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Diversity, Function, and Ecology of Soil Microbial Communities

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (30 November 2025) | Viewed by 5745

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Prof. Dr. Adijailton José de Souza

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Program of Agricultural Microbiology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
Interests: agronomy; soil microbiology; pesticide environmental behavior; microbial ecology; composing; plant growth-promoting bacteria; biological control; sewage treatment and agricultural use; regenerative agriculture; biological nitrogen fixation; pesticide biod
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Dear Colleagues,

Soil microbial communities are fundamental to ecosystem functioning, driving key processes such as nutrient cycling, organic matter decomposition, and plant health. Their diversity reflects a complex interplay of biotic and abiotic factors, including soil type, climate, vegetation, and land use. Recent advances in molecular and metagenomic techniques have revealed extraordinary taxonomic and functional diversity within these communities, uncovering new microbial taxa and metabolic pathways. This diversity supports critical ecological functions, from nitrogen fixation to carbon sequestration, and mediates soil resilience to environmental stressors. Understanding structure–function relationships in soil microbiomes is essential for predicting ecosystem responses to global climate change and for developing sustainable agricultural practices. This Special Issue highlights current research on the composition, functional roles, and ecological interactions of soil microorganisms, emphasizing their importance in maintaining soil health, stability and resilience of agroecosystems to ensure food security and sustainability. The scope of this Special Issue covers research on soil microbiome, land use change and its impact on soil health; advances in biotechnology to promote soil and plant health; responses of the soil microbiome to input of synthetic microbial communities, and microbial ecology.

Prof. Dr. Adijailton José de Souza
Guest Editor

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Keywords

soil microbial communities
metabolic pathways
ecological functions
agroecosystems

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Published Papers (9 papers)

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Research

13 pages, 3861 KB

Open AccessArticle

Fungal Diversity Drives Non-Linear Trajectories of Soil Multifunctionality During Alpine Grassland Restoration

by Minghui Meng, Jiakai Shi, Sha Zhou, Danni Peng, Yihan Fu, Mengmeng Wen, Jun Wang and Fazhu Zhao

Microorganisms 2026, 14(3), 562; https://doi.org/10.3390/microorganisms14030562 - 1 Mar 2026

Viewed by 317

Abstract

Despite the widely recognized importance of grassland restoration for soil multifunctionality (SMF), its temporal dynamics along the restoration chronosequence and the relative contributions of bacterial and fungal diversity to SMF remain poorly understood, particularly in alpine grasslands. Here, we examined SMF along an alpine grassland restoration chronosequence (1, 5, 7, 13, and 20 years) on the Qinghai–Tibet Plateau. We found that SMF exhibited a pronounced non-linear trajectory, increasing by 39.13% from year 1 to year 7, subsequently declining by 50% and 46.88% at years 13 and 20, respectively, relative to the peak at year 7. Fungal richness varied markedly across the restoration chronosequence, peaking in year 5 with a 16.03% increase relative to year 1, and was positively associated with SMF, whereas bacterial richness showed no significant relationship. Structural equation modeling further confirmed that, along with soil moisture, fungal richness was significantly associated with SMF. Together, our findings highlight fungal diversity as a key driver of SMF during alpine grassland restoration and improve process-based predictions of alpine grassland functioning under ongoing climate change. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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17 pages, 2663 KB

Open AccessArticle

Morphology and Molecular Phylogeny of Two Soil Ciliate Species (Protozoa, Ciliophora) from the Changbai Mountain Region, China, Including a New Species

by Yuxuan Wang, Yunhan Wang, Huan Li, Sitong Li and Xuming Pan

Microorganisms 2026, 14(3), 559; https://doi.org/10.3390/microorganisms14030559 - 28 Feb 2026

