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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 (31 December 2022) | Viewed by 26530

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Dr. Tim J. Dumonceaux

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Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2, Canada
Interests: molecular diagnostics; agricultural microbiology; microbial communities; biofuels; plant pathology
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Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, "Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems".

The contribution of the microbial component of terrestrial ecosystems to an array of ecosystem services is increasingly recognized, and a corresponding increase in research aimed at understanding and characterizing microbial ecosystems has been observed. However, while technology and analytical capacity continues to improve, significant gaps remain in our ability to identify taxa of importance, to analyze microbial communities including all domains of life (bacteria, archaea, and eukarya), and to understand the complexities and implications of these interdomain interactions at the mechanistic level. Despite an increase in the feasibility of whole-metagenome sequencing in beginning to address some of these questions, the analysis of amplicon data targeting taxonomic genes such as 16S rRNA for bacteria and certain archaea or internal transcribed spacer (ITS) for fungi remains a predominant experimental approach. Improvements to the ability to generate and analyze such data, including paradigm-shifting approaches such as microbial co-occurrence network analysis, can provide novel means of identifying taxa that are critical to the functioning of these ecosystems, along with interspecific and even inter-domain relationships of importance. The second edition of our Special Issue on terrestrial microbial ecosystems aims to address some of these gaps by inviting scientists to submit novel research that employs tools that can provide novel insights into the composition, structure, and function of human-impacted agricultural and forest ecosystems. Manuscripts describing the development or implementation of novel methods for microbial community analysis or review papers highlighting research gaps and proposing approaches to address them are welcomed.

Dr. Tim J. Dumonceaux
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.

Related Special Issue

Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems in Microorganisms (11 articles)

Published Papers (12 papers)

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Editorial

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6 pages, 222 KiB

Open AccessEditorial

Composition and Dynamics of Plant- and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems

by Tim Dumonceaux

Microorganisms 2023, 11(7), 1782; https://doi.org/10.3390/microorganisms11071782 - 10 Jul 2023

Cited by 1 | Viewed by 999

Abstract

Peter Kropotkin (1842–1921) is well known as an anarchist intellectual, an amiable mass of contradictions who loved humanity and was highly regarded in academic and intellectual circles, yet also penned “fiery peans to violence” in Le Révolté, the anarchist journal he established [...] Read more.

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

Research

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15 pages, 2631 KiB

Open AccessArticle

Characterization of Phytopythium Species Involved in the Establishment and Development of Kiwifruit Vine Decline Syndrome

by Simona Prencipe, Giada Schiavon, Marco Rosati, Luca Nari, Leonardo Schena and Davide Spadaro

Microorganisms 2023, 11(1), 216; https://doi.org/10.3390/microorganisms11010216 - 15 Jan 2023

Cited by 6 | Viewed by 2541

Abstract

Since 2012, the kiwifruit vine decline syndrome (KVDS) has progressively compromised Italian kiwifruit orchards. Different abiotic and biotic factors have been associated with the establishment and development of KVDS. During monitoring of orchards affected by KVDS in north-western Italy during 2016–2019, 71 Phytopythium spp. were isolated. Based on maximum likelihood concatenated phylogeny on the ITS1-5.8S-ITS2 region of the rDNA, large subunit rDNA, and cytochrome oxidase I, isolates were identified as P. vexans (52), P. litorale (10), P. chamaehyphon (7) and P. helicoides (2). Phytopythium litorale and P. helicoides are reported for the first time as agents of KVDS in Italy. To demonstrate pathogenicity and fulfil Koch’s postulates, representative isolates of P. vexans, P. litorale, P. chamaehyphon and P. helicoides were inoculated in potted plants. In these trials, waterlogging was applied to stress plant with a temporary anoxia and to favour the production of infective zoospores by the oomycetes. In experiments in vitro, the four species showed the highest growth at 25–30 °C, depending on the media used. P. helicoides was able to grow also at 40 °C. The four species were able to grow in vitro at a pH ranging from 5.0 to 8.0, showing that pH had less effect on growth than temperature. The present study suggests a strong role of different species of Phytopythium in the establishment and development of KVDS. Phytopythium spp. could be favoured by the average increase in soil temperatures during summer, associated with global warming. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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13 pages, 2471 KiB

