Microorganisms

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26 pages, 3928 KiB

Open AccessArticle

Physicochemical Properties and Microbiome of Vineyard Soils from DOP Ribeiro (NW Spain) Are Influenced by Agricultural Management

by Pilar Blanco, Isaac Rodríguez, Victoria Fernández-Fernández, María Ramil, David Castrillo, Marta Acín-Albiac, Irene Adamo, Clara Fernández-Trujillo, Beatriz García-Jiménez, Alberto Acedo, Noemi Calvo-Portela, Andrea Parente-Sendín, Lara Acemel-Míguez and Flora Alonso-Vega

Microorganisms 2024, 12(3), 595; https://doi.org/10.3390/microorganisms12030595 - 16 Mar 2024

Viewed by 1326

Abstract

Agricultural management influences the soil ecosystem by affecting its physicochemical properties, residues of pesticides and microbiome. As vineyards grow crops with the highest incidence of pesticides, the aim of this study was to evaluate the impact of conventional and sustainable management systems of [...] Read more.

Agricultural management influences the soil ecosystem by affecting its physicochemical properties, residues of pesticides and microbiome. As vineyards grow crops with the highest incidence of pesticides, the aim of this study was to evaluate the impact of conventional and sustainable management systems of vineyards from DOP Ribeiro on the soil’s condition. Samples from soils under three different management systems were collected, and the main soil physicochemical properties were evaluated. A selection of 50 pesticides were investigated by liquid chromatography with tandem mass spectrometry. The bacterial and fungal microbiomes were characterized through amplicon sequencing. The results show that organic agriculture positively influences soil pH and the concentration of some nutrients compared to conventional management. Our microbiome analysis demonstrated that transitioning from conventional to organic management significantly improves several BeCrop^® indexes related to key microbial metabolism and soil bio-sustainability. Such a transition does not affect soil alpha diversity, but leads to a higher interconnected microbial network structure. Moreover, differential core genera and species for each management system are observed. In addition, the correlation of the microbiome with geographical distance is evidence of the existence of different microbial terroirs within DOP Ribeiro. Indeed, sustainable management leads to higher nutrient availability and enhances soil health in the short term, while lowering pesticide usage. Full article

(This article belongs to the Special Issue Advances in Soil Microbiome 2.0)

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18 pages, 5688 KiB

Open AccessArticle

Impact of Straw Incorporation on the Physicochemical Profile and Fungal Ecology of Saline–Alkaline Soil

by Weiming Ma, Li Ma, Jintang Jiao, Abbas Muhammad Fahim, Junyan Wu, Xiaolei Tao, Yintao Lian, Rong Li, Yapeng Li, Gang Yang, Lijun Liu, Yuanyuan Pu, Wancang Sun and Wangtian Wang

Microorganisms 2024, 12(2), 277; https://doi.org/10.3390/microorganisms12020277 - 28 Jan 2024

Viewed by 1203

Abstract

Improving the soil structure and fertility of saline–alkali land is a major issue in establishing a sustainable agro-ecosystem. To explore the potential of different straw returning in improving saline–alkaline land, we utilized native saline–alkaline soil (SCK), wheat straw-returned saline–alkaline soil (SXM) and rapeseed [...] Read more.

Improving the soil structure and fertility of saline–alkali land is a major issue in establishing a sustainable agro-ecosystem. To explore the potential of different straw returning in improving saline–alkaline land, we utilized native saline–alkaline soil (SCK), wheat straw-returned saline–alkaline soil (SXM) and rapeseed straw-returned saline–alkaline soil (SYC) as our research objects. Soil physicochemical properties, fungal community structure and diversity of saline–alkaline soils were investigated in different treatments at 0–10 cm, 10–20 cm and 20–30 cm soil depths. The results showed that SXM and SYC reduced soil pH and total salinity but increased soil organic matter, alkali-hydrolyzable nitrogen, available phosphorus, total potassium, etc., and the enhancement effect of SYC was more significant. The total salinity of the 0–10 cm SCK soil layer was much higher than that of the 10–30 cm soil layers. Fungal diversity and abundance were similar in different soil layers in the same treatment. SXM and SYC soil had higher fungal diversity and abundance than SCK. At the genus level, Plectosphaerella, Mortierella and Ascomycota were the dominant groups of fungal communities in SXM and SYC. The fungal diversity and abundance in SXM and SYC soils were higher than in SCK soils. Correlation network analysis of fungal communities with environmental factors showed that organic matter, alkali-hydrolyzable nitrogen and available phosphorus were the main environmental factors for the structural composition of fungal communities of Mortierella, Typhula, Wickerhamomyces, Trichosporon and Candida. In summary, straw returning to the field played an effective role in improving saline–alkaline land, improving soil fertility, affecting the structure and diversity of the fungal community and changing the interactions between microorganisms. Full article

