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17 pages, 5695 KiB

Open AccessArticle

Assembly Characteristics and Influencing Factors of the Soil Microbial Community in the Typical Forest of Funiu Mountain

by Kunrun He, Yiran Lai, Shurui Hu, Meiyi Song, Ye Su, Chunyang Li, Xinle Wu, Chunyue Zhang, Yuanhang Hua, Jinyong Huang, Shujuan Guo and Yadong Xu

Microorganisms 2024, 12(11), 2355; https://doi.org/10.3390/microorganisms12112355 - 18 Nov 2024

Viewed by 452

Abstract

Assessing the relationship between litter characteristics and soil microbial community traits across different forest types can enhance our understanding of the synergistic interactions among litter, soil, and microorganisms. This study focused on three representative forest types in the Funiu Mountains—Larix gmelinii (LG), [...] Read more.

Assessing the relationship between litter characteristics and soil microbial community traits across different forest types can enhance our understanding of the synergistic interactions among litter, soil, and microorganisms. This study focused on three representative forest types in the Funiu Mountains—Larix gmelinii (LG), Quercus aliena var. acutiserrata (QA), and Quercus aliena var. acutiserrata + Pinus armandii (QAPA). The findings indicated no significant differences in Chao1 among the three forests; however, the Shannon index exhibited an initial increase followed by a decline. NMDS and ANOSIM analyses revealed significant structural differences across these forest types. Network topological metrics (nodes, edges, average degree, and average path distance) for bacterial taxa were higher in LG and QA compared with QAPA. Additionally, LG and QA demonstrated significantly greater average niche breadth than QAPA. The results from the null models (the proportion occupied by dispersal limitation is 62.2%, 82.2%, and 64.4% in LG, QA, and QAPA), modified stochasticity ratio (LG: 0.708, QA: 0.664, and QAPA: 0.801), and neutral community models (LG: R² = 0.665, QA: R² = 0.630, and QAPA: R² = 0.665) suggested that stochastic processes predominantly govern the assembly of soil bacterial communities. Random forest analysis alongside Mantel tests highlighted LTP (litter total phosphorus), STN (soil total nitrogen), MCP (carbon-to-phosphorus ratio of microbial biomass), and SCN (soil carbon-to-nitrogen ratio) as critical factors affecting bacterial niche width; conversely LCN (litter carbon-to-nitrogen ratio), RCP (ratio of dissolved carbon to phosphorus), MCP, and SCN emerged as key determinants influencing community assembly processes. Furthermore, the PLS-SEM results underscored how both litter characteristics along with soil properties—and their associated alpha diversity—impact variations in niche breadth while also shaping community assembly dynamics overall. This research provides vital insights into understanding synergistic relationships between litter quality, soil characteristics, and microbial community across diverse forest ecosystems. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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16 pages, 5508 KiB

Open AccessArticle

Litter Removal Counteracts the Effects of Warming on Soil Bacterial Communities in the Qinghai–Tibet Plateau

by Guanwen Li, Yang Wu, Wenjing Chen, Ziwen Zhao, Yuanze Li, Leilei Qiao, Guobin Liu and Sha Xue

Microorganisms 2024, 12(11), 2274; https://doi.org/10.3390/microorganisms12112274 - 9 Nov 2024

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Abstract

Climate warming and high-intensity human activities threaten the stability of alpine meadow ecosystems. The stability of the soil microbial community is crucial for maintaining ecological service function. However, the effects of warming and litter removal on microbial interactions, community-building processes, and species coexistence [...] Read more.

