Effect of Sugarcane Straw and Goat Manure on Soil Nutrient Transformation and Bacterial Communities

Response of total belowground soil biota in Alhagi sparsifolia monoculture at different soil vertical profiles in desert ecosystem

The soil organisms are extremely important for the land-based ecosystem. There is a growing interest in studying the variety and composition of the entire underground soil organism community at a large ecological scale. Soil organisms show different patterns in relation to soil physiochemical properties (SPPs) in various ecosystems. However, there is limited knowledge regarding their response to soil vertical profiles (SVPs) in monoculture of Alhagi sparsifolia, which is the primary shrub in the deserts of China, and is well-known for its contributions to sand dune stabilization, traditional Chinese medicine, and forage. Here, we investigated the population dynamics of soil bacteria, fungi, archaea, protists and metazoa across six different SVPs ranging from 0 to 100 cm in monoculture of A. sparsifolia, in its natural desert ecosystem. Our findings indicate that the soil biota communities displayed a declining pattern in the alpha diversity of bacteria, protists, and metazoa with an increase in soil depth. However, the opposite trend was observed for fungi and archaea. The beta diversity of soil biota was significantly affected by SVPs, particularly for metazoa, fungi and protists as revealed by Non-Metric Dimensional Scaling. The most prevalent soil bacterial, fungal, archaeal, protist, and metazoa classes were Actinobacteria, Sordariomycetes, Nitrososphaeria, Filosa-Sarcomonadea, and Nematoda, respectively. The correlation among vertical distribution of the most abundant biotic communities and variations in SPPs exhibited that the variations in total carbon (TC) and total nitrogen (TN) had the most significant influence on bacterial changes, while available potassium (AK) had an impact on fungi. Archaea were affected by TC and pH, protists by the C/N-Ratio and TP, and metazoa by TN, AK, and soil water capacity (SWC). Collectively, our findings provide a new perspective on the vertical distribution and distinct response patterns of soil biota in A. sparsifolia monoculture under natural desert ecosystem of China.

Free-living bacteria stimulate sugarcane growth traits and edaphic factors along soil depth gradients under contrasting fertilization

Free-living bacterial community and abundance have been investigated extensively under different soil management practices. However, little is known about their nitrogen (N) fixation abilities, and how their contributions to N budgets impact plant growth, yield, and carbon (C) and N cycling enzymes in a long-term consecutive sugarcane monoculture farming system, under contrasting amendments, along different soil horizons. Here, nifH gene amplicon was used to investigate diazotrophs bacterial community and abundance by leveraging high-throughput sequencing (HTS). Moreover, edaphic factors in three soil depths (0-20, 20-40, and 40-60 cm) under control (CK), organic matter (OM), biochar (BC), and filter mud (FM) amended soils were investigated. Our analysis revealed that β-glucosidase activity, acid phosphatase activity, ammonium (NH₄⁺-N), nitrate (NO₃^-N), total carbon (TC), total nitrogen (TN), and available potassium (AK) were considerably high in 0-20 cm in all the treatments. We also detected a significantly high proportion of Proteobacteria and Geobacter in the entire sample, including Anabaena and Enterobacter in 0-20 cm soil depth under the BC and FM amended soils, which we believed were worthy of promoting edaphic factors and sugarcane traits. This phenomenon was further reinforced by network analysis, where diazotrophs bacteria belonging to Proteobacteria exhibited strong and positive associations soil electrical conductivity (EC), soil organic matter content (SOM) available phosphorus (AP), TN, followed by NH4⁺-N and NO₃^-N, a pattern that was further validated by Mantel test and Pearson's correlation coefficients analyses. Furthermore, some potential N-fixing bacteria, including Burkholderia, Azotobacter, Anabaena, and Enterobacter exhibited a strong and positive association with sugarcane agronomic traits, namely, sugarcane stalk, ratoon weight, and chlorophyll content. Taken together, our findings are likely to broaden our understanding of free-living bacteria N-fixation abilities, and how their contributions to key soil nutrients such as N budgets impact plant growth and yield, including C and N cycling enzymes in a long-term consecutive sugarcane monoculture farming system, under contrasting amendments, along different soil horizons.

