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A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Agroecology Innovation: Achieving System Resilience".

Deadline for manuscript submissions: closed (10 December 2024) | Viewed by 13204

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Dr. Wenjie Wan

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Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China
Interests: agriculture; soil fertility; soil degradation; land use; crop production; phosphorus cycling; plant-growth-promoting bacteria; microbial ecology; ecosystem multifunctionality
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Dear Colleagues，

Soil microorganisms play important ecological roles, including carbon decomposition, nitrogen fixation, phosphorus mineralization, and sulfur transformation. Soil ecosystem multifunctionality, regarded as an important indicator for reflecting nutrient cycling and retention, as well as plant diversity, makes it possible to qualitatively estimate the linkage between nutrient cycling and soil microorganisms. In agroecosystems, microbial diversity maintenance is subjected to the nutrient level, environmental filtering, ecological risk, biotic interaction, and so on. Microbial diversity relates closely to ecosystem multifunctionality in various agroecosystems. However, nutrient cycling, ecosystem multifunctionality, and microbial diversity maintenance in response to agricultural management (e.g., fertilization and irrigation) and climatic change remain largely unknown. Additionally, the contribution of core microorganisms mediating nutrient cycling to soil ecosystem multifunctionality is rarely investigated. Prosperous bioinformatic technology, including metagenomics, amplicon sequencing, and fast species identification system, can provide crucial information, and can advance our understanding of nutrient cycling and microorganisms in agroecosystem at a given site or on a global scale, allowing for better agricultural management.

With this Special Issue of Agronomy, we welcome papers on key nutrient cycling, nutrient cycling functional gene diversity in agroecosystems, the linkage between soil ecosystem multifunctionality and microbial diversity, and mechanisms underlying microbial diversity maintenance in agroecosystems. Moreover, we also encourage colleagues to submit papers on the contribution of ecosystem multifunctionality to crop yield in agroecosystems and papers that expose reasons underlying ecosystem multifunctionality difference between agricultural and nonagricultural soils.

Dr. Wenjie Wan
Guest Editor

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Keywords

nutrient cycling
microorganisms
agroecosystem
ecosystem multifunctionality
microbial biodiversity
crop yield

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Published Papers (8 papers)

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Research

16 pages, 4031 KiB

Open AccessArticle

Mechanisms of Biochar in Modulating Soil Organic Selenium Transformation and Enhancing Soil Selenium Availability

by Zhenya Tang, Xin Feng, Ruijiang Li, Fangling Fan and Zhen Miao

Agronomy 2025, 15(3), 701; https://doi.org/10.3390/agronomy15030701 - 13 Mar 2025

Viewed by 376

Abstract

Selenium deficiency poses a significant threat to human health. The low bioavailability of selenium in soil largely limits the improvement of selenium content in crops. Selenium in soil mainly exists in an organically bound form. Biochar has the ability to regulate the organic matter content of soil; however, the impact of biochar on the transformation of organically bound selenium in soil remains poorly understood. Therefore, this study investigates the effect of biochar on organically bound selenium in typical medium–to–high selenium soils from Yimen County, Yuxi City, Yunnan Province. Reed straw (RS), apple wood (AW), and walnut shells (WS) were used as biomass materials for biochar preparation. The study utilized organically bound selenium transformation incubation and pot experiments to explore the role of biochar in transforming organically bound selenium in soil. The results showed that organically bound selenium was the dominant selenium form in the soil, accounting for 66.31% of the total selenium content. Both pot experiments and incubation trials indicated that the addition of biochar significantly increased the levels of water–soluble and exchangeable selenium in the soil. The addition of biochar mainly promotes the conversion of fulvic acid–bound selenium into water–soluble and exchangeable selenium. In the absence of carbon sources, humic acid–bound selenium can also be converted to water–soluble and exchangeable selenium. Correlation analysis revealed that soil water–soluble selenium was significantly negatively correlated with soil total selenium (r = −0.792 **, p < 0.01), soil phosphatase activity (r = −0.645 *, p < 0.05), abundance taxa of Chloroflexi (r = −0.751 *, p < 0.05), Chytridiomycota (r = −0.674 *, p < 0.05), and Basidiomycota (r = 0.722 **, p < 0.05), while it was significantly positively correlated with soil urease activity (r = 0.809 **, p < 0.01), and significantly negatively correlated with abundance taxa of Myxococcota (r = −0.800 **, p < 0.01). Compared with the initial soil, the WS treatment (initial soil water–soluble selenium 0.31 μg·kg⁻¹, exchangeable selenium 0.11 μg·kg⁻¹) significantly increased the soil water–soluble selenium by 34.9 times and exchangeable selenium by 100.2 times. Additionally, the selenium content in garlic increased by 170% compared to the control group. Full article

