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A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (15 December 2020) | Viewed by 39407

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Prof. Dr. Tongmin Sa

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Guest Editor

Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
Interests: soil salinity; plant growth promotion; ethylene; bacterial inoculant; soil microbiology; long-term fertilization
Special Issues, Collections and Topics in MDPI journals

Dr. Rangasamy Anandham

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Co-Guest Editor

Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore 641003, India
Interests: plant growth promotion; plant–microbe interaction; sulfur oxidation; insect gut microbiota; soil microbiota; microbiome of contaminated environment; molecular microbial taxonomy
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Special Issue Information

Dear Colleagues,

We are inviting submissions to the Special Issue on “Environmental Factors Shaping the Soil Microbiome”.

The soil microenvironment is controlled by the dynamics of soil microbial diversity and community profiles. The microbial community profiles define the quality of soil, and various abiotic and biotic factors are responsible for shaping the soil microbiome. Different environmental factors such as long-term fertilization, soil salinization, soil contamination, atmospheric CO₂ concentration and altered precipitation effect the microbial community of the soil. The preliminary idea about the microbial community profiles of the particular soil sample will enable us to screen potential microbes, which could be helpful in developing technologies to improve soil quality.

In this Special Issue, we invite submissions concentrating on soil microbial community profiles shaped by multifactorial environmental conditions. Both research and review articles are open to submission in this issue.

Prof. Dr. Tongmin Sa
Dr. Rangasamy Anandham
Guest Editors

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Keywords

Soil microbial community
Environmental factors
Abiotic and biotic factors
Pyrosequencing
Sequence analysis
Long-term fertilization
Soil contamination
Soil pollutant
Atmospheric CO₂ concentration
Precipitation
Microbial diversity

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review

4 pages, 185 KiB

Open AccessEditorial

Editorial for Special Issue “Environmental Factors Shaping the Soil Microbiome”

by Rangasamy Anandham and Tongmin Sa

Appl. Sci. 2021, 11(21), 10387; https://doi.org/10.3390/app112110387 - 5 Nov 2021

Viewed by 1708

Abstract

Soil is a complex system consisting of various abiotic and biotic factors interacting among themselves in a particular time period. These biotic factors are particularly affected by a large number of disturbances or perturbations occurring in the micro-niches. Soil microbiome is the paramount biotic factor responsible for nutrient cycling that in turn determines soil health and quality. However, there are limitations in studying soil systems as there are a number of unknown boxes that need to be checked before understanding their full-fledged contribution to the environment. The microbial diversity in the soil can be affected by salinity, contaminant, fertilization, nutrient accumulation, and cultivation practices. Additionally, plants can also benefit from these changes in microbial community composition, and novel microbial isolates can be used for enhancing their growth under various stress conditions. Collectively, this Special Issue includes various studies that determine key abiotic and biotic factors that can result in changes in microbial community composition in the soil system. These studies are carried out in specified environmental niches rather than microcosms, which provides a broader context in which to understand microbial dynamics. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

Research

Jump to: Editorial, Review

10 pages, 1862 KiB

Open AccessCommunication

Structural and Functional Shift in Soil Bacterial Community in Response to Long-Term Compost Amendment in Paddy Field

by Sookjin Kim, Sandipan Samaddar, Poulami Chatterjee, Aritra Roy Choudhury, Jeongyun Choi, Jongseo Choi and Tongmin Sa

Appl. Sci. 2021, 11(5), 2183; https://doi.org/10.3390/app11052183 - 2 Mar 2021

Cited by 12 | Viewed by 2409

Abstract

Microbial community composition and diversity of agricultural soils primarily depend on management practices. The application of compost on agricultural fields is known to increase soil fertility, which can also help to enhance agricultural productivity. The effects of long-term application of compost along with nitrogen (N), phosphorus (P), and potassium (K) (+Compost) on soil bacterial diversity and community profiles were assessed by amplicon sequencing targeting the 16S rRNA gene of bacteria and compared with those on soils that received only NPK but not compost (−Compost). Ordination plot showed treatments to cluster differently, implying changes in community composition, which were validated with taxonomical data showing Firmicutes, Actinobacteria, and their related classes to be significantly higher in +Compost than in −Compost soils. The predicted abundance of functional genes related to plant growth promotion, development, and decomposition was significantly higher in compost-amended soil than in soils without compost. The results are of particular importance as they provide insights into designing management practices to promote agricultural sustainability. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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11 pages, 2325 KiB