Viewed by 318

Abstract

Soil ciliates are an important component of the soil micro-food web, playing key roles in organic matter decomposition and nutrient cycling. However, research on the species diversity and taxonomy of this group in the temperate forest soils of China is still limited. This study investigates the morphology and ciliary pattern of two ciliate species discovered in the Changbai Mountain region of northeastern China: Bryometopus changbaishanensis sp. n. and Apocolpodidium etoschense Foissner et al., 2002, using live observation and silver carbonate impregnation. B. changbaishanensis sp. n. is characterized by the following morphological features: size in vivo approximately 40–48 × 20–29 μm, 11–14 somatic kineties; the paroral membrane consists of about 16–26 dikinetids; and there are 11–15 oral membranelles. This species differs from B. atypicus in its smaller body size in vivo, fewer somatic kineties, and fewer oral membranelles. Apocolpodidium etoschense Foissner et al., 2002, exhibits the following morphological features: in vivo size approximately 48–85 × 19–35 μm, 16–20 somatic kineties, and a gently curved paroral membrane composed of about 13–20 dikinetids; its hypostomial organelle consists of three to five files, each containing approximately three to five monokinetids. Additionally, DNA extraction and SSU rRNA gene sequencing were performed to elucidate their evolutionary relationships. Phylogenetic analyses based on SSU rRNA gene data indicated that Bryometopus changbaishanensis sp. n. clusters with B. atypicus. This study also provides a redescription and supplementary definition of A. etoschense, with the Changbai Mountain population forming a fully supported cluster with previously sequenced data. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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28 pages, 10753 KB

Open AccessArticle

Response of Soil Microbial Communities to Karst Desertification in Soil and Water Conservation Agroforestry Systems

by Wanmei Hu, Kangning Xiong, Anjun Lan, Min Zhang, Liheng You, Jifeng Zhang and Zhenquan Zhong

Microorganisms 2026, 14(3), 556; https://doi.org/10.3390/microorganisms14030556 - 28 Feb 2026

Viewed by 275

Abstract

Karst desertification (KD) severely constrains regional ecological security and sustainable development. As an important ecological restoration measure, soil and water conservation agroforestry (SWCAF) systems have unclear mechanisms for soil microbial responses. This study investigated the effects of potential–light (PL), light–moderate (LM), and moderate–high (MH) KD on soil physicochemical properties and microbial communities in Karst SWCAF (KSWCAF) systems. It explored the drivers of microbial community changes. The results showed that (1) Soil physicochemical properties exhibited nonlinear changes along the KD gradient. Key soil-fertility indicators including silt, clay, total porosity (TP), total phosphorus (Total_P), total nitrogen (Total_N), soil organic carbon (SOC), and carbon nitrogen ratio (C_N) showed significant unimodal patterns, peaking at the LM stage with optimal overall soil quality; (2) The dominant bacterial phyla were Pseudomonadota, Acidobacteriota, Actinomycetota, and Planctomycetota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. The overall abundance of these dominant phyla increased with intensifying KD, except that the relative abundance of Pseudomonadota was lowest in the QZ study area, while Acidobacteriota was highest in the QZ area. The dominant fungal phylum Ascomycota increased with KD intensification; (3) KD significantly influenced microbial community structure and beta diversity. Fungi showed stronger responses to the KD gradient than bacteria. Bacterial alpha diversity was significantly higher in the LM stage compared to the PL and MH stages (p < 0.05), while fungal alpha diversity was significantly lowest in the MH stage (p < 0.05); (4) Bacterial networks exhibited highest complexity but reduced stability at the LM stage, whereas fungal networks enhanced stability at the MH stage by increasing modularization and positive correlation proportions; (5) RDA revealed that soil physicochemical factors explained 66.89% and 98.82% of bacterial and fungal community variation, respectively, with pH, moisture, and C_N as key drivers. Overall, KD regulates microbial community structure and functional allocation by reshaping the soil environmental gradient, with the LM stage potentially representing a “transitional optimization window” for KSWCAF ecosystem structure and function. This study provides a theoretical basis for microbial regulation strategies in KD control and soil and water conservation (SWC) processes. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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18 pages, 4918 KB

Open AccessArticle

Synthetic Microbial Communities Enhance Artificial Cyanobacterial Crusts Formation via Spatiotemporal Synergy

by Qi Li, Pingting Zhu, Guoxia Tian, Qingliang Cui, Pengyu Zhang, Lingyan Dong, Chensi Min and Linchuan Fang

Microorganisms 2026, 14(1), 243; https://doi.org/10.3390/microorganisms14010243 - 21 Jan 2026