(This article belongs to the Special Issue Nutrient Cycling and Microorganisms in Agroecosystems)

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20 pages, 12885 KiB

Open AccessArticle

Combination of Nitrogen-Enriched Zeolite and Arbuscular Mycorrhizal Symbiosis to Improve Growth of Maize (Zea mays L.)

by Luis G. Sarmiento-López, Arny Matos-Alegria, Mariana E. Cesario-Solis, Daniel Tapia-Maruri, Paul H. Goodwin, Carmen Quinto, Olivia Santana and Luis Cardenas

Agronomy 2025, 15(1), 156; https://doi.org/10.3390/agronomy15010156 - 10 Jan 2025

Viewed by 983

Abstract

Zeolite, a microporous mineral with strong ion binding, can enhance nutrient availability and growth of plants, such as maize (Zea mays L.). Arbuscular mycorrhizal (AM) symbiosis has also been shown to enhance nutrient availability and growth of plants, including maize. However, the interaction between AM symbiosis and zeolite is poorly understood. In this study, the effect on growth of maize was examined following soil treatment with N-enriched (ZN+) zeolite, which could retain 19.68% N, or N-free zeolite (ZN−), compared to N-enriched or N-free vermiculite (VN+ and VN−). There was a 2.7-times increase in the growth of maize under ZN+ treatment compared to ZN−, indicating that N could be released from zeolite for plant growth, and a 3.8-times increase with ZN+ treatment compared to VN− or VN+, indicating that zeolite was more effective than vermiculite in releasing N for plant growth. Subsequently, ZN+ and ZN− treatments were examined with non-AM (M−) and AM (M+) treatments using Rhizophagus irregularis. ZN+ M+ treatment led to higher AM colonization and development compared to M+ ZN−treatment, indicating an interaction of AM in roots with N from zeolite. PCA revealed improvements in leaf N content, photosynthetic pigments, photosynthetic performance, and secondary metabolites with M+ ZN+ treatment, which was also observed in comparison to M−ZN+ and M− ZN−treatments, further supporting the benefit of combining N from zeolite with an AM fungus. The combination of N released from N-enriched zeolite and AM symbiosis offers a promising alternative to chemical fertilizers to improve maize growth. Full article

(This article belongs to the Special Issue Nutrient Cycling and Microorganisms in Agroecosystems)

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18 pages, 4062 KiB

Open AccessArticle

Altitude Distribution Patterns and Driving Factors of Rhizosphere Soil Microbial Diversity in the Mountainous and Hilly Region of Southwest, China

by Yanlin Li, Yonggang Wang, Yunpeng Liu, Yangyang Chen and Shuangrong Yang

Agronomy 2024, 14(10), 2441; https://doi.org/10.3390/agronomy14102441 - 21 Oct 2024