Amelioration of Organic Carbon and Physical Health of Structurally Disturbed Soil through Microbe–Manure Amalgam

Less precipitation, high temperature, and minimal natural vegetation are characteristic of regions having an arid climate. The harsh environment massively destructs the soil structure of that area by burning soil organic carbon, leading to deteriorated soil nutritional quality, creating a significant threat to agricultural production and food security. Direct application of organic wastes not only substitutes lost organic carbon but also restores soil structure and fertility. This study was conducted to assess the impact of organic amendments, i.e., farm manure (FM), poultry manure (PM), molasses (MO), and Exo-Poly Saccharides (EPS) producing rhizobacterial strains i.e., M2, M19, M22 amalgams as treatments. To assess the impact of treatments on soil carbon and structure restoration to hold more water and nutrients, a 42-day incubation experiment using a completely randomized design (CRD) under the two-factor factorial arrangement was conducted. Macro aggregation (0.25 to >1 mm), carbon retention in macro aggregates, active carbon (dissolved organic carbon, a mineral-associated organic carbon, microbial biomass carbon), total organic carbon, the carbon mineralization activities, and water retention capacities were observed to be highest in soils that were treated with (FM + M2, FM + M22, PM + M19, and MO + M19). Finally, we conclude that organics mineralization by microbial actions releases organic glues that not only impart particle aggregation but also conserve organics as aggregate entrapped carbon. Amalgamated application of microbe–manure combinations directly impacts soil structure and organic carbon contents, but in an indirect scenario, it improves the fertility and productivity of the soil. Therefore, it is strongly recommended to use organic manures and microbes in combination to restore structurally degraded lands.

Effects of biodegradable film mulching on bacterial diversity in soils

The spread of biodegradable plastic films (BDFs) not only increases grain yield but also reduces environmental pollution from plastic film to a large extent. Soil microbes are considered to be involved in biodegradation processes. However, the study of microbe diversity in soil mulched with biodegradable plastic film remains limited. Here, we compared the diversity of microbes between soils with biodegradable film and nonbiodegradable film (NBDF) mulch. The results showed that BDFs affected total C, P and NH₄⁺-N, especially organism C content, as well as microbe species richness (ACE; Chao1) and diversity (Simpson index; Shannon index). In terms of dominant phyla and genera, BDFs and NBDF can influence the abundance of disparate species. Furthermore, BDFs could also contribute to improving the richness of the important functional bacterial groups in soil, e.g., Pedomicrobium and Comamonas, both of which are involved in the degradation of plastic residues in soil. Finally, we found that BDFs improved the transformation of nitrogen by significantly increasing the abundances of Nitrobacter and Nitrospira. Our results highlight the impact of BDF mulch on the abundance of functional bacteria in the soil.

Filtered mud improves sugarcane growth and modifies the functional abundance and structure of soil microbial populations

BACKGROUND

Exploring high-quality organic amendments has been a focus of sustainable agriculture. Filtered mud (FM), a sugar factory waste derived from sugarcane stems, could be an alternative organic amendment for sugarcane production. However, the effects of its application proportions on soil fertility, nutrient cycling, structure of soil bacterial and fungal communities, and the growth of sugarcane in clay-loam soils remain unexplored.

METHODS

Three application proportions of FM: (FM1-(FM: Soil at 1:4), FM2-(FM: Soil at 2:3), and FM3-(FM: Soil at 3:2)) were evaluated on sugarcane growth and soil nutrient cycling. High throughput sequencing was also employed to explore soil microbial dynamics.

RESULTS

We observed that FM generally increased the soil's nutritional properties while improving NO₃ ^- retention compared to the control, resulting in increased growth parameters of sugarcane. Specifically, FM1 increased the concentration of NH₄ ⁺-N, the N fraction preferably taken up by sugarcane, which was associated with an increase in the plant height, and more improved growth properties, among other treatments. An increase in the proportion of FM also increased the activity of soil nutrient cycling enzymes; urease, phosphatase, and β-glucosidase. High throughput sequencing revealed that FM reduced the diversity of soil bacteria while having insignificant effects on fungal diversity. Although increasing FM rates reduced the relative abundance of the phyla Proteobacteria, its class members, the Gammaproteobacteria and Betaproteobacteria containing some N-cycling related genera, were stimulated. Also, FM stimulated the abundance of beneficial and lignocellulose degrading organisms. These included the bacterial phyla Actinobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and the fungal phylum Ascomycota. The distribution of the soil microbial community under FM rates was regulated by the changes in soil pH and the availability of soil nutrients. Since FM1 showed more promise in improving the growth properties of sugarcane, it could be more economical and sustainable for sugarcane production in clay-loam soils.

