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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: 28 February 2025 | Viewed by 10909

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Special Issue Editor

Dr. Alejandro Rodriguez-Sanchez

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Guest Editor

Institute of Water Research, University of Granada, Granada, Spain
Interests: water and wastewater engineering; water quality; water treatment; emerging pollutants in wastewater; applied microbiology; next-generation sequencing; biological wastewater treatment
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Special Issue Information

Dear Colleagues,

Microorganisms are significantly small life forms; however, they are represented in enormous numbers in every environment worldwide and, thus, play very important roles in the ecosystem functioning in both natural and engineered environments. Their different capabilities are already being used for many applications, among which agriculture is one of the most prominent. In this way, the fate of planet Earth and humanity lies substantially on the microbial communities that inhabit our planet.

Unfortunately, human progress is subjecting our planet to environmental deterioration. This fact is tied to human progress and cannot be avoided, though it can be addressed. There is a crucial need for engineering solutions to remediate the affection that the human population has for the ecosystems of our world. The enormous impact that microbial communities play on the ecosystem functioning on Earth can, thus, be a very important tool for harnessing and alleviating the negative impact that humanity has worldwide, as well as potentiating human processes that rely on their activities. Environmental engineering solutions for the protection of the environment and enhancement of agricultural production are, therefore, essential.

For these reasons, this Special Issue is important for environmental protection and agriculture potentiation based on microbial engineering. Novel approaches for applying microbes to the bioremediation of environments, prevention of pollution, and enhancement of agricultural activity deserve an important spotlight, which we aim to provide. In addition, studies that successfully apply microbial engineering in the environment and agricultural fields are welcome due to the fact that they provide initial frameworks for the regional application of these techniques to further protect the environment and enhance agricultural yield.

Thus, this new Special Issue of Microorganisms entitled ‘Effect of Microbial Communities for Environmental Protection and Development of Agriculture’ gathers contributions on the following topics:

Novel techniques for the bioremediation of environmental pollution in the environment;
The effects of pollutants on environmental microbial communities and the adaptation process of microbes to environmental stresses of pollution;
The use of microbial communities to increase agricultural yield and quality;
The use of microorganisms for the protection of plants in agricultural fields against biotic and abiotic stresses;
Regional applications of environmental engineering strategies based on microbial communities.

Dr. Alejandro Rodriguez-Sanchez
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

environmental microbial communities
environmental protection
agriculture potentiation
bioremediation
ecosystem functioning
biotic and abiotic stresses

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Published Papers (9 papers)

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Research

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23 pages, 6644 KiB

Open AccessArticle

Bioremediation Potential of Rhodococcus qingshengii PM1 in Sodium Selenite-Contaminated Soil and Its Impact on Microbial Community Assembly

by Mu Peng, Guangai Deng, Chongyang Hu, Xue Hou and Zhiyong Wang

Microorganisms 2024, 12(12), 2458; https://doi.org/10.3390/microorganisms12122458 - 29 Nov 2024

Viewed by 592

Abstract

Soil microbial communities are particularly sensitive to selenium contamination, which has seriously affected the stability of soil ecological environment and function. In this study, we applied high-throughput 16S rRNA gene sequencing to examine the effects of low and high doses of sodium selenite and the selenite-degrading bacterium, Rhodococcus qingshengii PM1, on soil bacterial community composition, diversity, and assembly processes under controlled laboratory conditions. Our results indicated that sodium selenite and strain PM1 were key predictors of bacterial community structure in selenium-contaminated soils. Exposure to sodium selenite initially led to reductions in microbial diversity and a shift in dominant bacterial groups, particularly an increase in Actinobacteria and a decrease in Acidobacteria. Sodium selenite significantly reduced microbial diversity and simplified co-occurrence networks, whereas inoculation with strain PM1 partially reversed these effects by enhancing community complexity. Ecological modeling, including the normalized stochasticity ratio (NST) and Sloan’s neutral community model (NCM), suggested that stochastic processes predominated in the assembly of bacterial communities under selenium stress. Null model analysis further revealed that heterogeneous selection and drift were primary drivers of community turnover, with PM1 inoculation promoting species dispersal and buffering against the negative impacts of selenium. These findings shed light on microbial community assembly mechanisms under selenium contamination and highlight the potential of strain PM1 for the bioremediation of selenium-affected soils. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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17 pages, 2832 KiB