(This article belongs to the Special Issue Advances in Soil Microbiome 2.0)

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17 pages, 3881 KiB

Open AccessArticle

Effects of Polycyclic Aromatic Hydrocarbons on the Composition of the Soil Bacterial Communities in the Tidal Flat Wetlands of the Yellow River Delta of China

by Yue Qi, Yuxuan Wu, Qiuying Zhi, Zhe Zhang, Yilei Zhao and Gang Fu

Microorganisms 2024, 12(1), 141; https://doi.org/10.3390/microorganisms12010141 - 11 Jan 2024

Cited by 1 | Viewed by 861

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are pervasive organic pollutants in coastal ecosystems, especially in tidal flat wetlands. However, the mechanisms through which PAHs impact the soil bacterial communities of wetlands featuring a simple vegetation structure in the Yellow River Delta (China) remain largely unclear. [...] Read more.

Polycyclic aromatic hydrocarbons (PAHs) are pervasive organic pollutants in coastal ecosystems, especially in tidal flat wetlands. However, the mechanisms through which PAHs impact the soil bacterial communities of wetlands featuring a simple vegetation structure in the Yellow River Delta (China) remain largely unclear. In this study, we examined soil samples from two sites featuring a single vegetation type (Suaeda salsa) in the Yellow River Delta. Specifically, we investigated the impacts of PAHs on the diversity and composition of soil bacteria communities through high-throughput 16 S rRNA sequencing. PAHs significantly increased the soil organic carbon content but decreased the total phosphorus content (p = 0.02). PAH contamination notably reduced soil bacterial community α diversity (Shannon index) and β diversity. Furthermore, PAHs significantly altered the relative abundance of bacterial phyla, classes, and genera (p < 0.05). Specifically, PAHs increased the relative abundance of the bacterial phyla Acidobacteriota and Gemmatimonadota (p < 0.05), while decreasing the relative abundance of Bacteroidota, Desulfobacterota, and Firmicutes compared to the control wetland (p < 0.05). Moreover, PAHs and certain soil properties [total nitrogen (TN), soil organic carbon (SOC), total phosphorus (TP), and total salt (TS)] were identified as key parameters affecting the community of soil bacteria, with the abundance of specific bacteria being both negatively and positively affected by PAHs, SOC, and TN. In summary, our findings could facilitate the identification of existing environmental problems and offer insights for improving the protection and management of tidal flat wetland ecosystems in the Yellow River Delta of China. Full article

(This article belongs to the Special Issue Advances in Soil Microbiome 2.0)

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16 pages, 1570 KiB

Open AccessArticle

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

by Késia Silva Lourenço, Heitor Cantarella and Eiko Eurya Kuramae

Microorganisms 2023, 11(12), 2905; https://doi.org/10.3390/microorganisms11122905 - 1 Dec 2023

Viewed by 824

Abstract

Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we [...] Read more.

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

(This article belongs to the Special Issue Advances in Soil Microbiome 2.0)

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18 pages, 6546 KiB

Open AccessArticle

Different Responses of Soil Bacterial and Fungal Communities in Three Typical Vegetations following Nitrogen Deposition in an Arid Desert

by Zhihao Zhang, Gangliang Tang, Xutian Chai, Bo Liu, Xiaopeng Gao, Fanjiang Zeng, Yun Wang and Bo Zhang

Microorganisms 2023, 11(10), 2471; https://doi.org/10.3390/microorganisms11102471 - 1 Oct 2023

Cited by 2 | Viewed by 1237

Abstract

The effects of increased nitrogen (N) deposition on desert ecosystems have been extensively studied from a plant community perspective. However, the response of soil microbial communities, which play a crucial role in nutrient cycling, to N inputs and plant community types remains poorly [...] Read more.