Liming improves the stability of soil microbial community structures against the application of digestate made from dairy wastes

Lime is used to reduce soil acidification in agricultural soils. However, its effects on the soil microbial community are not well understood. Additionally, the soil microbial community is known to be influenced by fertilizers. However, the question remains whether liming influences the magnitude of fertilizers' impact on soil microbial communities. Therefore, an incubation experiment was performed to understand the effect of lime application (pH = 6.5 and 5.5 for the soils with and without lime, respectively) and fertilizer (digestate, urea and control) on the soil microbial community structures, stability and gene functions. Soils were sampled weekly after the application of fertilizers for a month. For microbial community analysis, DNA was extracted and sequenced targeting 16 S rRNA region. For gene abundances i.e 16 S rRNA, ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB), nitrous oxide reductase (nosZ) and nitrite reductase (nirS) quantitative PCR was conducted. In results, the relative abundance of Actinobacteria was influenced more strongly by digestate in lime soils, while Alphaproteobacteria was influenced more strongly by digestate in the no lime soil. In NL treatments, digestate had a significant effect on more operational taxonomic units (146) compared to lime (127), indicating that lime application increased soil microbial community's stability. Liming and fertilizer had a significant effect on 16 S rRNA gene copy numbers with the highest values observed in lime plus digestate treatments. Soil pH had a significant effect on AOA, nosZ and nirS gene copy numbers with the highest values observed in lime treatments. In the lime treatments digestate application had a positive impact on AOB gene copy numbers but this was not the case for soils without liming treatments. These results indicate that soil pH and fertilizer type should be taken into consideration for the management of functional gene abundance in agricultural soils.

Continuous Sugarcane Planting Negatively Impacts Soil Microbial Community Structure, Soil Fertility, and Sugarcane Agronomic Parameters

Continuous planting has a negative impact on sugarcane plant growth and reduces global sugarcane crop production, including in China. The response of soil bacteria, fungal, and arbuscular mycorrhizae (AM) fungal communities to continuous sugarcane cultivation has not been thoroughly documented. Using MiSeq sequencing technology, we analyzed soil samples from sugarcane fields with 1, 10, and 30 years of continuous cropping to see how monoculture time affected sugarcane yield, its rhizosphere soil characteristics and microbiota. The results showed that continuous sugarcane planting reduced sugarcane quality and yield. Continuous sugarcane planting for 30 years resulted in soil acidification, as well as C/N, alkali hydrolyzable nitrogen, organic matter, and total sulfur content significantly lower than in newly planted fields. Continuous sugarcane planting affected soil bacterial, fungal, and AM fungal communities, according to PCoA and ANOSIM analysis. Redundancy analysis (RDA) results showed that bacterial, fungal, and AM fungal community composition were strongly associated with soil properties and attributes, e.g., soil AN, OM, and TS were critical environmental factors in transforming the bacterial community. The LEfSe analysis revealed bacterial families (e.g., Gaiellaceae, Pseudomonadaceae, Micromonosporaceae, Nitrosomonadaceae, and Methyloligellaceae) were more prevalent in the newly planted field than in continuously cultivated fields (10 and 30 years), whereas Sphingomonadaceae, Coleofasciculaceae, and Oxyphotobacteria were depleted. Concerning fungal families, the newly planted field was more dominated than the continuously planted field (30 years) with Mrakiaceae and Ceratocystidaceae, whereas Piskurozymaceae, Trimorphomycetaceae, Lachnocladiaceae, and Stigmatodisc were significantly enriched in the continuously planted fields (10 and 30 years). Regarding AMF families, Diversisporaceae was considerably depleted in continuously planted fields (10 and 30 years) compared to the newly planted field. These changes in microbial composition may ultimately lead to a decrease in sugarcane yield and quality in the monoculture system, which provides a theoretical basis for the obstruction mechanism of the continuous sugarcane planting system. However, continuous planting obstacles remain uncertain and further need to be coupled with root exudates, soil metabolomics, proteomics, nematodes, and other exploratory methods.

