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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 April 2024) | Viewed by 21127

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Prof. Dr. Acacio Aparecido Navarrete

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Graduate Program in Environmental Sciences, Universidade Brasil, Estrada Projetada F1, Fernandópolis 15613-899, SP, Brazil
Interests: soil microbial ecology; microbial indicators for soil quality; functional and taxonomical soil microbial diversity; microbial interactions
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Dear Colleagues,

Microorganisms are constantly faced with environmental stimuli and stresses. Some of the major environmental issues that are causing concern are land-use changes, climate change, anthropic and natural disturbances, pollution, built environments, etc. Climate change, as well as changes in land use and urbanization, are affecting soil microbial community structure, composition, diversity and function. The complex ecology of soil microbes support a better understanding of the multi-functionality of soils. In this respect, the importance of developing microbiological indicators for the monitoring of soil quality has been emphasized, in order to establish an early-warning bioindicator of potential losses of the multi-functionality of soils faced with environmental changes. Therefore, studies focusing on soil microbial communities and their relationships with key environmental factors constitute important research not only to reveal the effects of environmental changes, but also to identify microbial indicators to monitor such changes in the soil environment from agricultural, urban and natural landscapes.

The aim of this Special Issue is to provide an adequate collection of recent articles (both basic and applied research) that contributes to our understanding of the effects of environmental changes on soil microbial communities.

As a Guest Editor of the Special Issue, I invite you to submit research articles, review articles, and short communications related to soil microbial communities faced with land-use changes, climate change, anthropic and natural disturbances, pollution, built environments, etc.

Prof. Dr. Acacio Aparecido Navarrete
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

land use changes
climate change
pollution
microbiome of the built environment
anthropic and natural disturbances
microbial indicators for soil quality

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Published Papers (10 papers)

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Research

18 pages, 4022 KiB

Open AccessArticle

Microbial Community Shifts in Tea Plant Rhizosphere under Seawater Stress: Enrichment of Beneficial Taxa

by Xiaohua Zhang, Haozhen Li, Bin Li, Kangkang Song, Yuxue Sha, Ying Liu, Shaolin Dong, Di Wang and Long Yang

Microorganisms 2024, 12(7), 1287; https://doi.org/10.3390/microorganisms12071287 - 25 Jun 2024

Viewed by 1356

Abstract

Seawater intrusion has a significant impact on the irrigation quality of agricultural water, thereby posing a threat to plant growth and development. We hypothesized that the rhizosphere of tea plants harbors beneficial microorganisms, which may improve the tolerance of tea plants to seawater stress. This study utilized 16s and ITS techniques to analyze microbial community shifts in the tea plant rhizosphere and non-rhizosphere under seawater stress conditions. The findings suggest that seawater stress leads to a reduction in microbial diversity, although the rhizosphere microbial diversity in stressed soils showed a relatively higher level. Moreover, the rhizosphere of the tea plant under seawater stress exhibited an enrichment of plant growth-promoting rhizobacteria alongside a higher presence of pathogenic fungi. Network analysis revealed that seawater stress resulted in the construction of a more complex and stable rhizosphere microbial network compared to normal conditions. Predictions of bacterial potential functions highlighted a greater diversity of functional groups, enhancing resource utilization efficiency. In general, the rhizosphere microorganisms of tea plants are jointly selected by seawater and the host. The microorganisms closely related to the rhizosphere of tea plants are retained and, at the same time, attract beneficial microorganisms that may alleviate stress. These findings provide new insights into plant responses to saline stress and have significant implications for leveraging vegetation to enhance the resilience of coastal saline soils and contribute to economic progress. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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16 pages, 1998 KiB

Open AccessArticle

Vermicompost Supply Enhances Fragrant-Rice Yield by Improving Soil Fertility and Eukaryotic Microbial Community Composition under Environmental Stress Conditions

by Anas Iqbal, Quaid Hussain, Zhaowen Mo, Tian Hua, Abd El-Zaher M. A. Mustafa and Xiangru Tang

Microorganisms 2024, 12(6), 1252; https://doi.org/10.3390/microorganisms12061252 - 20 Jun 2024