Open AccessArticle

Characteristics of Soil Physicochemical Properties and Microbial Community of Mulberry (Morus alba L.) and Alfalfa (Medicago sativa L.) Intercropping System in Northwest Liaoning

by Muzi Li, Yawei Wei, You Yin, Wenxu Zhu, Xuejiao Bai and Yongbin Zhou

Microorganisms 2023, 11(1), 114; https://doi.org/10.3390/microorganisms11010114 - 01 Jan 2023

Cited by 4 | Viewed by 2260

Abstract

Medicinal plant intercropping is a new intercropping method. However, as a new intercropping model, the influence of intercropping of alfalfa on microorganisms has not been clarified clearly. In this study, the composition and diversity of microbial communities in alfalfa intercropping were studied, and the differences of bacterial and fungal communities and their relationships with environmental factors are discussed. Intercropping significantly decreased soil pH and significantly increased soil total phosphorus (TP) content, but did not increase soil total carbon (TC) and total nitrogen (TN). Intercropping can increase the relative abundance of Actinobacteria and reduce the relative abundance of Proteobacteria in soil. The relative abundance and diversity of bacteria were significantly correlated with soil pH and TP, while the diversity of fungi was mainly correlated with TC, TN and soil ecological stoichiometry. The bacterial phylum was mainly related to pH and TP, while the fungal phylum was related to TC, TN, C: P and N: P. The present study revealed the stoichiometry of soil CNP and microbial community characteristics of mulberry-alfalfa intercropping soil, clarified the relationship between soil stoichiometry and microbial community composition and diversity, and provided a theoretical basis for the systematic management of mulberry-alfalfa intercropping in northwest Liaoning. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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14 pages, 4135 KiB

Open AccessArticle

Investigating the Biocontrol Potential of the Natural Microbiota of the Apple Blossom

by Anya Schnyder, Leo Eberl and Kirsty Agnoli

Microorganisms 2022, 10(12), 2480; https://doi.org/10.3390/microorganisms10122480 - 15 Dec 2022

Cited by 1 | Viewed by 1530

Abstract

Erwinia amylovora, the causative agent of fire blight, leads to important economic losses of apple and pear crops worldwide. This study aimed to investigate the potential of the resident microbiota of the apple blossom in combatting plant disease-causing organisms, with a focus on controlling fire blight. We obtained 538 isolates from sites around Canton Zurich, which we tested for activity against Pectobacterium carotovorum and E. amylovora. We also evaluated the isolates’ activity against oomycete and fungal pathogens. Nine isolates showed activity against P. carotovorum, and eight of these against E. amylovora. Furthermore, 117 showed antifungal, and 161 anti-oomycete, activity. We assigned genera and in some cases species to 238 of the isolates by sequencing their 16S RNA-encoding gene. Five strains showed activity against all pathogens and were tested in a detached apple model for anti-E. amylovora activity. Of these five strains, two were able to antagonize E. amylovora, namely Bacillus velezensis #124 and Pantoea agglomerans #378. We sequenced the P. agglomerans #378 genome and analyzed it for secondary metabolite clusters using antiSMASH, revealing the presence of a putative bacteriocin cluster. We also showed that B. velezensis #124 exhibits strong activity against three different fungi and two oomycetes in vitro, suggesting a broader capacity for biocontrol. Our results showcase the protective potential of the natural apple blossom microbiota. We isolated two candidate biocontrol strains from apple blossoms, suggesting that they might persist at the most common entry point for the causative agent of fire blight. Furthermore, they are probably already part of the human diet, suggesting they might be safe for consumption, and thus are promising candidates for biocontrol applications. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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19 pages, 3907 KiB

Open AccessArticle

Comparison of the Peel-Associated Epiphytic Bacteria of Anthocyanin-Rich “Sun Black” and Wild-Type Tomatoes under Organic and Conventional Farming

by Susanna Gorrasi, Marcella Pasqualetti, Barbara Muñoz-Palazon, Giorgia Novello, Andrea Mazzucato, Enio Campiglia and Massimiliano Fenice

Microorganisms 2022, 10(11), 2240; https://doi.org/10.3390/microorganisms10112240 - 12 Nov 2022