Long-term effects of liquid swine manure land surface application in an apple orchard field on soil bacterial community and heavy metal contents in apple (Malus pumila Mill.)

This study investigated the impact of liquid swine manure (LSM) land surface application in an apple orchard on soil health and copper (Cu) and zinc (Zn) in soil and apple. Three apple plots were selected, among which two for LSM application for 5 (AY5) and 11 (AY11) years with different application rates, a long-term inorganic fertilizer application plot as the control treatment (AY0). The soil and apple samples were collected for analysis of soil physicochemical properties, bacterial diversity and abundance, and the contents of Cu and Zn in soil and apple. Results showed that the LSM application significantly increased the concentration of soil nutrients with the highest in AY5, which has a high application rate of LSM. After 5 or 11 years applied, the content of total nitrogen (TN) in AY5 and AY11 increased by 125.2% and 96.7%, total phosphorus (TP) increased by 167.6% and 148.6%, and soil organic matter (SOM) increased by 180.7% and 120.6%, respectively. The AY5 treatment significantly lowered OTUs and decreased Shannon index trend with a negative correlation between soil organic matter and Shannon index. The six predominant bacterial phyla in different treatments were similar, but the LSM application significantly increased the abundance of Chloroflexi and Firmicutes. However, the abundance of Actinobacteria and Acidobacteria significantly decreased in AY5 as compared to control treatment, followed by a significant positive correlation between the abundance of Acidobacteria and soil pH. Besides, LSM application significantly increased the contents of soil Cu, Zn, and apple Zn. Overall, the results illustrated that appropriate application rate of LSM can effectively improve apple orchard soil quality and bacterial community structure, but it will increase the risk of heavy metal accumulation in soil and apples.

Sugarcane monoculture drives microbial community composition, activity and abundance of agricultural-related microorganisms

Sugarcane monoculture (SM) often leads to soil problems, like soil acidification, degradation, and soil-borne diseases, which ultimately pose a negative impact on agricultural productivity and sustainability. Understanding the change in microbial communities' composition, activities, and functional microbial taxa associated with the plant and soil under SM is unclear. Using multidisciplinary approaches such as Illumina sequencing, measurements of soil properties, and enzyme activities, we analyzed soil samples from three sugarcane fields with different monoculture histories (1-, 2-, and 4-year cultivation times, respectively). We observed that SM induced soil acidity and had adverse effects on soil fertility, i.e., soil organic matter (OM), total nitrogen (TN), total carbon (TC), and available potassium (AK), as well as enzyme activities indicative for carbon, phosphorus, and nitrogen cycles. Non-metric multidimensional scaling (NMDS) analysis showed that SM time greatly affected soil attribute patterns. We observed strong correlation among soil enzymes activities and soil physiochemical properties (soil pH, OM, and TC). Alpha diversity analysis showed a varying response of the microbes to SM time. Bacterial diversity increased with increasing oligotrophs (e.g., Acidobacteria and Chloroflexi), while fungal diversity decreased with reducing copiotrophs (e.g., Ascomycota). β-Diversity analysis showed that SM time had a great influence on soil microbial structure and soil properties, which led to the changes in major components of microbial structure (soil pH, OM, TC, bacteria and soil pH; TC, fungi). Additionally, SM time significantly stimulated (four bacterial and ten fungal) and depleted (12 bacterial and three fungal) agriculturally and ecologically important microbial genera that were strongly and considerably correlated with soil characteristics (soil pH, OM, TC, and AK). In conclusion, SM induces soil acidity, reduces soil fertility, shifts microbial structure, and reduces its activity. Furthermore, most beneficial bacterial genera decreased significantly due to SM, while beneficial fungal genera showed a reverse trend. Therefore, mitigating soil acidity, improving soil fertility, and soil enzymatic activities, including improved microbial structure with beneficial service to plants and soil, can be an effective measure to develop a sustainable sugarcane cropping system.