Climate warming and high-intensity human activities threaten the stability of alpine meadow ecosystems. The stability of the soil microbial community is crucial for maintaining ecological service function. However, the effects of warming and litter removal on microbial interactions, community-building processes, and species coexistence strategies remain unclear. In this study, we used a fiberglass open-top chamber to simulate global change, and moderate grazing in winter was simulated by removing above-ground litter from all plants in the Qinghai–Tibet Plateau, China, to investigate the effects of warming, litter removal, and interactions on soil microbial communities. The treatments included (1) warming treatment (W); (2) litter removal treatment (L); (3) the combined treatment (WL); and (4) control (CK). The results show that compared with the control treatment, warming, litter removal, and the combined treatments increased bacterial Shannon diversity but reduced fungal Shannon diversity, and warming treatment significantly changed the bacterial community composition. Warming, litter removal, and the combined treatments reduced the colinear network connectivity among microorganisms but increased the modularity of the network, and the average path distance and average clustering coefficient were higher than those in the control group. Stochastic processes played a more important role in shaping the microbial community composition, and soil–available phosphorus and soil ammonium contributed more to the βNTI of the bacterial community, while total phosphorus and NAG enzyme in the soil contributed more to the βNTI of the fungal community. Notably, litter removal counteracts the effects of warming on bacterial communities. These results suggest that litter removal may enhance bacterial community stability under warming conditions, providing insights for managing alpine meadow ecosystems in the context of climate change. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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22 pages, 3549 KiB

Open AccessArticle

Soil Fungal Community Diversity, Co-Occurrence Networks, and Assembly Processes under Diverse Forest Ecosystems

by Bing Yang, Zhisong Yang, Ke He, Wenjia Zhou and Wanju Feng

Microorganisms 2024, 12(9), 1915; https://doi.org/10.3390/microorganisms12091915 - 20 Sep 2024

Viewed by 1139

Abstract

Fungal communities are critical players in the biogeochemical soil processes of forest ecosystems. However, the factors driving their diversity and community assembly are still unclear. In the present study, five typical vegetation types of soil fungal communities in Liziping Nature Reserve, China, were [...] Read more.

Fungal communities are critical players in the biogeochemical soil processes of forest ecosystems. However, the factors driving their diversity and community assembly are still unclear. In the present study, five typical vegetation types of soil fungal communities in Liziping Nature Reserve, China, were investigated using fungal ITS sequences. The results show that the topsoil fungal community is mainly dominated by the phyla Ascomycota, Basidiomycota, and Mortierellomycota. Although there was no significant difference in α diversity (Shannon, Simpson, and Pielou evenness indices) among different forest types, there was a significant difference in β diversity (community composition). This study found that soil pH, soil organic carbon, total nitrogen (TN), total phosphorus (TP), and the total nitrogen/total phosphorus (N/P) ratio are the main environmental factors that affect soil fungal communities. Each forest type has a specific co-occurrence network, indicating that these community structures have significant specificities and complexities. Deciduous evergreen broad-leaved forests as well as deciduous broad-leaved and evergreen broad-leaved mixed forests showed high modularity and average path lengths, indicating their highly modular nature without distinct small-scale characteristics. Furthermore, our findings indicate that the structures of topsoil fungal communities are mainly shaped by stochastic processes, with the diffusion limitation mechanism playing a particularly significant role. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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24 pages, 4316 KiB

Open AccessArticle

Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing

by Joseline Jiménez-Venegas, Leonardo Zamora-Leiva, Luciano Univaso, Jorge Soto, Yasna Tapia and Manuel Paneque

Microorganisms 2024, 12(9), 1820; https://doi.org/10.3390/microorganisms12091820 - 3 Sep 2024

Viewed by 1477

Abstract

Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace [...] Read more.

Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace metals in solid copper (Cu) mine tailings from the Ovejería Tailings Dam of the National Copper Corporation of Chile and used high-throughput sequencing techniques to determine the microbial community diversity of the tailings using 16S rRNA gene-based amplicon sequence analysis. The concentrations of the detected metals were highest in the following order: iron (Fe) > Cu > manganese (Mn) > molybdenum (Mo) > lead (Pb) > chromium (Cr) > cadmium (Cd). Furthermore, 16S rRNA gene-based sequence analysis identified 12 phyla, 18 classes, 43 orders, 82 families, and 154 genera at the three sampling points. The phylum Proteobacteria was the most dominant, followed by Chlamydiota, Bacteroidetes, Actinobacteria, and Firmicutes. Genera, such as Bradyrhizobium, Aquabacterium, Paracoccus, Caulobacter, Azospira, and Neochlamydia, showed high relative abundance. These genera are known to possess adaptation mechanisms in high concentrations of metals, such as Cd, Cu, and Pb, along with nitrogen-fixation capacity. In addition to their tolerance to various metals, some of these genera may represent pathogens of amoeba or humans, which contributes to the complexity and resilience of bacterial communities in the studied Cu mining tailings. This study highlights the unique microbial diversity in the Ovejería Tailings Dam, including the discovery of the genus Neochlamydia, reported for the first time for heavy metal resistance. This underscores the importance of characterizing mining sites, particularly in Chile, to uncover novel bacterial mechanisms for potential biotechnological applications. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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15 pages, 6500 KiB

Open AccessArticle

The Effect of Intercropping with Different Leguminous Green Manures on the Soil Environment and Tea Quality in Tea Plantations

by Pinqian Zhou, Mengjuan Chen, Qiang Bao, Hua Wang, Yuanjiang Wang and Haiping Fu

Microorganisms 2024, 12(8), 1721; https://doi.org/10.3390/microorganisms12081721 - 21 Aug 2024

Viewed by 856

Abstract

Intercropping with green manure is a soil-sustainable cultivation practice that has demonstrated positive impacts on tea growth and the soil environment in tea plantations. Nevertheless, research examining the effect of leguminous green manure varieties in tea plantations is scarce. This study aimed to [...] Read more.

Intercropping with green manure is a soil-sustainable cultivation practice that has demonstrated positive impacts on tea growth and the soil environment in tea plantations. Nevertheless, research examining the effect of leguminous green manure varieties in tea plantations is scarce. This study aimed to analyze the tea quality and soil environment components in response to intercropping with three distinct leguminous green manures, Cassia sophera cv. Chafei 1 (CF), Sesbania cannabina (Retz.) Pers. (SC), and Chamaecrista rotundifolia (Pers.) Greene (CR), with 70% chemical fertilizer, and compare them to non-intercropped green manures with 100% chemical fertilizer (CK) in tea plantations. The findings indicated that intercropping with SC increased the amino acids content of tea leaves, the soil organic carbon (SOC), the soil acid phosphatase (ACP), the soil acid protease (ACPT), and the bacterial diversity compared to the CK treatment. Intercropping with CR improved the ACP activity and bacterial diversity while intercropping with CF improved the polyphenols. Proteobacteria, Acidobacteria, Actinomycetes, and Firmicutes were identified as the dominant bacterial taxa in tea plantations with intercropped green manure. A strong positive correlation was indicated between the SOC contents and the amino acids content in tea leaves after intercropping. A canonical correspondence analysis indicated significant associations between the ACP and the urease activity, and between the ACP and ACPT, and both were closely linked to SC. This finding provides an explanation that intercropping with SC may positively affect tea quality by influencing the SOC content, the soil enzyme activity, and the soil bacterial diversity. Green manure intercropping may replace part of chemical fertilizers, improve the soil environment in tea gardens, and enhance the quality of tea. These findings offer a theoretical reference for selecting leguminous green manure and advancing the sustainable development of tea plantations. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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15 pages, 3390 KiB

Open AccessArticle

Enzymatic Stoichiometry Reveals the Metabolic Limitations of Soil Microbes under Nitrogen and Phosphorus Addition in Chinese Fir Plantations

by Yan Ren, Ying Wang, Xiulan Zhang, Xionghui Liu, Pei Liu and Liang Chen

Microorganisms 2024, 12(8), 1716; https://doi.org/10.3390/microorganisms12081716 - 20 Aug 2024

Viewed by 803

Abstract

Increasing nitrogen (N) deposition alters the availability of soil nutrients and is likely to intensify phosphorus (P) limitations, especially in P-limited tropical and subtropical forests. Soil microorganisms play vital roles in carbon (C) and nutrient cycling, but it is unclear whether and how [...] Read more.