Cited by 5 | Viewed by 1504

Abstract

Tomatoes are among the most consumed vegetables worldwide and represent a source of health-beneficial substances. Our study represents the first investigating the peel-associated epiphytic bacteria of red and purple (anthocyanin-rich) tomatoes subjected to organic and conventional farming systems. Proteobacteria was the dominant phylum (relative abundances 79–91%) in all experimental conditions. Enterobacteriaceae represented a large fraction (39.3–47.5%) of the communities, with Buttiauxella and Atlantibacter as the most represented genera. The core microbiota was composed of 59 operational taxonomic units (OTUs), including the majority of the most abundant ones. The occurrence of the most abundant OTUs differed among the experimental conditions. OTU 1 (Buttiauxella), OTU 2 (Enterobacteriales), and OTU 6 (Bacillales) were higher in red and purple tomatoes grown under organic farming. OTU 5 (Acinetobacter) had the highest abundance in red tomatoes subjected to organic farming. OTU 3 (Atlantibacter) was among the major OTUs in red tomatoes under both farming conditions. OTU 7 (Clavibacter) and OTU 8 (Enterobacteriaceae) had abundances ≥1% only in red tomatoes grown under conventional farming. PCA and clustering analysis highlighted a high similarity between the bacterial communities of red and purple tomatoes grown under organic farming. Furthermore, the bacterial communities of purple tomatoes grown under organic farming showed the lowest diversity and evenness. This work paves the way to understand the role of nutritional superior tomato genotypes, combined with organic farming, to modulate the presence of beneficial/harmful bacteria and supply healthier foods within a sustainable agriculture. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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19 pages, 5634 KiB

Open AccessArticle

A Case Study Demonstrates That the Litter of the Rare Species Cinnamomum migao Composed of Different Tissues Can Affect the Chemical Properties and Microbial Community Diversity in Topsoil

by Yuangui Xie, Xiaofeng Liao, Jiming Liu and Jingzhong Chen

Microorganisms 2022, 10(6), 1125; https://doi.org/10.3390/microorganisms10061125 - 30 May 2022

Cited by 2 | Viewed by 1399

Abstract

The decomposition of litter plays an important role in the return of forest soil nutrients, as well as the growth and productivity of plants. With this study, we aimed to determine the impact of litter mulching on different tissues of Cinnamomum migao, a rare Chinese endemic species. In particular, seeds and pericarp are easily overlooked components of C. migao litter. In this study, we tested control (uncovered litter) and litter (leaf, branch, seed, and pericarp) mulching conditions and conducted a one-year litter decomposition experiment. The enzyme activities of urease enzyme (UE) and invertase enzyme (INV) were significantly improved by litter mulching. Catalase (CAT) enzyme activities in leaf, branch, and seed litter mulching were lower than in the control, whereas CAT activity in pericarp mulching was significantly higher than in the control. Although Mortierella, Cladophialophora, Acidothermus, Sphingomonas, and Burkholderia were the dominant microbes of topsoil in different mulching treatments, there were differences in the number and connectivity of microbial communities, and this change was correlated with soil organic carbon (SOC) and CAT enzyme activity. Compared with leaves and branches, seeds and pericarp as litter are also very important for nutrient return and affect topsoil microbes in C. migao forest, which may be of significance for the growth feedback of C. migao in biennial bearing. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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21 pages, 5375 KiB

Open AccessArticle

Effects of Mixed Decomposition of Pinus sylvestris var. mongolica and Morus alba Litter on Microbial Diversity

by Jiaying Liu, Yawei Wei, You Yin, Keye Zhu, Yuting Liu, Hui Ding, Jiawei Lei, Wenxu Zhu and Yongbin Zhou

Microorganisms 2022, 10(6), 1117; https://doi.org/10.3390/microorganisms10061117 - 28 May 2022