Depth-dependent influence of biochar application on the abundance and community structure of diazotrophic under sugarcane growth

Despite progress in understanding diazotrophic distribution in surface soils, few studies have investigated the distribution of diazotrophic bacteria in deeper soil layers. Here, we leveraged high-throughput sequencing (HTS) of nifH genes obtained to assess the influence of biochar amended soil (BC) and control (CK), and soil depths (0–20, 20–40 and 40–60 cm) on diazotrophic abundance and community structures, soil enzyme activities and physio-chemical properties. Multivariate ANOVA analysis revealed that soil depth had profound impact on majority of the soil parameters measured than fertilization. Although soil physio-chemical properties, enzymes activities, diazotrophic genera and enriched operational taxonomic units (OTUs) were significantly influenced across the entire soil profiles, we also observed that BC amended soil significantly increased cane stalk height and weight, nitrate (NO₃^-), ammonium (NH₄⁺), organic matter (OM), total carbon (TC) and available potassium (AK), and enhanced diazotrophic genera in soil depth 0–20 cm compared to CK treatment. Soil TC, total nitrogen (TN), OM and NH₄⁺ were the major impact factors shifting diazotrophic community structures in soil depth 0–20 cm. Overall, these results were more pronounced in 0–20 cm soil depth in BC than CK treatment.

Application of Fourier transform ion cyclotron resonance mass spectrometry in deciphering molecular composition of soil organic matter: A review

Swiftly deciphering soil organic matter (SOM) composition is critical for research on soil degradation and restoration. Recent advances in analytical techniques (e.g., optical methods and mass spectrometry) have expanded our understanding of the composition, origin, and evolution of SOM. In particular, the use of Fourier transform ion cyclotron resonance mass spectrometers (FTICR-MS) makes it possible to interpret SOM compositions at the molecular level. In this review, we discuss extraction, enrichment, and purification methods for SOM using FTICR-MS analysis; summarize ionization techniques, FTICR-MS mechanisms, data analysis methods, and molecular compositions of SOM in different environments (providing new insights into its origin and evolution); and discuss factors affecting its molecular diversity. Our results show that digenesis, combustion, pyrolysis, and biological metabolisms jointly contribute to the molecular diversity of SOM molecules. The SOM thus formed can further undergo photodegradation during transportation from land to fresh water (and subsequently oceans), resulting in the formation of dissolved organic matter (DOM). Better understanding the molecular features of DOM therefore accelerates our understanding of SOM evolution. In addition, we assess the degradation potential of SOM in different environments to better inform soil remediation methods. Finally, we discuss the merits and drawbacks of applying FTICR-MS on the analysis of SOM molecules, along with existing gaps in knowledge, challenges, and new opportunities for research in FTICR-MS applications and SOM identification.

Straw retention efficiently improves fungal communities and functions in the fallow ecosystem

BACKGROUND

Straw retention is a substitute for chemical fertilizers, which effectively maintain organic matter and improve microbial communities on agricultural land. The purpose of this study was to provide sufficient information on soil fungal community networks and their functions in response to straw retention. Hence, we used quantitative real-time PCR (qRT-PCR), Illumina MiSeq (ITS rRNA) and FUNGuild to examine ITS rRNA gene populations, soil fungal succession and their functions under control (CK) and sugarcane straw retention (SR) treatments at different soil layers (0-10, 10-20, 20-30, and 30-40 cm) in fallow fields.

RESULT

The result showed that SR significantly enhanced ITS rRNA gene copy number and Shannon index at 0-10 cm soil depth. Fungi abundance, OTUs number and ACE index decreased with the increasing soil depth. The ANOSIM analysis revealed that the fungal community of SR significantly differed from that of CK. Similarly, significant difference was also observed between topsoil (0-20 cm) and subsoil (20-40 cm). Compared with CK, SR decreased the relative abundance of the pathogen, while increased the proportion of saprotroph. Regarding soil depth, pathogen relative abundance in topsoil was lower than that in subsoil. Besides, both sugarcane straw retention and soil depths (topsoil and subsoil) significantly altered the co-occurrence patterns and fungal keystone taxa closely related to straw decomposition. Furthermore, both SR and topsoil had higher average clustering coefficients (aveCC), negative edges and varied modularity.

CONCLUSIONS

Overall, straw retention improved α-diversity, network structure and fungal community, while reduced soil pathogenic microbes across the entire soil profile. Thus, retaining straw to improve fungal composition, community stability and their functions, in addition to reducing soil-borne pathogens, can be an essential agronomic practice in developing a sustainable agricultural system.