Increasing nitrogen (N) deposition alters the availability of soil nutrients and is likely to intensify phosphorus (P) limitations, especially in P-limited tropical and subtropical forests. Soil microorganisms play vital roles in carbon (C) and nutrient cycling, but it is unclear whether and how much N and P imbalances affect the soil’s microbial metabolism and mechanisms of nutrient limitations. In this study, a 3-year field experiment of N and P addition (control (CK), 100 kg N ha⁻¹ yr⁻¹ (N), 50 kg P ha⁻¹ yr⁻¹ (P), and NP) was set up to analyze the extracellular enzyme activities and stoichiometry characteristics of the top mineral soils in Chinese fir plantations with different stand ages (7, 20, and 33 years old). The results showed that the enzyme activities associated with the acquisition of C (β-1,4-glucosidase (BG) and β-d-cellobiohydrolase (CBH)) and P (acid phosphatases (APs)) in the N treatment were significantly higher than those in the CK treatment. Moreover, vector analysis revealed that both the vector’s length and angle increased in stands of all ages, which indicated that N addition aggravated microbial C and P limitations. The P and NP treatments both significantly decreased the activity of AP and the enzymes’ N:P ratio, thereby alleviating microbial P limitations, as revealed by the reduction in the vector’s angle. Stand age was found to promote all enzymatic activities but had no obvious effects on the limitation of microbial metabolism with or without added nutrients in the soils under Chinese fir. Available N, Olsen-P, and pH were the main drivers of microbial metabolic limitations related to C nutrients. These results provide useful data for understanding the change in soil microbial activity in response to environmental changes, and suggest that P fertilization should be considered for management to improve productivity and C sequestration in Chinese fir plantation in the context of increased deposition of N. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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16 pages, 2927 KiB

Open AccessArticle

Core Bacterial Taxa Determine Formation of Forage Yield in Fertilized Soil

by Xiangtao Wang, Ningning Zhao, Wencheng Li, Xin Pu, Peng Xu and Puchang Wang

Microorganisms 2024, 12(8), 1679; https://doi.org/10.3390/microorganisms12081679 - 15 Aug 2024

Viewed by 774

Abstract

Understanding the roles of core bacterial taxa in forage production is crucial for developing sustainable fertilization practices that enhance the soil bacteria and forage yield. This study aims to investigate the impact of different fertilization regimes on soil bacterial community structure and function, [...] Read more.

Understanding the roles of core bacterial taxa in forage production is crucial for developing sustainable fertilization practices that enhance the soil bacteria and forage yield. This study aims to investigate the impact of different fertilization regimes on soil bacterial community structure and function, with a particular focus on the role of core bacterial taxa in contributing to soil nutrient content and enhancing forage yield. Field experiments and high-throughput sequencing techniques were used to analyze the soil bacterial community structure and function under various fertilization regimes, including six treatments, control with no amendment (CK), double the standard rate of organic manure (T01), the standard rate of organic manure with nitrogen input equal to T04 (T02), half the standard rate of inorganic fertilizer plus half the standard rate of organic manure (T03), the standard rate of inorganic fertilizer reflecting local practice (T04), and double the standard rate of inorganic fertilizer (T05). The results demonstrated that organic manure treatments, particularly T01, significantly increased the forage yield and the diversity of core bacterial taxa. Core taxa from the Actinomycetota, Alphaproteobacteria, and Gammaproteobacteria classes were crucial in enhancing the soil nutrient content, directly correlating with forage yield. Fertilization significantly influenced functions relating to carbon and nitrogen cycling, with core taxa playing central roles. The diversity of core microbiota and soil nutrient levels were key determinants of forage yield variations across treatments. These findings underscore the critical role of core bacterial taxa in agroecosystem productivity and advocate for their consideration in fertilization strategies to optimize forage yield, supporting the shift towards sustainable agricultural practices. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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26 pages, 5132 KiB

Open AccessArticle

Microbial Diversity of Soil in a Mediterranean Biodiversity Hotspot: Parque Nacional La Campana, Chile

by Carolina Quinteros-Urquieta, Jean-Pierre Francois, Polette Aguilar-Muñoz, Roberto Orellana, Rodrigo Villaseñor, Andres Moreira-Muñoz and Verónica Molina

Microorganisms 2024, 12(8), 1569; https://doi.org/10.3390/microorganisms12081569 - 31 Jul 2024

Viewed by 965

Abstract

Parque Nacional La Campana (PNLC) is recognized worldwide for its flora and fauna, rather than for its microbial richness. Our goal was to characterize the structure and composition of microbial communities (bacteria, archaea and fungi) and their relationship with the plant communities typical [...] Read more.