Cited by 5 | Viewed by 1669

Abstract

Pinus sylvestris var. mongolica is widely planted in China as a windbreak and sand fixation tree. To improve the current situation of large-scale declines of forested areas planted as P. sylvestris var. mongolica monocultures, we investigated the biological and microbial effects of stand establishment using mixed tree species. The interactions during the mixed decomposition of the litter and leaves of different tree species are an important indicator in determining the relationships among species. In this experiment, a method of simulating the mixed decomposition of P. sylvestris var. mongolica and Morus alba litter under P. sylvestris var. mongolica forest was used to determine the total C, total N, and total P contents in the leaf litter, and the microbial structures were determined by using Illumina MiSeq high-throughput sequencing. It was found that with samples with different proportions of P. sylvestris var. mongolica and M. alba litters, the decomposition rate of P. sylvestris var. mongolica × M. alba litter was significantly higher than that of the pure P. sylvestris var. mongolica forest, and the microbial community and composition diversity of litter in a pure P. sylvestris var. mongolica forest could be significantly improved. The possibility of using M. alba as a mixed tree species to address the declines of pure P. sylvestris var. mongolica forest was verified to provide guidance for pure P. sylvestris var. mongolica forests by introducing tree species with coordinated interspecific relationships and creating a mixed forest. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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18 pages, 3994 KiB

Open AccessArticle

Tillage Practices and Residue Management Manipulate Soil Bacterial and Fungal Communities and Networks in Maize Agroecosystems

by Yupeng Guan, Bei Xu, Ximei Zhang and Wei Yang

Microorganisms 2022, 10(5), 1056; https://doi.org/10.3390/microorganisms10051056 - 20 May 2022

Cited by 9 | Viewed by 2336

Abstract

Tillage practices and residue management are highly important agricultural practices. However, very few studies have examined the influence of tillage practices and residue management on both bacterial and fungal communities and network patterns in consecutive years. We examined the effects of different tillage practices, including no tillage, rotary tillage, and deep tillage, on soil bacterial and fungal communities and co-occurrence networks following residue removal and residue retention in 2017 and 2018. This study showed that both bacterial and fungal communities were unaffected by tillage practices in 2017, but they were significantly impacted in 2018. Soil fungal operational taxonomic unit (OTU) richness was significantly enhanced by deep tillage compared with no tillage in 2018, while bacterial OTU richness was unaffected in either year. Tillage practices had differing effects on soil microbial co-occurrence networks, with rotary and deep tillage increasing the complexity of bacterial networks but simplifying fungal networks. However, residue retention only induced a shift in the fungal community and simplified soil bacterial and fungal networks in 2018. This study highlights the dissimilar responses of bacterial and fungal networks to tillage practices and emphasizes that tillage practice is more important than residue management in shaping soil microbial communities. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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14 pages, 3223 KiB

Open AccessArticle

The Genome of Bacillus velezensis SC60 Provides Evidence for Its Plant Probiotic Effects

by Xiaoyan Dong, Chen Tu, Zhihong Xie, Yongming Luo, Lei Zhang and Zhaoyi Li

Microorganisms 2022, 10(4), 767; https://doi.org/10.3390/microorganisms10040767 - 01 Apr 2022

Cited by 10 | Viewed by 2480

Abstract

Root colonization and plant probiotic function are important traits of plant growth-promoting rhizobacteria (PGPR). Bacillus velezensis SC60, a plant endophytic strain screened from Sesbania cannabina, has a strong colonization ability on various plant roots, which indicates that SC60 has a preferable adaptability to plants. However, the probiotic function of the strain SC60 is not well-understood. Promoting plant growth and suppressing soil-borne pathogens are key to the plant probiotic functions. In this study, the genetic mechanism of plant growth-promoting and antibacterial activity of the strain SC60 was analyzed by biological and bioinformatics methods. The complete genome size of strain SC60 was 3,962,671 bp, with 4079 predicted genes and an average GC content of 46.46%. SC60 was designated as Bacillus velezensis according to the comparative analysis, including average nucleotide polymorphism (ANI), digital DNA–DNA hybridization (dDDH), and phylogenetic analysis. Genomic secondary metabolite analyses indicated two clusters encoding potential new antimicrobials. The antagonism experiments revealed that strain SC60 had the ability to inhibit the growth of a variety of plant pathogens and its closely related strains of Bacillus spp., which was crucial to the rhizospheric competitiveness and growth-promoting effect of the strain. The present results further suggest that B. velezensis SC60 could be used as a PGPR strain to develop new biocontrol agents or microbial fertilizers. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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Review