Cited by 5 | Viewed by 1354

Abstract

Heavy-metal contamination in agricultural soil, particularly of cadmium (Cd), poses serious threats to soil biodiversity, rice production, and food safety. Soil microbes improve soil fertility by regulating soil organic matter production, plant nutrient accumulation, and pollutant transformation. Addressing the impact of Cd toxicity on soil fungal community composition, soil health, and rice yield is urgently required for sustainable rice production. Vermicompost (VC) is an organic fertilizer that alleviates the toxic effects of Cd on soil microbial biodiversity and functionality and improves crop productivity sustainably. In the present study, we examined the effects of different doses of VC (i.e., 0, 3, and 6 tons ha⁻¹) and levels of Cd stress (i.e., 0 and 25 mg Cd kg⁻¹) on soil biochemical attributes, soil fungal community composition, and fragrant-rice grain yield. The results showed that the Cd toxicity significantly reduced soil fertility, eukaryotic microbial community composition and rice grain yield. However, the VC addition alleviated the Cd toxicity and significantly improved the soil fungal community; additionally, it enhanced the relative abundance of Ascomycota, Chlorophyta, Ciliophora, Basidiomycota, and Glomeromycta in Cd-contaminated soils. Moreover, the VC addition enhanced the soil’s chemical attributes, including soil pH, soil organic carbon (SOC), available nitrogen (AN), total nitrogen (TN), and microbial biomass C and N, compared to non-VC treated soil under Cd toxicity conditions. Similarly, the VC application significantly increased rice grain yield and decreased the Cd uptake in rice. One possible explanation for the reduced Cd uptake in plants is that VC amendments influence the soil’s biological properties, which ultimately reduces soil Cd bioavailability and subsequently influences the Cd uptake and accumulation in rice plants. RDA analysis determined that the leading fungal species were highly related to soil environmental attributes and microbial biomass C and N production. However, the relative abundance levels of Ascomycota, Basidiomycota, and Glomeromycta were strongly associated with soil environmental variables. Thus, the outcomes of this study reveal that the use of VC in Cd-contaminated soils could be useful for sustainable rice production and safe utilization of Cd-polluted soil. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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18 pages, 3633 KiB

Open AccessArticle

Spatial Distribution Patterns and Assembly Processes of Abundant and Rare Fungal Communities in Pinus sylvestris var. mongolica Forests

by Reyila Mumin, Dan-Dan Wang, Wen Zhao, Kai-Chuan Huang, Jun-Ning Li, Yi-Fei Sun and Bao-Kai Cui

Microorganisms 2024, 12(5), 977; https://doi.org/10.3390/microorganisms12050977 - 13 May 2024

Viewed by 1200

Abstract

Revealing the biogeography and community assembly mechanisms of soil microorganisms is crucial in comprehending the diversity and maintenance of Pinus sylvestris var. mongolica forests. Here, we used high-throughput sequencing techniques and null model analysis to explore the distribution patterns and assembly processes of abundant, rare, and total fungal communities in P. sylvestris var. mongolica forests based on a large-scale soil survey across northern China. Compared to the abundant and total taxa, the diversity and composition of rare taxa were found to be more strongly influenced by regional changes and environmental factors. At the level of class, abundant and total taxa were dominated by Agaricomycetes and Leotiomycetes, while Agaricomycetes and Sordariomycetes were dominant in the rare taxa. In the functional guilds, symbiotrophic fungi were advantaged in the abundant and total taxa, and saprotrophic fungi were advantaged in the rare taxa. The null model revealed that the abundant, rare, and total taxa were mainly governed by stochastic processes. However, rare taxa were more influenced by deterministic processes. Precipitation and temperature were the key drivers in regulating the balance between stochastic and deterministic processes. This study provides new insights into both the biogeographical patterns and assembly processes of soil fungi in P. sylvestris var. mongolica forests. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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14 pages, 2985 KiB

Open AccessArticle

Interruption after Short-Term Nitrogen Additions Improves Ecological Stability of Larix olgensis Forest Soil by Affecting Bacterial Communities

by Tongbao Qu, Xiaoting Zhao, Siyu Yan, Yushan Liu, Muhammad Jamal Ameer and Lei Zhao

Microorganisms 2024, 12(5), 969; https://doi.org/10.3390/microorganisms12050969 - 11 May 2024

