also expected that fluctuations in soil microbial diversity and composition could be complemented by plant phenological stages and different fertilizer amendments. Thus, we investigated bacterial community composition in soil treated with phosphate-based inorganic and organic fertilizers, in the presence of Vicia faba plants at flowering and fruiting time using NGS 16S rRNA gene amplicon sequencing. Further, the evaluation of plant biomass parameters under different fertilizer treatments was also carried out. The presence of the Vicia faba plant increased the abundance of N fixing bacterial such as Bardyrhizobium, Microvirga (Rhizobiales), Arthrobacter, and Psuedoarthrobacter (Actinomycetales) in soil. Fluctuation in composition and diversity of bacterial community was further supplemented by plant phenological stages. These alterations could be due to changes that occurred in the plant nutrient requirement and varied root exudation patterns at a specific phenological stage. Further, fertilizer treatments also have a profound effect on the diversity and structure of the bacterial community. Organic fertilizers, especially vegetable tanned leather waste (VTLW), have a stronger effect on the composition and diversity of bacterial community compared to inorganic fertilizer (PT&mdash, triple superphosphate). Alpha-diversity was significantly decreased by both organic and inorganic amendments, especially a species evenness because each fertilizer tends to stimulate the growth of distinctive microbes that dominated the community of amended soil. Proteobacteria, Actinobacteria, and Cyanobacteria were the most abundant phyla, and Chelatococcus, Cyanobacteria, Sphingomonas, and Microvirga were a most abundant genus that contributed most in co-occurrence pattern, which suggests that these generalists are adapted to a variety of environments. These indicate that plant presence was a key, dominating factor, followed by fertilizers and time, in affecting soil bacterial diversity and composition. Plant recruits system (fertilization and time) -specific taxa due to differences in available nutrients and energy sources among different treatments during different growth stages. Further, fertilizer treatments did not have a stronger effect on plant production as compared to the effect on microbial community, which highlights that organic fertilizers did not tend to increase plant production. Thus, organic and inorganic amendments with matched macronutrients could have a similar impact on crop yields.

Soil structure degradation, declining soil organic matter and nutrient losses are among major drawbacks of continuous conventional tillage with large-scale environmental consequences including decreasing soil productivity, groundwater contamination and greenhouse gases emissions. This becomes especially true in conventionally-tilled Mediterranean croplands which are also affected by severe climatic conditions. In this study, a one-year field experiment was carried out to investigate the impact of different tillage practices on the soil fertility status in two tree orchards (olive, citrus) soils with contrasting texture (clay, sandy loam), carbonate content (non-calcareous, slightly calcareous) and pH (strongly acid, slightly alkaline), located in Southern Italy. Treatments included in this study were conventional tillage, conventional tillage combined with the incorporation of solid anaerobic digestate, and no-tillage. Changes in the aggregate stability and dynamics of various C and N pools were assessed by monitoring a large set of physical (aggregate stability index), chemical (pH, electrical conductivity, total organic C, total N, nitrate-N, ammonium-N, total soluble N, extractable organic N), biochemical (microbial biomass C and N, basal respiration, potentially mineralizable N) and eco-physiological (microbial and metabolic quotients, mineralization coefficient) soil variables. Results showed that the stability of soil aggregates declined under conventional tillage, remained unaltered under no-tillage, improved after digestate amendment. Moreover, following incorporation of digestate large and long-lasting increase of the organic pool, microbial C-use efficiency and release of soluble C and N forms were observed in the fine-textured soil. Whereas opposite responses were found in the moderately coarse alkaline soil, where incorporation of digestate stimulated C resources depletion, microbial respiration and N losses due to ammonia volatilization with less beneficial effects on soil organic pools. On the other hand, no-tillage prevented soil C and N resources from over-exploitation (as observed in conventionally-tilled soils) with greater beneficial effects on microbial C-use efficiency and biomass found in the coarse than in the fine-textured soil. Our findings suggest that improved management practices such as no-tillage or conventional tillage combined with incorporation of solid anaerobic digestate should specifically deal with soil and climate conditions to became effective for restoring the fertility status in Mediterranean orchard soils.