Parque Nacional La Campana (PNLC) is recognized worldwide for its flora and fauna, rather than for its microbial richness. Our goal was to characterize the structure and composition of microbial communities (bacteria, archaea and fungi) and their relationship with the plant communities typical of PNLC, such as sclerophyllous forest, xerophytic shrubland, hygrophilous forest and dry sclerophyllous forest, distributed along topoclimatic variables, namely, exposure, elevation and slope. The plant ecosystems, the physical and chemical properties of organic matter and the soil microbial composition were characterized by massive sequencing (iTag-16S rRNA, V4 and ITS1-5F) from the DNA extracted from the soil surface (5 cm, n = 16). A contribution of environmental variables, particularly related to each location, is observed. Proteobacteria (35.43%), Actinobacteria (32.86%), Acidobacteria (10.07%), Ascomycota (76.11%) and Basidiomycota (15.62%) were the dominant phyla. The beta diversity (~80% in its axes) indicates that bacteria and archaea are linked to their plant categories, where the xerophytic shrub stands out with the most particular microbial community. More specifically, Crenarchaeote, Humicola and Mortierella were dominant in the sclerophyllous forest; Chloroflexi, Cyanobacteria and Alternaria in the xerophytic shrubland; Solicoccozyma in the dry sclerophyllous forest; and Cladophialophora in the hygrophilous forest. In conclusion, the structure and composition of the microbial consortia is characteristic of PNLC’s vegetation, related to its topoclimatic variables, which suggests a strong association within the soil microbiome. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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16 pages, 4487 KiB

Open AccessArticle

Effect of Plateau pika on Soil Microbial Assembly Process and Co-Occurrence Patterns in the Alpine Meadow Ecosystem

by Xiangtao Wang, Zhencheng Ye, Chao Zhang and Xuehong Wei

Microorganisms 2024, 12(6), 1075; https://doi.org/10.3390/microorganisms12061075 - 26 May 2024

Viewed by 755

Abstract

Burrowing animals are a critical driver of terrestrial ecosystem functioning, but we know little about their effects on soil microbiomes. Here, we evaluated the effect of burrowing animals on microbial assembly processes and co-occurrence patterns using soil microbiota from a group of habitats [...] Read more.

Burrowing animals are a critical driver of terrestrial ecosystem functioning, but we know little about their effects on soil microbiomes. Here, we evaluated the effect of burrowing animals on microbial assembly processes and co-occurrence patterns using soil microbiota from a group of habitats disturbed by Plateau pikas (Ochtona curzoniae). Pika disturbance had different impacts on bacterial and fungal communities. Fungal diversity generally increased with patch area, whereas bacterial diversity decreased. These strikingly different species–area relationships were closely associated with their community assembly mechanisms. The loss of bacterial diversity on larger patches was largely driven by deterministic processes, mainly due to the decline of nutrient supply (e.g., organic C, inorganic N). In contrast, fungal distribution was driven primarily by stochastic processes that dispersal limitation contributed to their higher fungal diversity on lager patches. A bacterial co-occurrence network exhibited a positive relationship of nodes and linkage numbers with patch area, and the fungal network presented a positive modularity–area relationship, suggesting that bacteria tended to form a closer association community under pika disturbance, while fungi tended to construct a higher modularity network. Our results suggest that pikas affects the microbial assembly process and co-occurrence patterns in alpine environments, thereby enhancing the current understanding of microbial biogeography under natural disturbances. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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15 pages, 12780 KiB