Viewed by 1107

Abstract

The distribution characteristics of the microbial community in rhizosphere soils of different altitudinal gradients were explored to uncover ecological factors affecting microbial community composition. In this study, the community variations of bacteria and fungi in the rhizosphere soil of Chrysanthemum indicum L. were analyzed. Samples were distributed along an altitudinal gradient of 300–1500 m above sea level in the Fuling watershed of the Three Gorges Reservoir area, China. The analysis was conducted using Illumina MiSeq high-throughput sequencing and bioinformatics analyses. Through correlation analysis with ecological factors, the altitude distribution pattern and driving factors of soil microbial diversity in the mountainous and hilly region of Chongqing were explored. According to the results, the richness and diversity of rhizosphere soil bacteria increased with altitude, while fungi were the richest and most diverse at an altitude of 900 m. The composition of the microbial community differed among different altitudes. Actinobacteria, Proteobacteria, Acidobacteriota, Chloroflexi, Bacteroidota, Ascomycota, unclassified_k_Fungi, Basidiomycota, and Mortierellomycota dominated the microbial community in rhizosphere soil. Correlation analysis showed that the distribution of rhizosphere soil microbial communities correlated with soil ecological factors at different altitudes. Moisture, pH, total nitrogen, total potassium, available potassium, urease, and catalase were significantly positively correlated with rhizosphere soil bacterial α-diversity, while their correlations with fungi were not significant. Variation partition analysis showed that the combined effects of soil physical and chemical factors, enzyme activity, and microbial quantity regulated bacterial community structure and composition. Their combined contributions (19.21%) were lower than the individual effects of soil physical and chemical factors (48.49%), enzyme activity (53.24%), and microbial quantity (60.38%). The effects of ecological factors on fungal communities differed: While the soil physical and chemical factors (44.43%) alone had a clear effect on fungal community structures, their combined contributions had no apparent effect. The results of this study not only contribute to a deeper understanding of the impact mechanism of altitude gradient on the diversity of rhizosphere soil microbial communities, but also provide a scientific basis for the protection and management of mountainous and hilly ecosystems. It lays a foundation for the future exploration of the relationship between microbial communities and plant–soil interactions. Full article

(This article belongs to the Special Issue Nutrient Cycling and Microorganisms in Agroecosystems)

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15 pages, 1661 KiB

Open AccessArticle

Reinoculation in Topdressing of Rhizobium tropici, Azospirillum brasilense, and the Micronutrients Mo/Co in Common Bean

by Brenda B.A. Ribeiro, Itamar R. Teixeira, Gisele C. Silva, Tamires Ester P. Bravo, Nathan Mickael B. Cunha, Maurílio R. Benício Neto, Gessiele P.C. Alves, Alexandre M. Sbroggio Filho and Elton F. Reis

Agronomy 2024, 14(7), 1368; https://doi.org/10.3390/agronomy14071368 - 26 Jun 2024

Cited by 2 | Viewed by 1600

Abstract

Biological nitrogen fixation (BNF) can provide the necessary nitrogen for bean crops; however, for this to occur, important limitations involving the inoculant application technology need to be overcome.The use of co-inoculation is a management technique used to obtain benefits and increase the potential of N₂ fixation from the association between bacteria from the rhizobia group, such as R. tropici, and bacteria that promote plant growth, such as A. brasilense, in association with the addition of nutrients that allow greater efficiency of bacteria fixing atmospheric N₂. This study aimed to evaluate the bean response to the reinoculation of R. tropici in co-inoculation with A. brasilense in a mixture with the micronutrients Co/Mo, in the winter season of 2021, in Anápolis-GO, Brazil. A randomized block design was used, with four replications, and the following treatments (TRs) were studied: TR1—reinoculation with R. tropici; TR2—reinoculation with co-inoculation of R. tropici + A. brasilense; TR3—reinoculation of R. tropici + Mo/Co micronutrients; TR4—reinoculation with co-inoculation R. tropici + A. brasilense + Mo/Co micronutrients; TR5—inoculation via seed, without reinoculation; TR6—mineral N fertilization in the sowing furrow and topdressing; TR7—control, without any N source. At stage R6, nodulation characteristics (number and dry mass of nodules) and the morphophysiological parameters of the plants (main root length, root dry mass, plant height, shoot dry mass, leaf area, and leaf N content in the shoot) were evaluated. At harvest, the final plant stand and components (number of pods per plant, number of grains per pod, and average weight of one hundred grains) were determined, in addition to grain yield. It was concluded that inoculation followed by reinoculation in topdressing with R. tropici in co-inoculation with A. brasilense plus Mo/Co, compared to mineral nitrogen fertilization, improves the efficiency of the nodulation process and the morphophysiological characteristics of the common bean crop. Seed inoculation and topdressing application with R. tropici, associated with co-inoculation with A. brasilense + Mo and Co, have the potential to completely replace mineral nitrogen fertilization in common bean crops. Full article