Open AccessArticle

Root Endophytic Microorganisms Contribute to the Attribute of Full-Year Shooting in Woody Bamboo Cephalostachyum pingbianense

by Lushuang Li, Bin Li, Qing Li, Lianchun Wang and Hanqi Yang

Microorganisms 2024, 12(9), 1927; https://doi.org/10.3390/microorganisms12091927 - 22 Sep 2024

Viewed by 1080

Abstract

Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang is unique among bamboo species for its ability to produce bamboo shoots in all seasons under natural conditions. Apart from the physiological mechanism, information regarding the effects of endophytic microorganisms on this full-year shooting characteristic is limited. We hypothesize that root endophytic microorganisms will have a positive impact on the full-year bamboo shooting characteristic of C. pingbianense by increasing the availability or supply of nutrients. To identify the seasonal variations in the root endophytic bacterial and fungal communities of C. pingbianense, and to assess their correlation with bamboo shoot productivity, the roots of C. pingbianense were selected as research materials, and the 16S rRNA and ITS rDNA genes of root endophytic microorganisms were sequenced using the Illumina platform. Following this sequencing, raw sequencing reads were processed, and OTUs were annotated. Alpha and beta diversity, microbial composition, and functional predictions were analyzed, with correlations to bamboo shoot numbers assessed. The results showed that seasonal changes significantly affected the community diversity and structure of root endophytic microbes of C. pingbianense. Bacterial communities in root samples from all seasons contained more nitrogen-fixing microorganisms, with members of the Burkholderiales and Rhizobiales predominating. The relative abundances of ectomycorrhizal and arbuscular mycorrhizal fungi in the autumn sample were significantly higher than in other seasons. Correlation analysis revealed that the bamboo shoot productivity was significantly and positively correlated with bacterial functions of nitrogen fixation, arsenate detoxification, and ureolysis, as well as with symbiotrophic fungi, ectomycorrhizal fungi, and arbuscular mycorrhizal fungi. At the genus level, the bacterial genus Herbaspirillum and the fungal genera Russula, unclassified_f_Acaulosporaceae, and unclassified_f_Glomeraceae were found to have a significant positive correlation with bamboo shoot number. Our study provides an ecological perspective for understanding the highly productive attribute of C. pingbianense and offers new insights into the forest management of woody bamboos. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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36 pages, 8562 KiB

Open AccessArticle

Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer

by Valentina Gonzalez, Josefina Abarca-Hurtado, Alejandra Arancibia, Fernanda Claverías, Miguel R. Guevara and Roberto Orellana

Microorganisms 2024, 12(9), 1796; https://doi.org/10.3390/microorganisms12091796 - 29 Aug 2024

Cited by 1 | Viewed by 1214

Abstract

Some sulfate-reducing bacteria (SRB), mainly belonging to the Desulfovibrionaceae family, have evolved the capability to conserve energy through microbial extracellular electron transfer (EET), suggesting that this process may be more widespread than previously believed. While previous evidence has shown that mobile genetic elements drive the plasticity and evolution of SRB and iron-reducing bacteria (FeRB), few have investigated the shared molecular mechanisms related to EET. To address this, we analyzed the prevalence and abundance of EET elements and how they contributed to their differentiation among 42 members of the Desulfovibrionaceae family and 23 and 59 members of Geobacteraceae and Shewanellaceae, respectively. Proteins involved in EET, such as the cytochromes PpcA and CymA, the outer membrane protein OmpJ, and the iron–sulfur cluster-binding CbcT, exhibited widespread distribution within Desulfovibrionaceae. Some of these showed modular diversification. Additional evidence revealed that horizontal gene transfer was involved in the acquiring and losing of critical genes, increasing the diversification and plasticity between the three families. The results suggest that specific EET genes were widely disseminated through horizontal transfer, where some changes reflected environmental adaptations. These findings enhance our comprehension of the evolution and distribution of proteins involved in EET processes, shedding light on their role in iron and sulfur biogeochemical cycling. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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14 pages, 3895 KiB