Viewed by 573

Abstract

Artificial cyanobacterial crusts (ACCs) are a potentially effective biological strategy for combating desertification. However, while functional microorganisms influence ACCs formation efficiency, research on their role is limited, and their underlying promotion mechanisms remain unclear. Here, we investigated the effects of three functional synthetic microbial communities (SynComs), each dominated by microorganisms specialized in exopolysaccharide (EPS) production (3 strains), siderophore production (3 strains), or nitrogen fixation (4 strains), on ACCs formation following inoculation with Microcoleus vaginatus. This study was carried out in a controlled laboratory setting with a 12 h light/dark cycle and a light intensity of 2400–2700 lux. Following a 24-day cultivation period, EPS-producing or nitrogen-fixing SynComs significantly increased the chlorophyll-a content by 16.0–16.3%. Except for the nitrogen-fixing bacteria treatment, other SynComs enhanced the soil organic matter content of ACCs by 9.1% to 27.3%. The content of EPS was significantly improved by all three SynComs by 14.1~19.2%. Urease activity rose by 6.7% when siderophore-producing bacteria were added. The impacts of SynComs on ammonium nitrogen (NH₄⁺-N) showed different temporal dynamics: nitrogen-fixing SynComs significantly increased NH₄⁺-N early (≤10 days), while EPS-producing and siderophore-producing SynComs enhanced accumulation later (17–24 days). SynComs inoculation markedly accelerated cyanobacterial and general microbial colonization and growth. In comparison to day 0, the 16S rRNA gene copy number of ACCs increased by 24.1% and 43.0%, respectively, in the EPS-producing and nitrogen-fixing SynComs. Additionally, correlation analysis showed that SynComs transformed the weak correlations in the control into a strong positive correlation between NH₄⁺-N and both Chl-a and microbial biomass. Our findings demonstrate SynComs, particularly the EPS-producing or nitrogen-fixing SynComs, enhance ACCs formation through elucidated mechanisms, providing a theoretical basis for optimizing ACCs-based desertification control strategies. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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16 pages, 12627 KB

Open AccessArticle

Forest Type Shapes Soil Microbial Carbon Metabolism: A Metagenomic Study of Subtropical Forests on Lushan Mountain

by Dan Xi, Feifei Zhu, Zhaochen Zhang, Saixia Zhou and Jiaxin Zhang

Microorganisms 2026, 14(1), 220; https://doi.org/10.3390/microorganisms14010220 - 17 Jan 2026

Viewed by 481

Abstract

Forest type strongly influences soil microbial community composition and associated carbon cycling, yet its influence on microbial functional traits remains poorly understood. In this study, metagenomics sequencing was used to investigate soil microbial communities and carbon metabolism genes across three forest types: deciduous broadleaf (DBF), mixed coniferous–broadleaf (CBMF), and coniferous forest (CF) at two soil depths (0–20 cm and 20–40 cm) on Lushan Mountain in subtropical China. The results showed that CF exhibited higher bacterial diversity and a distinct microbial composition, with an increase in Actinomycetota and Bacteroidota and a decrease in Acidobacteriota and Pseudomonadota. The Calvin cycle was the dominant carbon fixation pathway in all forests, while the relative abundance of secondary pathways (i.e., the 3-hydroxypropionate bi-cycle and reductive citrate cycle) varied significantly with forest type. Key carbon fixation genes (sucD, pckA) were more abundant in CF and CBMF, with higher levels of rpiA/B and ackA in DBF. Functional profiling further indicated that CF soils, especially in the surface layer, were enriched in glycoside hydrolases (GHs) and carbohydrate esterases (CEs), while CBMF showed a greater potential for starch and lignin degradation. Multivariate statistical analyses identified soil available phosphorus (AP) and pH as primary factors shaping microbial community variation, with AP emerging as being the dominant regulator of carbon-related functional gene abundance. Overall, the prevalence of these distinct genetic potentials across forest types underscores how vegetation composition may shape microbial functional traits, thereby influencing the stability and dynamics of the soil carbon pool in forest ecosystem. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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21 pages, 1897 KB

Open AccessArticle

Predicted Bacterial Metabolic Landscapes of the Sumaco Volcano: A Picrust2 Analysis of 16S rRNA Data from Amazonian Ecuador

by Pablo Jarrín-V, Julio C. Carrión-Olmedo, Pamela Loján, Daniela Reyes-Barriga, María Lara, Andrés Oña, Cristian Quiroz-Moreno, Pablo Castillejo, Gabriela N. Tenea, Magdalena Díaz, Pablo Monfort-Lanzas and C. Alfonso Molina