(This article belongs to the Special Issue Nutrient Cycling and Microorganisms in Agroecosystems)

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14 pages, 1224 KiB

Open AccessArticle

Sustainable Agriculture Practices: Utilizing Composted Sludge Fertilizer for Improved Crop Yield and Soil Health

by Lijun Li, He Li, Lihong Tong and Yizhong Lv

Agronomy 2024, 14(4), 756; https://doi.org/10.3390/agronomy14040756 - 6 Apr 2024

Cited by 4 | Viewed by 2840

Abstract

It is desirable to recycle sewage sludge as fertilizer for agricultural fields. The application of sludge to agricultural soils is a measure that replaces chemical fertilizers and plays an important role in improving soil’s physicochemical and biological properties. However, there are concerns that the pollutants in sewage sludge will cause negative impacts on soil health. To closely monitor the soil–sludge interactions, a field study was conducted over a 20-year period in the North China Plain. In this study, the long-term effects of sewage sludge on the soil properties and soil microbial diversity were investigated. We examined the effects of various fertilization methods (control, chemical fertilizer, uncomposted sludge fertilizer, composted sludge fertilizer) on wheat production and several soil health indicators, such as the soil’s enzymatic activities, microbial biomass, microbial diversity, and crop yield. This long-term experiment supports that the composted sludge fertilizer increased crop production by 124.2% compared to the control treatment. The soil’s biological quality (e.g., the concentration of soil microbial biomass carbon) was also improved under the composted sludge fertilizer treatment. The concentrations of soil microbial biomass carbon under the uncomposted sludge fertilizer and composted sludge fertilizer treatments were 560.07 mg/kg and 551.07 mg/kg, respectively. The effect of the composted sludge fertilizer was greater than that of the uncomposted sludge fertilizer. The content of heavy metals did not exceed the national standard. The highest soil health index was 0.79 with the composted sludge fertilizer. Therefore, these results suggest that the application of composted sludge fertilizer has the potential to enhance long-term soil health and promote sustainable agricultural practices. Full article

(This article belongs to the Special Issue Nutrient Cycling and Microorganisms in Agroecosystems)

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16 pages, 3182 KiB

Open AccessArticle

Effects of Conventional Non-Biodegradable Film-Derived Microplastics and New Biodegradable Film-Derived Microplastics on Soil Properties and Microorganisms after Entering Sub-Surface Soil

by Xiaowei Liu, Wenliang Wei, Guocheng Liu, Bo Zhu, Jie Cui and Tao Yin

Agronomy 2024, 14(4), 753; https://doi.org/10.3390/agronomy14040753 - 5 Apr 2024

Cited by 2 | Viewed by 1748

Abstract

Plastic film mulching, widely used in agriculture, leads to microplastic (MP) pollution in soils. While biodegradable polybutylene adipate terephthalate (PBAT) films may offer a solution, their impacts on subsurface soils and microorganisms remain unclear. To investigate the effects of conventional non-biodegradable polyethylene (PE) and biodegradable PBAT MPs on the properties of sub-surface soils and microbial communities, MPs were added at varying doses in a field experiment and incubated for 160 days. Physicochemical characteristics, nutrient dynamics, and microbial composition, diversity, and networks of soils were analyzed using standard techniques and 16S rRNA/ITS gene sequencing. Correlations between soil properties and microbes were assessed. Both MP types significantly altered soil characteristics, with PBAT-MP elevating pH and the levels of available phosphorus and potassium more than PE-MP. Microbial composition shifts occurred, with low-addition PBAT-MP promoting plastic-degrading genera. The assessment of α/β-diversity indicated that PBAT-MP predominantly influenced fungi while PE-MP impacted bacteria. An examination of microbial co-occurrence networks highlighted that PE-MP primarily disrupted fungal interactions, whereas PBAT-MP streamlined network complexity. Correlation analyses revealed that PBAT-MP promoted fungal diversity/network resilience correlating to nutrients. PE-MP and PBAT-MP significantly altered native soil/microbe relationships. PBAT-MP may exert greater, yet unknown, impacts over time through its biodegradation into newer and smaller fragments. Future research needs to integrate multi-omics and stable isotope science to elucidate the deep mechanistic impacts of degraded film-derived MPs on microbial ecological functions and biogeochemical cycles. Attention should also be paid to the long-term accumulation/transport of MPs in agricultural soils. Overall, this work deepens the impact and understanding of MPs from plastic film on sub-surface soil ecology. Furthermore, it provides a theoretical foundation for managing ‘white pollution’ in the film-covered farmlands of arid and semi-arid regions in China. Full article