Open AccessArticle

Effect of Altitude Gradients on the Spatial Distribution Mechanism of Soil Bacteria in Temperate Deciduous Broad-Leaved Forests

by Wenxin Liu, Shengqian Guo, Huiping Zhang, Yun Chen, Yizhen Shao and Zhiliang Yuan

Microorganisms 2024, 12(6), 1034; https://doi.org/10.3390/microorganisms12061034 - 21 May 2024

Cited by 1 | Viewed by 1336

Abstract

Soil bacteria are an important part of the forest ecosystem, and they play a crucial role in driving energy flow and material circulation. Currently, many uncertainties remain about how the composition and distribution patterns of bacterial communities change along altitude gradients, especially in [...] Read more.

Soil bacteria are an important part of the forest ecosystem, and they play a crucial role in driving energy flow and material circulation. Currently, many uncertainties remain about how the composition and distribution patterns of bacterial communities change along altitude gradients, especially in forest ecosystems with strong altitude gradients in climate, vegetation, and soil properties. Based on dynamic site monitoring of the Baiyun Mountain Forest National Park (33°38′–33°42′ N, 111°47′–111°51′ E), this study used Illumina technology to sequence 120 soil samples at the site and explored the spatial distribution mechanisms and ecological processes of soil bacteria under different altitude gradients. Our results showed that the composition of soil bacterial communities varied significantly between different altitude gradients, affecting soil bacterial community building by influencing the balance between deterministic and stochastic processes; in addition, bacterial communities exhibited broader ecological niche widths and a greater degree of stochasticity under low-altitude conditions, implying that, at lower altitudes, community assembly is predominantly influenced by stochastic processes. Light was the dominant environmental factor that influenced variation in the entire bacterial community as well as other taxa across different altitude gradients. Moreover, changes in the altitude gradient could cause significant differences in the diversity and community composition of bacterial taxa. Our study revealed significant differences in bacterial community composition in the soil under different altitude gradients. The bacterial communities at low elevation gradients were mainly controlled by stochasticity processes, and bacterial community assembly was strongly influenced by deterministic processes at middle altitudes. Furthermore, light was an important environmental factor that affects differences. This study revealed that the change of altitude gradient had an important effect on the development of the soil bacterial community and provided a theoretical basis for the sustainable development and management of soil bacteria. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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20 pages, 4848 KiB

Open AccessArticle

Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics

by Rui Li, Haihua Jiao, Bo Sun, Manjiao Song, Gaojun Yan, Zhihui Bai, Jiancheng Wang, Xuliang Zhuang and Qing Hu

Microorganisms 2024, 12(4), 683; https://doi.org/10.3390/microorganisms12040683 - 28 Mar 2024

Viewed by 1666

Abstract

Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the [...] Read more.

Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity’s critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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12 pages, 5463 KiB

Open AccessArticle

Comparison of Microbial Diversity of Two Typical Volcanic Soils in Wudalianchi, China

by Qingyang Huang, Fan Yang, Hongjie Cao, Jiahui Cheng, Mingyue Jiang, Maihe Li, Hongwei Ni and Lihong Xie

Microorganisms 2024, 12(4), 656; https://doi.org/10.3390/microorganisms12040656 - 26 Mar 2024

Cited by 2 | Viewed by 1378

Abstract

Volcanic lava is an excellent model of primary succession, in which basalt-associated microorganisms drive the cycling of different elements such as nitrogen, carbon, and other nutrients. Microbial communities in volcanic soils are of particular interest for study on the emergence and evolution of [...] Read more.