Cited by 1 | Viewed by 1364

Abstract

Atmospheric nitrogen deposition can alter soil microbial communities and further impact the structure and function of forest ecosystems. However, most studies are focused on positive or negative effects after nitrogen addition, and few studies pay attention to its interruption. In order to investigate whether interruption after different levels of short-term N additions still benefit soil health, we conducted a 2-year interruption after a 4-year short-term nitrogen addition (10 and 20 kg N·hm⁻²·yr⁻¹) experiment; then, we compared soil microbial diversity and structure and analyzed soil physicochemical properties and their correlations before and after the interruption in Larix olgensis forest soil in northeast China. The results showed that soil ecological stabilization of Larix olgensis forest further improved after the interruption compared to pre-interruption. The TN, C:P, N:P, and C:N:P ratios increased significantly regardless of the previous nitrogen addition concentration, and soil nutrient cycling was further promoted. The relative abundance of the original beneficial microbial taxa Gemmatimonas, Sphingomonas, and Pseudolabrys increased; new beneficial bacteria Ellin6067, Massilia, Solirubrobacter, and Bradyrhizobium appeared, and the species of beneficial soil microorganisms were further improved. The results of this study elucidated the dynamics of the bacterial community before and after the interruption of short-term nitrogen addition and could provide data support and a reference basis for forest ecosystem restoration strategies and management under the background of global nitrogen deposition. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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17 pages, 2339 KiB

Open AccessArticle

Effect of Biogas Slurry on the Soil Properties and Microbial Composition in an Annual Ryegrass-Silage Maize Rotation System over a Five-Year Period

by Guangyan Feng, Feixiang Hao, Wei He, Qifan Ran, Gang Nie, Linkai Huang, Xia Wang, Suhong Yuan, Wenzhi Xu and Xinquan Zhang

Microorganisms 2024, 12(4), 716; https://doi.org/10.3390/microorganisms12040716 - 1 Apr 2024

Cited by 3 | Viewed by 1989

Abstract

Soil health is seriously threatened by the overuse of chemical fertilizers in agricultural management. Biogas slurry is often seen as an organic fertilizer resource that is rich in nutrients, and its use has the goal of lowering the amount of chemical fertilizers used while preserving crop yields and soil health. However, the application of continuous biogas slurry has not yet been studied for its long-term impact on soil nutrients and microbial communities in a rotation system of annual ryegrass-silage maize (Zea mays). This study aimed to investigate the impacts on the chemical properties and microbial community of farmland soils to which chemical fertilizer (NPK) (225 kg ha⁻¹), biogas slurry (150 t ha⁻¹), and a combination (49.5 t ha⁻¹ biogas slurry + 150 kg ha⁻¹ chemical fertilizer) were applied for five years. The results indicated that compared to the control group, the long-term application of biogas slurry significantly increased the SOC, TN, AP, and AK values by 45.93%, 39.52%, 174.73%, and 161.54%, respectively; it neutralized acidic soil and increased the soil pH. TN, SOC, pH, and AP are all important environmental factors that influence the structural composition of the soil’s bacterial and fungal communities. Chemical fertilizer application significantly increased the diversity of the bacterial community. Variation was observed in the composition of soil bacterial and fungal communities among the different treatments. The structure and diversity of soil microbes are affected by different methods of fertilization; the application of biogas slurry not only increases the contents of soil nutrients but also regulates the soil’s bacterial and fungal community structures. Therefore, biogas slurry can serve as a sustainable management measure and offers an alternative to the application of chemical fertilizers for sustainable intensification. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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15 pages, 3299 KiB

Open AccessArticle

How Organic Mulching Influences the Soil Bacterial Community Structure and Function in Urban Forests

by Wei Zhou, Xiangyang Sun, Suyan Li, Bingpeng Qu and Jianbing Zhang

Microorganisms 2024, 12(3), 520; https://doi.org/10.3390/microorganisms12030520 - 5 Mar 2024

Viewed by 1486

Abstract

Urban forest soil is often disturbed by frequent human activity. Organic mulching is effective for improving soil quality; however, the effects of organic mulching on soil bacterial communities in urban forests are still largely unexplored. This study evaluated how organic mulching changed the urban forest soil bacterial community through an incubation experiment. Four treatments were applied: (1) no organic mulch (CK); (2) wood chips alone (5 g, Mw); (3) wood compost alone (5 g, Mc); and (4) wood chips + wood compost (This mulch was divided into two layers, i.e., the upper layer of wood chips (2.5 g) and the lower layer wood compost (2.5 g, Mw+c).) We found significant differences in the soil physicochemical properties under organic mulching after incubation. Overall, organic mulching can alter soil bacterial community structure. Soil alkali-hydrolyzable nitrogen, soil organic carbon, soil total nitrogen, and carbon-nitrogen ratio were the main factors affecting soil microbial community structures. Soil bacterial groups under organic mulching treatments mainly acted on the C and N cycling of functional pathways in soil. This study suggests that organic mulching could maintain the development of soil bacteria, which establishes a theoretical foundation for enhancing the microbiological environment of urban forest soils. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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24 pages, 4709 KiB