We studied the molecular diversity of β-glucosidase-encoding genes, microbial biomass, cellulase, N-acetyl-glucosaminidase, β-glucosidase, and β-galactosidase activities in the rhizosphere and bulk soil of two maize lines differing in nitrogen use efficiency (NUE). The maize lines had significant differences in diversity of β-glucosidase-encoding genes in their rhizosphere, and Actinobacteria and Proteobacteria were the dominating phyla in all samples, but representatives of Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Cyanobacteria were also detected. Among the Proteobacteria, β-glucosidase genes from α-, β-, and γ-Proteobacteria were dominant in the rhizosphere of the high NUE maize line, whereas δ-Proteobacteria β-glucosidase genes were dominant in the rhizosphere of the low NUE maize line. The high NUE maize line also showed higher glucosidase activities in the rhizosphere than the low NUE maize line. We concluded that plants with high NUE select bacterial communities in the rhizosphere differing in the diversity of β-glucosidase-encoding genes which likely result in higher C-hydrolyzing enzyme activities. These effects on the diversity of β-glucosidase-encoding genes may influence the C dynamics in the agro-ecosystems.

Over centuries and even today, traditional farming practices are well performed without any ecological degradation. However, management practice such as conservative tillage combined with nutrient and residue could increase the crop production as well as soil fertility. A three-year replicated study was conducted to assess the effects of agronomic modification of traditional farming practices on productivity and sustainability of rice (wet season)–rice (dry season) system (RRS). The replacement of farmers practice (T2) with conservation effective tillage (no-till (NT)) and integrated nutrient management (INM) practice along with 30% residue retention (T5) enhanced the straw, root and biomass yield of both wet season rice (WR), dry season rice (DR) and system as a whole over T2. Treatment T5 recorded significantly lower soil bulk density (ρb) and higher pH than the T2 after three years of the experiment. Further, treatment T5 increased total soil organic carbon (2.8%), total soil organic carbon stock (2.8%), carbon sequestration rate (336.5 kg ha−1 year−1), cumulative carbon stock (142.9%) and carbon retention efficiency (141.0%) over T2 of 0–20 cm depth after three year. The soil microbial biomass carbon concentration was significantly the highest under T5. Similarly, the dehydrogenase activity was the maximum under T5. Adoption of conservation tillage and nutrient management practice involving NT and INM along with residue retention can enhance the system productivity, and C and N sequestration in paddy soils is thereby contributing to the sustainability of the RRS.

Transitional areas between two or more different biomes—ecotones—are clearly visible due to the sudden changes in vegetation structures and patterns. However, much is still unknown about the crucial soil factors that control such vegetational changes across ecotones and how different soil properties vary across ecotones. In this study, we try to understand the spatial variation in soil properties across a clearly defined ecotone from a forest stand to meadow field at the Training Forest Enterprise (T.F.E), Masaryk Forest Křtiny, Czechia. Thirteen sampling sites were selected: six in the forest region, six in the meadow and one in the ecotone zone between forest and meadow. Soil samples were taken at 5 cm below the soil surface once every month from April to November. All the collected soil samples were examined for minimal air capacity, actual and potential soil reaction and maximum capillary water. The results showed a pattern of soil acidity decreasing from the forest stand towards the meadow field but that increased sharply at the ecotone zone. The water holding capacity showed a decreasing trend approaching the ecotone zone from the meadow region and markedly decreased from the meadow site closest to the ecotone zone. The minimum air capacity showed an increasing trend from the forest region but suddenly declined at the ecotone region.

Study of the changes in soil microbial biomass, enzyme activity and the microbial community structure in the rhizosphere of two contrasting maize lines differing in the nitrogen use efficiency (NUE). The Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in rhizoboxes allowing precise sampling of rhizosphere and bulk soil and solution. We also determined microbial biomass, enzyme activities involved in the C, N, P and S cycles, and the microbial community structure using a phylogenetic group specific PCR-DGGE approach in the rhizosphere and bulk soil of both Lo5 and T250 maize lines. High NUE Lo5 maize induced faster inorganic N depletion in the rhizosphere and larger changes in microbial biomass and enzyme activities than the low NUE T250 maize line. The two maize lines induced differences in the studied microbial groups in the rhizosphere, with the larger modifications induced by the high NUE Lo5 maize line. The Lo5 maize line with higher NUE induced larger changes in soil chemical properties and in the enzyme activity, soil microbial biomass and community structure than the low NUE T250 maize line, probably due to differences in the root exudates of the two maize lines.