(This article belongs to the Special Issue Nutrient Cycling and Microorganisms in Agroecosystems)

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15 pages, 1361 KiB

Open AccessArticle

Apple Growth and Yield in Replant Soils Supplemented by Organic Soil Additives

by Roxana Djalali Farahani-Kofoet, Daniel Schneider and Carmen Feller

Agronomy 2024, 14(4), 678; https://doi.org/10.3390/agronomy14040678 - 26 Mar 2024

Cited by 1 | Viewed by 1174

Abstract

Repeated apple cultivation in the same area leads to apple replant disease (ARD), which can probably be reduced by the use of organic supplements and selected rootstock/variety combinations. Soils at two conventionally and one organically farmed site in north-eastern Germany were tested for ARD in pot trials. In subsequent field trials, the effects of champost, microbially carbonised compost, and coniferous wood shavings piled up like a dam (‘Müncheberger Damm’ (M)-dam) and of rootstock/variety combinations were tested. On the organic site, only leonardite and champost were tested. The pot trials indicated for all sites that the soil is affected by ARD. After five years, the growth increase in trunks in the M-dam was 20–40% higher than in controls and other treatments, depending on the site. On one site, the yield over four years was a 15.7% increase for M-dam and also for champost compared to controls, on the other site, it was 11.7% and 3.0%, respectively. The M.9 rootstock with the Gala variety had a higher, but insignificant, yield compared to G.11/Gala by 6.7 or 2.6%, depending on the site. No difference in trunk growth or yield with Topaz was observed at the organic farmed site. Further research on M-dam and champost is supported, as both are promising in terms of yield. Full article

(This article belongs to the Special Issue Nutrient Cycling and Microorganisms in Agroecosystems)

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19 pages, 1468 KiB

Open AccessArticle

Quantifying CO₂ Emissions and Carbon Sequestration from Digestate-Amended Soil Using Natural ¹³C Abundance as a Tracer

by Gregory Reuland, Steven Sleutel, Haichao Li, Harmen Dekker, Ivona Sigurnjak and Erik Meers

Agronomy 2023, 13(10), 2501; https://doi.org/10.3390/agronomy13102501 - 28 Sep 2023

Cited by 3 | Viewed by 2543

Abstract

The untapped potential for carbon sequestration in agricultural soils represents one of the most cost-effective tools for climate change mitigation. Increasing soil organic matter also brings other agronomic benefits such as improved soil structure, enhanced water-and-nutrient-retention capacity, and biological activity. Broadly, soil organic carbon storage is achieved by increasing carbon inputs (plant residues and organic amendments) and reducing carbon outputs (soil loss mechanisms, decomposition). With a focus on carbon inputs—more specifically, organic amendments—as leverage to increase soil organic carbon, we compared the respiration rates and carbon storage of incubated soil cores amended with maize straw, manure, two digestates and the solid fraction of digestate. Using the variation in the natural ¹³C abundance found in C4 and C3 plants as a tracer, we were able to partition the CO₂ emissions between the exogenous organic matter materials elaborated from maize (C4) and native soil organic carbon (C3). The addition of digestate resulted in an additional 65 to 77% of remaining organic carbon after 92 days. The digestate-derived CO₂ was fitted to a second-order kinetic carbon model that accounts for the substrate C that is assimilated into the microbial biomass. The model predicted a carbon sequestration potential of 56 to 73% of the total applied organic carbon after one to two years. For the solid fraction, the results were higher, with 89% of the applied organic carbon after 92 days and a sequestration potential of 86%. The soil priming ranged from −19% to +136% in relation to the unamended control soil, highlighting a surprisingly wide spectrum of results that warrants the need for further research on soil–digestate interactions. Full article

(This article belongs to the Special Issue Nutrient Cycling and Microorganisms in Agroecosystems)

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