Open AccessArticle

Characteristics of the Perianthic Endophytic Fungal Communities of the Rare Horticultural Plant Lirianthe delavayi and Their Changes under Artificial Cultivation

by Lang Yuan, Tongxing Zhao, Jing Yang, Nannan Wu, Pinzheng Zhang, Hanbo Zhang and Tao Xu

Microorganisms 2024, 12(7), 1491; https://doi.org/10.3390/microorganisms12071491 - 21 Jul 2024

Viewed by 955

Abstract

Flower endophytic fungi play a major role in plant reproduction, stress resistance, and growth and development. However, little is known about how artificial cultivation affects the endophytic fungal community found in the tepals of rare horticultural plants. In this research, we used high-throughput sequencing technology combined with bioinformatics analysis to reveal the endophytic fungal community of tepals in Lirianthe delavayi and the effects of artificial cultivation on the community composition and function of these plants, using tepals of L. delavayi from wild habitat, cultivated campus habitat, and cultivated field habitat as research objects. The results showed that the variety of endophytic fungi in the tepals of L. delavayi was abundant, with a total of 907 Amplicon sequencing variants (ASVs) obtained from all the samples, which were further classified into 4 phyla, 23 classes, 51 orders, 97 families, 156 genera, and 214 species. We also found that artificial cultivation had a significant impact on the community composition of endophytic fungi. Although there was no significant difference at the phylum level, with Ascomycota and Basidiomycota being the main phyla, there were significant differences in dominant and unique genera. Artificial cultivation has led to the addition of new pathogenic fungal genera, such as Phaeosphaeria, Botryosphaeria, and Paraconiothyrium, increasing the risk of disease in L. delavayi. In addition, the abundance of the endophytic fungus Rhodotorula, which is typical in plant reproductive organs, decreased. Artificial cultivation also altered the metabolic pathways of endophytic fungi, decreasing their ability to resist pests and diseases and reducing their ability to reproduce. A comparison of endophytic fungi in tepals and leaves revealed significant differences in community composition and changes in the endophytic diversity caused by artificial cultivation. To summarize, our results indicate that endophytic fungi in the tepals of L. delavayi mainly consist of pathogenic and saprophytic fungi. Simultaneously, artificial cultivation introduces a great number of pathogenic fungi that alter the metabolic pathways associated with plant resistance to disease and pests, as well as reproduction, which can increase the risk of plant disease and reduce plant reproductive capacity. Our study provides an important reference for the conservation and breeding of rare horticultural plants. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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21 pages, 4938 KiB

Open AccessArticle

Endophytic Fungi Inoculation Reduces Ramulosis Severity in Gossypium hirsutum Plants

by Isabella de Oliveira Silva, Layara Alexandre Bessa, Mateus Neri Oliveira Reis, Damiana Souza Santos Augusto, Charlys Roweder, Edson Luiz Souchie and Luciana Cristina Vitorino

Microorganisms 2024, 12(6), 1124; https://doi.org/10.3390/microorganisms12061124 - 31 May 2024