Role of environmental factors in shaping the soil microbiome

The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.

Short term effects of biochar with different particle sizes on phosphorous availability and microbial communities

Despite the increasing interest for biochar as a soil amendment, a knowledge gap remains on different particle size of biochar on soil phosphorous (P) availability and its impacts on microbial community. We hypothesized that biochar particle size and incubation temperature can significantly influence soil P availability and microbial community in subtropical acidic soil. A laboratory incubation study was established to investigate the effects of soil pH, available P and soil microbial responses to biochar addition having varying particle sizes using paddy soil and red soil under different incubation temperatures (15 °C & 25 °C). Biochar produced via pyrolysis of spent mushroom substrate feedstock was sieved into three particle sizes ((≤0.5 mm (fine), 0.5-1.0 mm (medium) and 1.0-2.0 mm (large)). The results exhibited that the fine particle biochar resulted in significantly higher release of P, soil pH, available P and bacterial species richness while simultaneously reducing the activities of phosphatase enzyme in both soils. Apprehending the impact of biochar particle size and incubation temperature, principal coordinate analysis (PCoA) predicted that soil microbial communities with fine particle biochar and high incubation temperature (25 °C) clustered separately. Redundancy analysis depicted that fine particle biochar had a direct association with available P and soil pH while high incubation temperature depicted a strong affinity for microbial communities. Hence, it is suggested that fine particle biochar and high incubation temperature may provide better habitat for microorganisms compared to the other particle sizes which may be due to improved soil pH and available P. However, a long term study of different biochar particles application in subtropical acidic soil needs to be pursued further for a more comprehensive understanding on this issue.

Effects of Different Fertilizer Treatments on Rhizosphere Soil Microbiome Composition and Functions

Fertilization influences the soil microbiome. However, little is known about the effects of long-term fertilization on soil microbial metabolic pathways. In this study, we investigated the soil microbiome composition and function and microbial participation in the N cycle according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) functional annotation of different genes in a metagenomic analysis after long-term fertilization. Fertilizer application significantly changed the soil C/N ratio. Chemical fertilizer (NPK) treatment decreased soil pH, and chemical fertilizer combined with straw (NPK+S0.5) treatment increased ammonium nitrogen (NH4+-N) but decreased nitrate nitrogen (NO3−-N). NPK, NPK+S0.5 and S0.5 applications did not change the soil microbiome composition or dominant phylum but changed the relative abundances of microbiome components. Moreover, fertilizer significantly influenced metabolic processes, cellular processes and single-organism processes. Compared with a no-fertilizer treatment (CK), the NPK treatment resulted in more differentially expressed gene (DEG) pathways than the NPK+S0.5 and S0.5 treatments, and these pathways significantly correlated with soil nitrate nitrogen (NO3−-N), available phosphorus (AP) and the moisture content of soil (MC). KEGG analysis found that fertilizer application mainly affected the ribosome, photosynthesis and oxidative phosphorylation pathways. S0.5 and NPK+S0.5 increased microbial nitrogen fixation, and NPK and NPK+S0.5 decreased amoA and amoB and accelerated denitrification. Thus, organic fertilizer increased N fixation and nitrification, and inorganic N fertilizer accelerated denitrification. We found that the function of the soil microbiome under different fertilizer applications could be important for the rational application of fertilizer and for environmental and sustainable development.

Organic soil additives for the remediation of cadmium contaminated soils and their impact on the soil-plant system: A review

Immobilization is among the most-suitable strategies to remediate cadmium (Cd) contaminated sites. Organic additives (OAs) have emerged as highly efficient and environment-friendly immobilizers to eradicate Cd contamination in a wide range of environments. This review article is intended to critically illustrate the role of different OAs in Cd immobilization and to highlight the key findings in this context. Owing to the unique structural features (high surface area, cation exchange capacity (CEC), presence of many functional groups), OAs have shown strong capability to remediate Cd polluted soils by adsorption, electrostatic interaction, complexation and precipitation. Research data is compiled about the efficiency of different OAs (bio-waste, biochar, activated carbon, composts, manure, and plant residues) applied alone or in combination with other amendments in stabilization and renovation of contaminated sites. In addition to their role in remediation, OAs are widely advocated for being classical sources of essential plant nutrients and as agents to improve the soil health and quality which has also been focused in this review. OAs may contain considerable amounts of metals and therefore it becomes essential to assess their final contribution. Elimination of Cd contamination is essential to attenuate the contaminant effect and to produce the safe food. Therefore, deployment of environment-friendly remediation strategies (alone or in combination with other suitable technologies) should be adopted especially at early stages of contamination.