Microorganisms 2026, 14(1), 94; https://doi.org/10.3390/microorganisms14010094 - 1 Jan 2026

Viewed by 854

Abstract

The Sumaco volcano in Ecuador, which has a distinct geological origin from the Andes and is located in the Amazon basin, offers an opportunity to study untouched microbiomes. We explored comparative patterns of abundance from predicted functional profiling in soil samples collected along the elevation and sulfur gradients on its slopes. Using 16S rRNA gene metabarcoding, we inferred metagenome functional profiles, contrasting sample groups by altitude or soil sulfur concentration. We inferred that high-altitude communities may have higher predicted abundance for anaerobic metabolism (crotonate fermentation), coenzyme B12 synthesis, and degradation of diverse carbon sources (sugars and octane). High-sulfur soils were associated with an inferred enrichment of pathways for degrading complex organic compounds and nitrogen metabolism, reflecting adaptation to unique geochemical conditions. In contrast, low-sulfur soils are consistent with a higher predicted abundance of glycerol degradation. Within the limitation imposed by the potential weak associations of the applied predicted functional profiling to actual gene content, we propose that the inferred metabolic changes represent different ecological strategies for resource acquisition, energy generation, and stress tolerance, and they are optimized for varying conditions in this unique volcanic ecosystem. Our findings highlight how environmental gradients shape soil microbiome functional diversity and offer insights into microbial adaptation in Sumaco’s exceptional geochemistry within the Amazon. Further efforts linking functional predictions back to specific taxa will offer a complete ecological perspective of the microbiome exploration in the Sumaco volcano. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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25 pages, 6146 KB

Open AccessArticle

Evaluation of Soil Amelioration Effects of Different Afforestation Measures in Alpine Sandy Land: A Case Study of the Gonghe Basin

by Shaobo Du, Huichun Xie, Gaosen Zhang, Feng Qiao, Tianyue Zhao, Guigong Geng and Chongyi E

Microorganisms 2025, 13(12), 2860; https://doi.org/10.3390/microorganisms13122860 - 16 Dec 2025

Viewed by 430

Abstract

Desertification poses a severe challenge in China. Although long-term sand control measures have proven effective, the extensive and challenging nature of sandy land necessitates systematic research to identify optimal sand control measures for soil amelioration, thereby promoting ecological restoration in sandy areas. This study focused on the Gonghe Basin to assess the effectiveness of four 24-year afforestation treatments—Salix cheilophila + Populus simonii, S. cheilophila, P. simonii (YY), and Caragana korshinskii—compared to untreated mobile dunes. Surface soils (0–10 cm and 10–20 cm) were analyzed for physicochemical properties, enzyme activities, and bacterial community structure using Illumina high-throughput sequencing and PICRUSt2 functional prediction. All afforestation treatments significantly improved soil quality, increasing fine particle content, moisture, nutrients, enzyme activity, and microbial richness and diversity, especially in the topsoil. Bulk density and pH were notably reduced. Among the treatments, YY demonstrated the most substantial improvements. pH emerged as the primary factor influencing bacterial community structure, with enzyme activities also playing a significant role. Metabolism was the dominant functional category across all sites, while YY enhanced environmental information processing functions in the topsoil. Secondary functions showed high redundancy across treatments. These findings confirm that afforestation can effectively rehabilitate degraded alpine sandy soils, with the YY treatment offering the greatest benefits. The study provides a scientific basis for optimizing sand control measures and supports broader ecological restoration efforts in similar environments worldwide. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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18 pages, 2194 KB

Open AccessArticle

Driving Effects of Soil Microbial Diversity on Soil Multifunctionality in Carya illinoinensis Agroforestry Systems

by Cheng Huang, Mengyu Zhou, Fasih Ullah Haider, Lin Wu, Jia Xiong, Songling Fu, Zhaocheng Wang, Fan Yang and Xu Li

Microorganisms 2025, 13(11), 2425; https://doi.org/10.3390/microorganisms13112425 - 23 Oct 2025