Viewed by 1029

Abstract

Biotic stress in cotton plants caused by the phytopathogenic fungus Colletotrichum gossypii var. cephalosporioides triggers symptoms of ramulosis, a disease characterized by necrotic spots on young leaves, followed by death of the affected branch’s apical meristem, plant growth paralysis, and stimulation of lateral bud production. Severe cases of ramulosis can cause up to 85% yield losses in cotton plantations. Currently, this disease is controlled exclusively by using fungicides. However, few studies have focused on biological alternatives for mitigating the effects of contamination by C. gossypii var. cephalosporioides on cotton plants. Thus, the hypothesis raised is that endophytic fungi isolated from an Arecaceae species (Butia purpurascens), endemic to the Cerrado biome, have the potential to reduce physiological damage caused by ramulosis, decreasing its severity in these plants. This hypothesis was tested using plants grown from seeds contaminated with the pathogen and inoculated with strains of Gibberella moniliformis (BP10EF), Hamigera insecticola (BP33EF), Codinaeopsis sp. (BP328EF), G. moniliformis (BP335EF), and Aspergillus sp. (BP340EF). C. gossypii var. cephalosporioides is a leaf pathogen; thus, the evaluations were focused on leaf parameters: gas exchange, chlorophyll a fluorescence, and oxidative metabolism. The hypothesis that inoculation with endophytic strains can mitigate physiological and photochemical damage caused by ramulosis in cotton was confirmed, as the fungi improved plant growth and stomatal index and density, increased net photosynthetic rate (A) and carboxylation efficiency (A/Ci), and decreased photochemical stress (ABS/RC and DI₀/RC) and oxidative stress by reducing enzyme activity (CAT, SOD, and APX) and the synthesis of malondialdehyde (MDA). Control plants developed leaves with a low adaxial stomatal index and density to reduce colonization of leaf tissues by C. gossypii var. cephalosporioides due to the absence of fungal antagonism. The Codinaeopsis sp. strain BP328EF can efficiently inhibit C. gossypii var. cephalosporioides in vitro (81.11% relative inhibition), improve gas exchange parameters, reduce photochemical stress of chlorophyll-a, and decrease lipid peroxidation in attacked leaves. Thus, BP328EF should be further evaluated for its potential effect as a biological alternative for enhancing the resistance of G. hirsutum plants and minimizing yield losses caused by C. gossypii var. cephalosporioides. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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13 pages, 1704 KiB

Open AccessArticle

Urea Fertilization Significantly Promotes Nitrous Oxide Emissions from Agricultural Soils and Is Attributed to the Short-Term Suppression of Nitrite-Oxidizing Bacteria during Urea Hydrolysis

by Yiming Jiang, Yueyue Zhu, Weitie Lin and Jianfei Luo

Microorganisms 2024, 12(4), 685; https://doi.org/10.3390/microorganisms12040685 - 28 Mar 2024

Viewed by 1460

Abstract

The application of urea in agricultural soil significantly boosts nitrous oxide (N₂O) emissions. However, the reason for nitrite accumulation, the period of nitrite-oxidizing bacteria (NOB) suppression, and the main NOB species for nitrite removal behind urea fertilization have not been thoroughly investigated. In this study, four laboratory microcosm experiments were conducted to simulate urea fertilization in agricultural soils. We found that within 36 h of urea application, nitrite oxidation lagged behind ammonia oxidation, leading to nitrite accumulation and increased N₂O emissions. However, after 36 h, NOB activity recovered and then removed nitrite, leading to reduced N₂O emissions. Urea use resulted in an N₂O emission rate tenfold higher than ammonium. During incubation, Nitrobacter-affiliated NOB growth decreased initially but increased later with urea use, while Nitrospira-affiliated NOB appeared unaffected. Chlorate suppression of NOB lasted longer, increasing N₂O emissions. Urease inhibitors effectively reduced N₂O emissions by slowing urea hydrolysis and limiting free ammonia production, preventing short-term NOB suppression. In summary, short-term NOB suppression during urea hydrolysis played a crucial role in increasing N₂O emissions from agricultural soils. These findings revealed the reasons behind the surge in N₂O emissions caused by extensive urea application and provided guidance for reducing N₂O emissions in agricultural production processes. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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Review

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10 pages, 598 KiB

Open AccessReview

Balancing Nature and Nurture: The Role of Biocontrol Agents in Shaping Plant Microbiomes for Sustainable Agriculture

by Suzana Moussa and Lilach Iasur Kruh

Microorganisms 2025, 13(2), 323; https://doi.org/10.3390/microorganisms13020323 - 2 Feb 2025