Volcanic lava is an excellent model of primary succession, in which basalt-associated microorganisms drive the cycling of different elements such as nitrogen, carbon, and other nutrients. Microbial communities in volcanic soils are of particular interest for study on the emergence and evolution of life within special and extreme conditions. The initial processes of colonization and subsequent rock weathering by microbial communities are still poorly understood. We analyzed the soil bacterial and fungal communities and diversities associated with lava (LBL) and kipuka (BK) sites in Wudalianchi using 16S and ITS rRNA Illumina Miseq sequencing techniques. The results showed that soil physical and chemical properties (pH, MC, TOC, TN, TP, AP, DOC, and DON) significantly differed between LBL and BK. The Shannon, Ace, and Pd indexes of fungi in the two sites showed a significant difference (p < 0.05). The dominant bacterial phyla forming communities at LBL and BK sites were Acidobacteria, Proteobacteria, Actinobacteria, and Basidiomycota, and their differences were driven by Gemmatimonadetes and Verrucomicrobia. The dominant fungal phyla of LBL and BK sites were Ascomycota, Zygomycota, and Rozellomcota, which differed significantly between the two sites. The microbial communities showed extremely significant differences (p < 0.05), with MC, pH, and nitrogen being the main influencing factors according to RDA/CCA and correlation analysis. Microbial functional prediction analysis across the two sites showed that the relative abundance of advantageous functional groups was significantly different (p < 0.05). The combined results drive us to conclude that the volcanic soil differences in the deposits appear to be the main factor shaping the microbial communities in Wudalianchi (WDLC) volcanic ecosystems. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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17 pages, 4616 KiB

Open AccessArticle

Nitrogen Application and Rhizosphere Effect Exert Opposite Effects on Key Straw-Decomposing Microorganisms in Straw-Amended Soil

by Yuanzheng Zhao, Shiyu Wang, Meiling Zhang, Li Zeng, Liyu Zhang, Shuyu Huang, Rong Zhang, Wei Zhou and Chao Ai

Microorganisms 2024, 12(3), 574; https://doi.org/10.3390/microorganisms12030574 - 13 Mar 2024

Viewed by 1450

Abstract

Crop residue decomposition is an important part of the carbon cycle in agricultural ecosystems, and microorganisms are widely recognized as key drivers during this process. However, we still know little about how nitrogen (N) input and rhizosphere effects from the next planting season [...] Read more.

Crop residue decomposition is an important part of the carbon cycle in agricultural ecosystems, and microorganisms are widely recognized as key drivers during this process. However, we still know little about how nitrogen (N) input and rhizosphere effects from the next planting season impact key straw-decomposing microbial communities. Here, we combined amplicon sequencing and DNA-Stable Isotope Probing (DNA-SIP) to explore these effects through a time-series wheat pot experiment with four treatments: ¹³C-labeled maize straw addition with or without N application (S1N1 and S1N0), and no straw addition with or without N application (S0N1 and S0N0). The results showed that straw addition significantly reduced soil microbial alpha diversity in the early stages. Straw addition changed microbial beta diversity and increased absolute abundance in all stages. Growing plants in straw-amended soil further reduced bacterial alpha diversity, weakened straw-induced changes in beta diversity, and reduced bacterial and fungal absolute abundance in later stages. In contrast, N application could only increase the absolute abundance of soil bacteria and fungi while having little effect on alpha and beta diversity. The SIP-based taxonomic analysis of key straw-decomposing bacteria further indicated that the dominant phyla were Actinobacteria and Proteobacteria, with overrepresented genera belonging to Vicinamibacteraceae and Streptomyces. Key straw-decomposing fungi were dominated by Ascomycota, with overrepresented genera belonging to Penicillium and Aspergillus. N application significantly increased the absolute abundance of key straw-decomposing microorganisms; however, this increase was reduced by the rhizosphere effect. Overall, our study identified key straw-decomposing microorganisms in straw-amended soil and demonstrated that they exhibited opposite responses to N application and the rhizosphere effect. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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31 pages, 10999 KiB

Open AccessArticle

The Molecular Profile of Soil Microbial Communities Inhabiting a Cambrian Host Rock

by Ting Huang, Daniel Carrizo, Laura Sánchez-García, Qitao Hu, Angélica Anglés, David Gómez-Ortiz, Liang-Liang Yu and David C. Fernández-Remolar

Microorganisms 2024, 12(3), 513; https://doi.org/10.3390/microorganisms12030513 - 2 Mar 2024

Viewed by 1607

Abstract

The process of soil genesis unfolds as pioneering microbial communities colonize mineral substrates, enriching them with biomolecules released from bedrock. The resultant intricate surface units emerge from a complex interplay among microbiota and plant communities. Under these conditions, host rocks undergo initial weathering [...] Read more.