Open AccessArticle

Impact of Ecological Restoration on the Physicochemical Properties and Bacterial Communities in Alpine Mining Area Soils

by Lingjian Kong, Lin Zhang, Yingnan Wang and Zhanbin Huang

Microorganisms 2024, 12(1), 41; https://doi.org/10.3390/microorganisms12010041 - 25 Dec 2023

Cited by 3 | Viewed by 1810

Abstract

Ecological restoration has notably impacted microbe and soil characteristics in abandoned open pit mines, especially in alpine regions. Yet, the adaptive responses of microbial communities in the initial years of mine site restoration remain largely unexplored. This study endeavors to offer a thorough comprehension of soil properties and microbial dynamics during the initial phases of alpine mining land reclamation. It places emphasis on physicochemical properties and microbial community composition and evaluates the feasibility of phytoremediation, along with proposing subsequent measures. Our study employs spatial sequence instead of time-sequenceal sequence to investigate early-stage changes in soil microbes and physicochemical properties in alpine mining land reclamation. We used high-throughput sequencing for the 16S rRNA amplicon study. Over time, soil physicochemical properties improved noticeably. Soil pH shifted from neutral to alkaline (7.04–8.0), while soil electrical conductivity (EC) decreased to 77 μS·cm⁻¹ in R_6a. Cation exchange capacity (CEC) initially decreased from R_2a (12.30–27.98 cmol·kg⁻¹) and then increased. Soil organic matter increased from 17.7 to 43.2 g·kg⁻¹ over time during mine reclamation and restoration. The dominant bacterial community consisted of Proteobacteria (33.94% to 52.09%), Acidobacteriota (4.94% to 15.88%), Bacteroidota (6.52% to 11.15%), Actinobacteriota (7.18% to 9.61%), and Firmicutes (4.52% to 16.80%) with varying relative abundances. Gene annotation of sequences from various reclamation years revealed general function prediction, translation, ribosome structure, cell wall/membrane/envelope biogenesis, nucleotide translocation, and metabolism, along with other related functions. Mine reclamation improved soil fertility and properties, with the R_6a treatment being the most effective. Starting in the 2nd year of reclamation, the effective phosphorus content and the dominance of microbial bacteria, notably the Bacillus content, decreased. Firmicute fertilization promoted phosphorus and bacterial growth. In conclusion, employing a blend of sequencing and experimental approaches, our study unveils early-stage enhancements in soil microbial and physicochemical properties during the reclamation of alpine mining areas. The results underscore the beneficial impacts of vegetation restoration on key properties, including soil fertility, pore structure, and bacterial community composition. Special attention is given to assessing the effectiveness of the R_6a treatment and identifying deficiencies in the R_2a treatment. It serves as a reference for addressing the challenges associated with soil fertility and microbial community structure restoration in high-altitude mining areas in Qinghai–Tibet. This holds great significance for soil and water conservation as well as vegetation restoration in alpine mining regions. Furthermore, it supports the sustainable restoration of local ecosystems. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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21 pages, 4884 KiB

Open AccessArticle

Exploring Microorganisms from Plastic-Polluted Sites: Unveiling Plastic Degradation and PHA Production Potential

by Diana A. Garza Herrera, Marija Mojicevic, Brana Pantelic, Akanksha Joshi, Catherine Collins, Maria Batista, Cristiana Torres, Filomena Freitas, Patrick Murray, Jasmina Nikodinovic-Runic and Margaret Brennan Fournet

Microorganisms 2023, 11(12), 2914; https://doi.org/10.3390/microorganisms11122914 - 3 Dec 2023

Cited by 5 | Viewed by 3721

Abstract

The exposure of microorganisms to conventional plastics is a relatively recent occurrence, affording limited time for evolutionary adaptation. As part of the EU-funded project BioICEP, this study delves into the plastic degradation potential of microorganisms isolated from sites with prolonged plastic pollution, such as plastic-polluted forests, biopolymer-contaminated soil, oil-contaminated soil, municipal landfill, but also a distinctive soil sample with plastic pieces buried three decades ago. Additionally, samples from Arthropoda species were investigated. In total, 150 strains were isolated and screened for the ability to use plastic-related substrates (Impranil dispersions, polyethylene terephthalate, terephthalic acid, and bis(2-hydroxyethyl) terephthalate). Twenty isolates selected based on their ability to grow on various substrates were identified as Streptomyces, Bacillus, Enterococcus, and Pseudomonas spp. Morphological features were recorded, and the 16S rRNA sequence was employed to construct a phylogenetic tree. Subsequent assessments unveiled that 5 out of the 20 strains displayed the capability to produce polyhydroxyalkanoates, utilizing pre-treated post-consumer PET samples. With Priestia sp. DG69 and Neobacillus sp. DG40 emerging as the most successful producers (4.14% and 3.34% of PHA, respectively), these strains are poised for further utilization in upcycling purposes, laying the foundation for the development of sustainable strategies for plastic waste management. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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15 pages, 13957 KiB