Liming Positively Modulates Microbial Community Composition and Function of Sugarcane Fields

Liming combined with an optimum quantity of inorganic fertilizer, as a soil amendment in intensive agriculture, is a viable agricultural practice in terms of improving soil nutrient status and productivity, as well as mitigating soil degradation. The chief benefits of this strategy are fundamentally dependent on soil microbial function. However, we have limited knowledge about lime’s effects on soil microbiomes and their functions, nor on its comprehensive influence on soil nutrient status and the productivity of sugarcane plantations. This study compares the impacts of lime application (1-year lime (L1), 2-year lime (L2), and no lime (CK) on microbial communities, their functions, soil nutrient status, and crop yield in a sugarcane cropping system. We employed Illumina sequencing and functional analysis (PICRUSt and FUNGuild) to decipher microbial communities and functions. In comparison with CK, lime application (L1 and L2) mitigated soil acidity, increased the level of base cations (Ca2+ and Mg2+), and improved soil nutrient status (especially through N and P) as well as soil microbial functions associated with nutrient cycling and that are beneficial to plants, thereby improving plant agronomic parameters and yield. Liming (L1 and L2) increased species richness and stimulated an abundance of Acidobacteria and Chloroflexi compared to CK. In comparison with CK, the two functional categories related to metabolism (amino acid and carbohydrate) increased in the L1 field, whereas cofactors and vitamin metabolites increased in the L2 field. Turning to fungi, compared to CK, liming enriched symbiotrophs (endophytes, ectomycorrhizae, and arbuscular mycorrhizae) and led to a reduction of saprotrophs (Zygomycota and wood saprotrophs) and pathotrophs. The observed benefits of liming were, in turn, ultimately reflected in improved sugarcane agronomic performance, such as increased stalk height and weight in the sugarcane planting system. However, the increase in the above-mentioned parameters was more prominent in the L2 field compared to the L1 field, suggesting consecutive liming could be a practical approach in terms of sustainable production of sugarcane.

Bacteria with Different Assemblages in the Soil Profile Drive the Diverse Nutrient Cycles in the Sugarcane Straw Retention Ecosystem

Straw retention, an alternative to artificial fertilization, commonly mitigates soil degradation and positively affects soil fertility. In this study, we investigated the succession of soil bacteria during two sugarcane straw retention treatments (control (CK) and sugarcane straw retention (SR)) and at four depths (0–10, 10–20, 20–30, and 30–40 cm) in fallow soil in a sugarcane cropping system. Using an Illumina MiSeq (16S rRNA) and soil enzyme activity, we explored the SR influence on soil bacterial communities and enzyme activities and its inclusive impact on soil fertility, with an emphasis on topsoil (0–10 cm) and subsoil (10–40 cm). Our results show that SR effectively improved soil fertility indicators (C, N, and P), including enzyme activities (C and N cycling), throughout the soil profile: these soil parameters greatly improved in the topsoil compared to the control. Sugarcane straw retention and soil depth (0–10 cm vs. 10–40 cm) were associated with little variation in bacterial species richness and alpha diversity throughout the soil profile. Subsoil and topsoil bacterial communities differed in composition. Compared to the CK treatment, SR enriched the topsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, and Nitrospirae, while the subsoil was depleted in Nitrospirae and Acidobacteria. Similarly, SR enriched the subsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes, while the topsoil was depleted in Acidobacteria, Gemmatimonadetes, and Planctomycetes compared to the CK. At the genus level, SR enriched the topsoil with Gp1, Gp2, Gp5, Gp7, Gemmatimonas, Kofleria, Sphingomonas, and Gaiella, which decompose lignocellulose and contribute to nutrient cycling. In summary, SR not only improved soil physicochemical properties and enzyme activities but also enriched bacterial taxa involved in lignocellulosic decomposition and nutrient cycling (C and N) throughout the soil profile. However, these effects were stronger in topsoil than in subsoil, suggesting that SR enhanced fertility more in topsoil than in subsoil in fallow land.