The process of soil genesis unfolds as pioneering microbial communities colonize mineral substrates, enriching them with biomolecules released from bedrock. The resultant intricate surface units emerge from a complex interplay among microbiota and plant communities. Under these conditions, host rocks undergo initial weathering through microbial activity, rendering them far from pristine and challenging the quest for biomarkers in ancient sedimentary rocks. In addressing this challenge, a comprehensive analysis utilizing Gas Chromatography Mass Spectrometry (GC-MS) and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) was conducted on a 520-Ma-old Cambrian rock. This investigation revealed a diverse molecular assemblage with comprising alkanols, sterols, fatty acids, glycerolipids, wax esters, and nitrogen-bearing compounds. Notably, elevated levels of bacterial C₁₆, C₁₈ and C₁₄ fatty acids, iso and anteiso methyl-branched fatty acids, as well as fungal sterols, long-chained fatty acids, and alcohols, consistently align with a consortium of bacteria and fungi accessing complex organic matter within a soil-type ecosystem. The prominence of bacterial and fungal lipids alongside maturity indicators denotes derivation from heterotrophic activity rather than ancient preservation or marine sources. Moreover, the identification of long-chain (>C22) n-alkanols, even-carbon-numbered long chain (>C20) fatty acids, and campesterol, as well as stigmastanol, provides confirmation of plant residue inputs. Furthermore, findings highlight the ability of contemporary soil microbiota to inhabit rocky substrates actively, requiring strict contamination controls when evaluating ancient molecular biosignatures or extraterrestrial materials collected. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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15 pages, 31140 KiB

Open AccessArticle

The Characteristics of the Root-Zone Soil’s Biological Properties and Microbial Community Structure in Grafted Star Anise Plantations

by Jian Xiao, Junxian Liu, Siyu Wu, Wenhui Liang and Shangdong Yang

Microorganisms 2024, 12(3), 431; https://doi.org/10.3390/microorganisms12030431 - 20 Feb 2024

Viewed by 1294

Abstract

Extensive management seriously affects the output, quality, and sustainable development of star anise, and grafting is commonly used to improve its production and quality. Although many studies have explored the effects of grafting on soil microorganisms for other plants, there is a lack [...] Read more.

Extensive management seriously affects the output, quality, and sustainable development of star anise, and grafting is commonly used to improve its production and quality. Although many studies have explored the effects of grafting on soil microorganisms for other plants, there is a lack of research on aromatic plants, especially on the soil ecosystems of star anise plantations. The effect of grafting star anise on the soil’s biological characteristics and microbial composition remains unclear. The soil’s enzyme activities, soil microbial biomass, and microbial community composition in grafted and non-grafted star anise plantations in Guangxi, China were studied using high-throughput sequencing technology. The results showed that the microbial biomass carbon and phosphorus contents in the soils of grafted star anise were significantly lower and the phosphatase activity was significantly higher than in the soils of non-grafted star anise. In comparison with the soils of non-grafted star anise plantations, the proportions of Proteobacteria, Acidobacteria, Actinobacteria, and WPS-2 decreased and the proportions of Chloroflexi, Planctomycetes, and Verrucomicrobia increased in the grafted star anise plantations. Meanwhile, Bacteroidetes was a dominant bacterial phylum unique to the soil of the grafted star anise plantations. Moreover, the proportions of Ascomycota and Basidiomycota increased and the proportions of Mortierellomycota and unclassified_k_Fungi decreased in the soils of the grafted star anise plantations. Furthermore, Basidiomycota and Rozellomycota had significant dominance in the grafted star anise plantations. In general, grafting can improve soil fertility and maintain soil health by promoting soil nutrient cycling and increasing the soil’s microbial diversity. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology)

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