Viewed by 201

Abstract

Microbial communities in the plant environment are highly dynamic, with bacterial populations rapidly responding to changes. Numerous studies have examined how both inherent plant characteristics and environmental factors shape plant-associated microbiota. These factors determine which bacterial communities thrive and how they interact with plants; certain conditions favor beneficial bacteria, and others support pathogens. In this mini-review, we focus on an additional factor influencing plant microbiomes and their surrounding environments: the use of biocontrol agents. The increasing application of microbial inoculants and their metabolites as biocontrol strategies in agriculture has created a critical knowledge gap about the effects of introducing non-native bacterial species into natural plant ecosystems. The inoculation of plants and their environments with exogenous biocontrol microorganisms has the potential to alter microbial community diversity and composition, presenting both opportunities and challenges for sustainable agricultural practices. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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20 pages, 6864 KiB

Open AccessReview

The Antimicrobial Effects of Coffee and By-Products and Their Potential Applications in Healthcare and Agricultural Sectors: A State-of-Art Review

by Rosa Castro-Díaz, Norma Patricia Silva-Beltrán, Nohemi Gámez-Meza and Kadiya Calderón

Microorganisms 2025, 13(2), 215; https://doi.org/10.3390/microorganisms13020215 - 21 Jan 2025

Viewed by 709

Abstract

Coffee is one of the most consumed beverages around the world. Its production is dominated by the species Coffea arabica and Coffea canephora. However, the coffee elaboration process leads to generating a significant amount of waste, which arises in various stages of coffee bean processing and is rich in natural bioactive compounds such as phenolic compounds and alkaloids. Particularly, chlorogenic and caffeic acids have a high antimicrobial potential and have been demonstrated to be effective against bacteria and viruses of healthcare and food relevance, including multi-resistant pathogens. However, the production and accumulation of coffee waste have a negative environmental impact since they can contaminate the surrounding environment due to the presence of organic molecules such as caffeine and tannins. In this context, exploiting natural resources as a source of compounds with the antimicrobial potential of, for example, the bioactive compounds obtained from coffee, has been evaluated in previous works. This review aims to summarize the current knowledge on the antimicrobial properties of coffee and its by-products and their potential application in the healthcare sector and disease control in agricultural crops, with particular emphasis on improving sustainability and efficiency in agriculture through making use of waste, which carries high importance in today’s society. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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17 pages, 2369 KiB

Open AccessReview

Sustainable Remediation of Soil and Water Utilizing Arbuscular Mycorrhizal Fungi: A Review

by Xueqi Zhang, Zongcheng Wang, Yebin Lu, Jun Wei, Shiying Qi, Boran Wu and Shuiping Cheng

Microorganisms 2024, 12(7), 1255; https://doi.org/10.3390/microorganisms12071255 - 21 Jun 2024

Cited by 4 | Viewed by 1934

Abstract

Phytoremediation is recognized as an environmentally friendly technique. However, the low biomass production, high time consumption, and exposure to combined toxic stress from contaminated media weaken the potential of phytoremediation. As a class of plant-beneficial microorganisms, arbuscular mycorrhizal fungi (AMF) can promote plant nutrient uptake, improve plant habitats, and regulate abiotic stresses, and the utilization of AMF to enhance phytoremediation is considered to be an effective way to enhance the remediation efficiency. In this paper, we searched 520 papers published during the period 2000–2023 on the topic of AMF-assisted phytoremediation from the Web of Science core collection database. We analyzed the author co-authorship, country, and keyword co-occurrence clustering by VOSviewer. We summarized the advances in research and proposed prospective studies on AMF-assisted phytoremediation. The bibliometric analyses showed that heavy metal, soil, stress tolerance, and growth promotion were the research hotspots. AMF–plant symbiosis has been used in water and soil in different scenarios for the remediation of heavy metal pollution and organic pollution, among others. The potential mechanisms of pollutant removal in which AMF are directly involved through hyphal exudate binding and stabilization, accumulation in their structures, and nutrient exchange with the host plant are highlighted. In addition, the tolerance strategies of AMF through influencing the subcellular distribution of contaminants as well as chemical form shifts, activation of plant defenses, and induction of differential gene expression in plants are presented. We proposed that future research should screen anaerobic-tolerant AMF strains, examine bacterial interactions with AMF, and utilize AMF for combined pollutant removal to accelerate practical applications. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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