Open AccessArticle

Responses of Soil Microbial Survival Strategies and Functional Changes to Wet–Dry Cycle Events

by Yaqi Zhang, Chunyi Mo, Yaqing Pan, Pengbin Yang, Xiaodong Ding, Qian Lei and Peng Kang

Microorganisms 2023, 11(11), 2783; https://doi.org/10.3390/microorganisms11112783 - 16 Nov 2023

Cited by 2 | Viewed by 2153

Abstract

Soil microbial taxa have different functional ecological characteristics that influence the direction and intensity of plant–soil feedback responses to changes in the soil environment. However, the responses of soil microbial survival strategies to wet and dry events are poorly understood. In this study, soil physicochemical properties, enzyme activity, and high–throughput sequencing results were comprehensively anal0079zed in the irrigated cropland ecological zone of the northern plains of the Yellow River floodplain of China, where Oryza sativa was grown for a long period of time, converted to Zea mays after a year, and then Glycine max was planted. The results showed that different plant cultivations in a paddy–dryland rotation system affected soil physicochemical properties and enzyme activity, and G. max field cultivation resulted in higher total carbon, total nitrogen, soil total organic carbon, and available nitrogen content while significantly increasing α–glucosidase, β–glucosidase, and alkaline phosphatase activities in the soil. In addition, crop rotation altered the r/K–strategist bacteria, and the soil environment was the main factor affecting the community structure of r/K–strategist bacteria. The co–occurrence network revealed the inter–relationship between r/K–strategist bacteria and fungi, and with the succession of land rotation, the G. max sample plot exhibited more stable network relationships. Random forest analysis further indicated the importance of soil electrical conductivity, total carbon, total nitrogen, soil total organic carbon, available nitrogen, and α–glucosidase in the composition of soil microbial communities under wet–dry events and revealed significant correlations with r/K–strategist bacteria. Based on the functional predictions of microorganisms, wet–dry conversion altered the functions of bacteria and fungi and led to a more significant correlation between soil nutrient cycling taxa and environmental changes. This study contributes to a deeper understanding of microbial functional groups while helping to further our understanding of the potential functions of soil microbial functional groups in soil ecosystems. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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14 pages, 2768 KiB

Open AccessArticle

Heterogeneous Habitats in Taiga Forests with Different Important Values of Constructive Species Changes Bacterial Beta Diversity

by Tian Zhou, Song Wu, Hong Pan, Xinming Lu, Jun Du and Libin Yang

Microorganisms 2023, 11(10), 2609; https://doi.org/10.3390/microorganisms11102609 - 23 Oct 2023

Cited by 3 | Viewed by 2132

Abstract

As a crucial link between the aboveground and belowground components of forest ecosystems, soil bacterial communities are extremely sensitive to changes in plant communities and soil conditions. To investigate the impact of the difference of constructive species on soil bacterial communities in taiga forests, we conducted a vegetation survey at the international monitoring plot of the Larix gmelinii forests in the Great Khingan Mountains and calculated the important value of Larix gmelinii to determine experimental groups based on this survey. Subsequently, we collected soil samples for high-throughput sequencing to analyze how the soil bacterial community composition and diversity changed, and which factors affected them. The results showed that taiga forests with different important values of Larix gmelinii had heterogeneous habitats, in which the soil AP content significantly increased, and the SOC, MBC, pH, and C/N content decreased significantly (p < 0.05). A total of 32 phyla, 91 classes, 200 orders, 308 families, 496 genera, and 975 species of soil bacteria were obtained by sequencing. Among them, Proteobacteria, Actinobacteriota, and Acidobacteriota were the dominant phyla, and Mycobacterium was the dominant genus, and the relative abundance of each bacterial group was varied. The beta diversity of soil bacteria showed extremely significant differences (p = 0.001), with SOC, C/N, MBC, AP, TN, pH, AN, and WC being the main influencing factors. Functional prediction analysis showed that chemoheterotrophy and aerobic chemoheterotrophy were the main bacterial functional groups, and the relative abundance of each functional group was significantly different (p < 0.05). Overall, taiga forests with differences in constructive species had heterogeneous habitats, which changed the community composition, beta diversity, and potential functions of soil bacteria. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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