The effects of increased nitrogen (N) deposition on desert ecosystems have been extensively studied from a plant community perspective. However, the response of soil microbial communities, which play a crucial role in nutrient cycling, to N inputs and plant community types remains poorly understood. In this study, we conducted a two-year N-addition experiment with five gradients (0, 10, 30, 60, and 120 kg N ha⁻¹ year⁻¹) to evaluate the effect of increased N deposition on soil bacterial and fungal communities in three plant community types, namely, Alhagi sparsifolia Shap., Karelinia caspia (Pall.) Less. monocultures and their mixed community in a desert steppe located on the southern edge of the Taklimakan Desert, Northwest China. Our results indicate that N deposition and plant community types exerted an independent and significant influence on the soil microbial community. Bacterial α-diversity and community dissimilarity showed a unimodal pattern with peaks at 30 and 60 kg N ha⁻¹ year^−1, respectively. By contrast, fungal α-diversity and community dissimilarity did not vary significantly with increased N inputs. Furthermore, plant community type significantly altered microbial community dissimilarity. The Mantel test and redundancy analysis indicated that soil pH and total and inorganic N (NH₄⁺ and NO₃⁻) levels were the most critical factors regulating soil microbial communities. Similar to the patterns observed in taxonomic composition, fungi exhibit stronger resistance to N addition compared to bacteria in terms of their functionality. Overall, our findings suggest that the response of soil microbial communities to N deposition is domain-specific and independent of desert plant community diversity, and the bacterial community has a critical threshold under N enrichment in arid deserts. Full article

(This article belongs to the Special Issue Advances in Soil Microbiome 2.0)

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20 pages, 5178 KiB

Open AccessArticle

Reforestation Increases the Aggregate Organic Carbon Concentration Induced by Soil Microorganisms in a Degraded Red Soil, Subtropical China

by Yunfang Ke, Hui Li, Tianyu Luo, Baodong Chen, Qiong Wang, Xueru Jiang and Wei Liu

Microorganisms 2023, 11(8), 2008; https://doi.org/10.3390/microorganisms11082008 - 4 Aug 2023

Cited by 1 | Viewed by 858

Abstract

In the process of biological carbon (C) sequestration during reforestation in degraded red soil, due to the decomposition of soil microorganisms, the interaction between soil organic carbon (SOC) and aggregates has an important effect on soil C sequestration. In this study, six common [...] Read more.

In the process of biological carbon (C) sequestration during reforestation in degraded red soil, due to the decomposition of soil microorganisms, the interaction between soil organic carbon (SOC) and aggregates has an important effect on soil C sequestration. In this study, six common reforestation models and three soil layers were selected in a degraded red soil area of the central subtropical region to determine the composition of soil aggregates and the distribution of SOC in soil aggregates. Based on the results of the soil physicochemical properties and microbial community composition biomass, we assessed the changes in aggregate-associated organic C storage during fluctuations in the stability of the aggregates. After reforestation, the SOC stock increased by 131.28–140.00%. Compared with the three pure forests and broad-leaved mixed forests, coniferous and broad-leaved mixed forests showed the largest proportion of macroaggregates (85.48–89.37%) and higher SOC accumulation. Soil microbial biomass mainly affected the decomposition process of SOC by affecting the stability of the soil aggregates, and the effect of bacteria was more significant. Coniferous and broad-leaved mixed forests can provide more soil microorganisms and C sources than pure forest, thus promoting macroaggregate formation and stability and related organic C storage. This reforestation model has greater C sequestration potential. Full article

(This article belongs to the Special Issue Advances in Soil Microbiome 2.0)

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18 pages, 3154 KiB

Open AccessArticle

Flavonoid Synthesis by Deinococcus sp. 43 Isolated from the Ginkgo Rhizosphere

by Jin Zhou, Kai Zou, Shaodong Fu, Zhenchun Duan, Guoqing Zhang, Xinhong Wu, Jingwen Huang, Shihui Li, Xueduan Liu, Shuangfei Zhang and Yili Liang

Microorganisms 2023, 11(7), 1848; https://doi.org/10.3390/microorganisms11071848 - 21 Jul 2023

Cited by 1 | Viewed by 1683

Abstract

Flavonoids are crucial in physiological and pharmaceutical processes, especially the treatment of cancer and the prevention of cardiovascular and cerebrovascular diseases. Flavonoid-producing plants and fungi have been extensively reported, but bacteria have been much less investigated as a source of flavonoid production. Deinococcus [...] Read more.