Restoration of Long-Term Monoculture Degraded Tea Orchard by Green and Goat Manures Applications System

Tea is an economic shrubby plant in tropical and subtropical regions of the world. To obtain high yield in tea cultivation, chemical fertilizer application rates have generally been used. However, a large quantity of chemical fertilizer application in a long-term continuously ratooned and monoculture tea orchard can inevitably lead to soil acidification and a decline in fertility. Therefore, the restoration of soil fertility and the sustainable development of tea planting by organic ways are critical for the tea industry. In this study, field trials were conducted in the tea orchard that was continuously ratooned and mono-cultured for 20 years. Nitrogen fertilizer (NF), Laredo soybeans green manure (LF), and goat manure (GM) treatments were applied to restore optimum acidity, soil fertility, microbial activity, and the community structure of a long-term continuously monoculture tea orchard. This paper investigated that the pH value was increased from 4.23 to 4.32 in GM and LF, respectively. Similarly, the content of exchangeable acidity (EA) was decreased by 1.21 and 1.46 cmol·kg−1 in GM and LF, respectively. Available nutrient results indicated that the content of NH4+-N was increased by 3.96, 4.38, NO3−-N by 1.07, 2.16, AP by 3.46, 6.86, AK by 0.26, 0.3 mg kg−1 in GM and LF treatments, respectively. Enzyme analysis revealed that the activity of urease and sucrase was promoted by 7.98 mg·g−1·24 h−1 and 6.77 mg·g−1·24 h−1, respectively, in LF treatment. Likewise, the activity of acid phosphatase and polyphenol oxidase was sharply increased by 2.3 mg·g−1 h−1 and 63.07 mg·g−1 h−1 in LF treatments. Additionally, the activity of urease, sucrase, acidic phosphatase, polyphenol oxidase, and peroxidase were also significantly increased by applying GM treatments. Meanwhile, LF and GM treatments significantly improved soil microbial biomass as well as low weight organic acid content in degraded tea rhizosphere. Furthermore, high throughput sequence results illustrated that the relative abundance of Rhizobiaceae and Bradyrhizobiaceae families increased in LF and GM treatments, respectively, which are mostly a kind of nitrogen fixer and plant growth promoting bacteria. Taken together, the physiological traits of the new sprouts and the biochemical components of new tea leaves were also significantly improved by GM and LF treatments. From this study, it is concluded that LF and GM are good agriculture management practices, which promote plant growth, yield, and nutrient availability by maintaining and improving pH, enhancing available nutrients status, improving the secretion of low molecular weight organic acids, and balancing the microbial community structure in the long-term mono-cultured tea orchard.

Short-Term Effects of Different Organic Amendments on Soil Fungal Composition

Fungi play an essential role in recovering the quality and fertility of soil. There is a limited understating of the complex response of fungal diversity to different organic materials in clay loam soil. Here, we report the response of soil fungi toward the short-term application of manure (M), sugarcane straw (S), and sugarcane straw plus manure (MS), including no organic material control (CK) at two different time points (50 and 100 days after application). Illumina sequencing was used to examine the fungal communities. Our results reveal a significant shift among the soil fungal community structure associated with each organic material application. After both time points, amendments—especially M and MS—decreased the fungal richness and stimulated the copiotrophic fungal group (Ascomycota) compared to the control soil (CK) and S-amended soil. On the contrary, as compared to the M and MS-amended soils, the CK and S-amended soils at both time points increased the fungal richness and stimulated the oligotrophic fungal groups. Organic material use, especially M and MS, showed variable results regarding pathogenic fungi enhancing the abundance of Lophodermium and Cercophora and decreasing Fusarium. Concerning the abundance of plant-beneficial fungi, Mortierella was reduced, and Podospora was increased by M and MS input. FUNGuild showed that the amendment of organic materials efficiently declined the abundance of endophytes and plant pathogens, but also enhanced the animal pathogens in terms of abundance with respect to CK at two time points. This study could be useful to provide a novel understanding of the management of soil-borne pathogens by organic amendments for the sustainable production of short-term crops.