Viewed by 893

Abstract

Sustainable soil management requires striking a balance between productivity and soil health. While agroforestry practices are known to improve soil health and ecosystem functions, the contribution of microbial diversity to maintaining multifunctional soil processes in pecan (Carya illinoinensis) cultivation has yet to be fully elucidated. This study examined microbial diversity, soil functions, and multifunctionality across different pecan intercropping setups. We compared a monoculture pecan plantation with three agroforestry models: pecan–Paeonia suffruticosa–Hemerocallis citrina (CPH), pecan–P. suffruticosa (CPS), and pecan–P. lactiflora (CPL). We employed high-throughput sequencing (16S and ITS) to determine the soil bacterial and fungal communities and analyzed the species diversity, extracellular enzyme activities, and physicochemical properties. Soil multifunctionality (SMF) was evaluated using 20 indicators for nutrient supply, storage, cycling, and environmental regulation. Agroforestry increased soil fungal diversity and improved multifunctionality when compared to monoculture. The CPS and CPH models were the most beneficial, increasing multifunctionality by 0.74 and 0.55 units, respectively. Structural equation modeling revealed two key pathways: bacterial diversity significantly enhanced nutrient cycling and environmental regulation, whereas fungal diversity primarily promoted nutrient cycling. These pathways together delivered clear gains in multifunctionality. Random forest analysis identified key predictors (total nitrogen, total carbon, available potassium, β-1,4-N-acetylglucosaminidase, and alkaline phosphatase), highlighting the joint importance of nutrients and microbial enzymes. Our results demonstrate that selecting species in pecan agroforestry alters microbial communities and activates key functions that support soil health and long-term resilience. Hence, pecan agroforestry maintains SMF through microbial processes, with CPS showing the strongest effect. These results can inform species selection and encourage broader testing for resilient, biodiversity-based farming practices. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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19 pages, 2329 KB

Open AccessArticle

Linking Soil Microbial Diversity to Nitrogen and Phosphorus Dynamics

by Bruna Arruda, Eduardo Mariano, Wilfrand Ferney Bejarano-Herrera, Fábio Prataviera, Elizabeth Mie Hashimoto, Fernando Ferrari Putti, Jéssica Pigatto de Queiroz Barcelos, Paulo Sergio Pavinato, Fernando Dini Andreote and Davey L. Jones

Microorganisms 2025, 13(10), 2401; https://doi.org/10.3390/microorganisms13102401 - 21 Oct 2025

Viewed by 1027

Abstract

Changes in the soil microbial community for studies of different novel communities can be promoted by different methodologies, among which soil autoclaving stands out as a quick and readily available tool. However, this procedure may also directly or indirectly alter nitrogen (N) and phosphorus (P) dynamics. The purposes of this study were as follows: (i) to characterize microbial activity after soil autoclaving through microbial ¹⁴CO₂-respiration; and (ii) to evaluate the effect of microbial manipulation and autoclaving on soil N and ³³P dynamics. For this, two sets of soil samples from two areas (forest and cultivated area) were used in the laboratory. Firstly, ¹⁴C-glucose was added to the soils and after 24 h five soil microbiomes were generated: AS (autoclaved soil), and AS re-inoculated with serial dilutions (w/v) prepared by successive mixing of soil suspensions in sterile deionized water obtaining 10⁻¹, 10⁻³, and 10⁻⁶, which generated the treatments AS + 10⁻¹, AS + 10⁻³, and AS + 10⁻⁶; and the treatment NS (non-autoclaved control), all incubated for 28 d. ¹⁴CO₂ emission was used to characterize microbial activity; additionally, N dynamics were assessed at the end of incubation. In a second assay, ³³P was applied to the soil before autoclaving and re-inoculation. Following further incubation (14 d), a ³³P chemical fractionation was performed. The following are based on the results: (i) ¹⁴CO₂ emission: microbial activity in the autoclaved soil is null, but after a reinoculation of AS + 10⁻¹ and AS + 10⁻³ soil dilution suspension, the ¹⁴CO₂-respiration is higher than in an NS. (ii) regarding the N dynamics, in autoclaved soils, the microbial levels increased N-NH₄⁺ concentration, with an evident increase in the AS + 10⁻³ and AS + 10⁻¹, and a reduction in the N-NO₃⁻ concentration in comparison to the NS. For ³³P, the autoclaving procedure itself reduced the ³³P lability, regardless of the levels of microbial community reinoculated. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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