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17 pages, 792 KiB

Open AccessReview

Perspectives on the Use of Biopolymeric Matrices as Carriers for Plant-Growth Promoting Bacteria in Agricultural Systems

by Jéssica F. Pereira, André Luiz M. Oliveira, Daniele Sartori, Fabio Yamashita and Suzana Mali

Microorganisms 2023, 11(2), 467; https://doi.org/10.3390/microorganisms11020467 - 13 Feb 2023

Cited by 5 | Viewed by 2416

Abstract

The subject of this review is to discuss some aspects related to the use of biopolymeric matrices as carriers for plant-growth promoting bacteria (PGPB) in agricultural systems as a possible technological solution for the establishment of agricultural production practices that result in fewer adverse impacts on the environment, reporting some promising and interesting results on the topic. Results from the encapsulation of different PGPB on alginate, starch, chitosan, and gelatin matrices are discussed, systematizing some advances made in this area of knowledge in recent years. Encapsulation of these bacteria has been shown to be an effective method for protecting them from unsuitable environments, and these new products that can act as biofertilizers and biopesticides play an important role in the establishment of a sustainable and modern agriculture. These new products are technological solutions for replacing deleterious chemical fertilizers and pesticides, maintaining soil fertility and stability, and improving crop productivity and food security. Finally, in the near future, scale-up studies will have to provide new information about the large-scale production of these materials as well as their application in the field under different biotic and abiotic stress conditions. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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13 pages, 2232 KiB

Open AccessReview

Weeds: An Insidious Enemy or a Tool to Boost Mycorrhization in Cropping Systems?

by Alessandra Trinchera and Dylan Warren Raffa

Microorganisms 2023, 11(2), 334; https://doi.org/10.3390/microorganisms11020334 - 29 Jan 2023

Cited by 4 | Viewed by 1676

Abstract

Weeds have always been considered an insidious enemy, capable of reducing crop production. Conversely, the agroecological vision attributes a key role to the spontaneous flora in promoting plant diversity and belowground interactions, which may improve the ecological performance of agroecosystems. We summarized the literature on the weeds’ arbuscular–mycorrhizae (AM) interaction and we analyzed evidence on the: (i) AM suppressive/selective effect on weed communities; (ii) effect of weeds on AM colonization, and (iii) positive role of AM-supporting weeds on forming shared mycorrhizal hyphal connections in agroecosystems. While some authors conceptualized AM as a weed control tool, others underlined their selective effect on weed communities. Recent studies suggest that AM-host weeds can participate in the development of a common mycorrhizal mycelial network (MMN) among different plants species. Nevertheless, direct evidence of the actual exchange of nutrients and C between coexisting plants through MMN in agroecosystems is missing. Although the effect of agricultural practices on plant community-AM interactions are complex, more conservative farming management seems to foster AM populations. Future studies should focus on: (i) field studies, (ii) weed communities and their traits, rather than on the most abundant species, and (iii) the use of advanced analytical techniques, able to monitor MMN development and functionality. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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14 pages, 318 KiB

Open AccessReview

Abundance, Diversity, and Function of Soil Microorganisms in Temperate Alley-Cropping Agroforestry Systems: A Review

by Lukas Beule, Anna Vaupel and Virna Estefania Moran-Rodas

Microorganisms 2022, 10(3), 616; https://doi.org/10.3390/microorganisms10030616 - 15 Mar 2022

Cited by 17 | Viewed by 4913

Abstract

Modern temperate alley-cropping systems combine rows of trees with rows of crops (agroforestry), which allows for diverse interspecific interactions such as the complementary and competitive use of resources. The complementary use of resources between trees and crops is considered the main advantage of these multifunctional land use systems over cropland monocultures. Moreover, several studies demonstrated that agroforestry systems are environmentally more sustainable than cropland monocultures. Over two decades of research on soil microorganisms in temperate alley-cropping systems are characterized by a variety of different methodological approaches and study designs to investigate the impact of agroforestry on the soil microbiome. Here, we review the available literature on the abundance, diversity, and functionality of soil microorganisms in temperate alley-cropping systems. Further, we identify current knowledge gaps as well as important experimental factors to consider in future studies. Overall, we found that temperate alley-cropping systems increase soil microbial abundance, diversity, and functions as compared to cropland monocultures, which is expected to contribute to enhanced biological soil fertility in these systems. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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