Flavonoids are crucial in physiological and pharmaceutical processes, especially the treatment of cancer and the prevention of cardiovascular and cerebrovascular diseases. Flavonoid-producing plants and fungi have been extensively reported, but bacteria have been much less investigated as a source of flavonoid production. Deinococcus sp. 43, a spherical flavonoid-producing bacteria from the Ginkgo rhizosphere, was reported in this study. First, the whole genome of Deinococcus sp. 43 was sequenced and a series of flavonoid anabolic genes were annotated. Simultaneously, High Performance Liquid Chromatography (HPLC) results showed that Deinococcus sp. 43 was capable of producing flavonoids, with a maximum quercetin output of 2.9 mg/L. Moreover, the relative expression of key genes involved in flavonoid synthesis was determined to test the completeness of the flavonoid anabolic pathway. The results of LC-MS analysis demonstrated that the flavonoids produced by Deinococcus sp. 43 were significantly different between intracellular and extracellular environments. The concentration of multiple glycosylated flavonoids was substantially higher in extracellular than intracellular environments, while the majority of flavonoids obtained in intracellular environments were hydroxylated multiple times. Lastly, the flavonoid biosynthetic pathway of Deinococcus sp. 43 was constructed based on the genomic analysis and the detected flavonoids. In conclusion, this study represents the first comprehensive characterization of the flavonoid-producing pathway of Deinococcus. The findings demonstrate that the strain has excellent potential as a genetically engineered strain for the industrial production of flavonoids. Full article

(This article belongs to the Special Issue Advances in Soil Microbiome 2.0)

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11 pages, 1336 KiB

Open AccessArticle

Changes to Soil Microbiome Resulting from Synergetic Effects of Fungistatic Compounds Pyrimethanil and Fluopyram in Lowbush Blueberry Agriculture, with Nine Fungicide Products Tested

by Austin W. Lloyd, David Percival, Morgan G. I. Langille and Svetlana N. Yurgel

Microorganisms 2023, 11(2), 410; https://doi.org/10.3390/microorganisms11020410 - 6 Feb 2023

Cited by 3 | Viewed by 1529

Abstract

Lowbush blueberries (Vaccinium spp.) are a crop of economic significance to Atlantic Canada, Quebec, and Maine. The fruit is produced by the management of naturally occurring plant populations. The plants have an intimate relationship with the soil microbiome and depend on it [...] Read more.

Lowbush blueberries (Vaccinium spp.) are a crop of economic significance to Atlantic Canada, Quebec, and Maine. The fruit is produced by the management of naturally occurring plant populations. The plants have an intimate relationship with the soil microbiome and depend on it for their health and productivity. Fungicides are an important tool in combatting disease pressure but pose a potential risk to soil health. In this study, amplicon sequencing was used to determine the effects of six fungistatic compounds both alone and in combination via nine commercially available fungicide products on the bacterial and fungal microbiomes associated with lowbush blueberries and to study whether these effects are reflected in crop outcomes and plant phenotypes. One fungicide, Luna Tranquility, a combination of fluopyram and pyrimethanil, was found to impart significant effects to fungal and bacterial community structure, fungal taxonomic abundances, and bacterial functions relative to control. The two fungicides which contained fluopyram and pyrimethanil as single ingredients (Velum Prime and Scala, respectively) did not induce significant changes in any of these regards. These results suggest the possibility that these microbiome changes are the result of the synergistic effect of fluopyram and pyrimethanil on soil microbiomes. While these results suggest a significant disruption to the soil microbiome, no corresponding changes to crop development and outcomes were noted. Ultimately, the majority of the fungicides analysed in this trial did not produce significant changes to the soil microbiome relative to the untreated group (UTG). However, one of the fungicide treatments, Luna Tranquility, did produce significant changes to the soil ecosystem that could have longer-term effects on soil health and its future use may merit additional investigation onto its ecotoxicological properties. Full article

(This article belongs to the Special Issue Advances in Soil Microbiome 2.0)

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