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Microorganisms
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Effect of Microbial Communities for Environmental Protection and Development of...
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Effect of Microbial Communities for Environmental Protection and Development of Agriculture

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

Deadline for manuscript submissions: 30 November 2024 | Viewed by 4462

Special Issue Editor

Dr. Alejandro Rodriguez-Sanchez

E-Mail Website
Guest Editor
Institute of Water Research, University of Granada, C/Ramón y Cajal, 4, 18071 Granada, Spain
Interests: environmental microbes; plant-soil-microbes interactions; molecular identification; crops pathogens; microbial ecology

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 (5 papers)

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Research

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40 pages, 8562 KiB  
Article
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
Viewed by 474
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 [...] Read more.
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  
Article
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 533
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 [...] Read more.
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  
Article
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 597
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 [...] Read more.
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  
Article
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 954
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 [...] Read more.
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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17 pages, 2369 KiB  
Review
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 1 | Viewed by 817
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 [...] Read more.
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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