Open AccessArticle

Interactive Effects of Scion and Rootstock Genotypes on the Root Microbiome of Grapevines (Vitis spp. L.)

by Stefanie Nicoline Vink, Francisco Dini-Andreote, Rebecca Höfle, Anna Kicherer and Joana Falcão Salles

Appl. Sci. 2021, 11(4), 1615; https://doi.org/10.3390/app11041615 - 10 Feb 2021

Cited by 24 | Viewed by 4863

Abstract

Diversity and community structure of soil microorganisms are increasingly recognized as important contributors to sustainable agriculture and plant health. In viticulture, grapevine scion cultivars are grafted onto rootstocks to reduce the incidence of the grapevine pest phylloxera. However, it is unknown to what extent this practice influences root-associated microbial communities. A field survey of bacteria in soil surrounding the roots (rhizosphere) of 4 cultivars × 4 rootstock combinations was conducted to determine whether rootstock and cultivar genotypes are important drivers of rhizosphere community diversity and composition. Differences in α-diversity was highly dependent on rootstock–cultivar combinations, while bacterial community structure primarily clustered according to cultivar differences, followed by differences in rootstocks. Twenty-four bacterial indicator genera were significantly more abundant in one or more cultivars, while only thirteen were found to be specifically associated with one or more rootstock genotypes, but there was little overlap between cultivar and rootstock indicator genera. Bacterial diversity in grafted grapevines was affected by both cultivar and rootstock identity, but this effect was dependent on which diversity measure was being examined (i.e., α- or β-diversity) and specific rootstock–cultivar combinations. These findings could have functional implications, for instance, if specific combinations varied in their ability to attract beneficial microbial taxa which can control pathogens and/or assist plant performance. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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11 pages, 1756 KiB

Open AccessCommunication

Correlation between Soil Bacterial Community Structure and Soil Properties in Cultivation Sites of 13-Year-Old Wild-Simulated Ginseng (Panax ginseng C.A. Meyer)

by Kiyoon Kim, Hyun Jun Kim, Dae Hui Jeong, Jeong Hoon Huh, Kwon Seok Jeon and Yurry Um

Appl. Sci. 2021, 11(3), 937; https://doi.org/10.3390/app11030937 - 20 Jan 2021

Cited by 5 | Viewed by 1905

Abstract

Soil properties are one of the major factors determining the growth of vegetation. These properties drive the selection of the dominant bacterial community profiles, which eventually determines the soil quality and fertility. The abundance of preferential bacterial community assists in better productivity of a particular type of vegetation. The increasing focus on the health and well-being of the human population has resulted in a shift in paradigm to concentrate on the cultivation of medicinal plants such as Wild-simulated ginseng (WSG). These plant species take a long time for their growth and are generally cultivated in the mountainous forest trenches of Far East countries like South Korea. This study was conducted to decipher the bacterial community profiles and their correlation with soil chemical properties, which would give a broader idea about the optimum growing conditions of such an important medicinal plant. The important edaphic factor determined in this study was the soil pH, which was recorded to be acidic in all the studied cultivation sites. In agreement with the edaphic factor, the relative abundance of Acidobacteria was found to be highest as this phylum prefers to grow in acidic soils. Moreover, the total organic matter, total nitrogen and cation exchange capacity were found to be significantly correlated with the bacterial community. Hence, these results will help to identify the suitable cultivation sites for WSG and increase the productivity of these medicinal plants. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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15 pages, 2563 KiB

Open AccessArticle

Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

by Lingzi Mo, Augusto Zanella, Xiaohua Chen, Bin Peng, Jiahui Lin, Jiaxuan Su, Xinghao Luo, Guoliang Xu and Andrea Squartini

Appl. Sci. 2021, 11(3), 918; https://doi.org/10.3390/app11030918 - 20 Jan 2021

Cited by 6 | Viewed by 2557

Abstract

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH₄NO₃ was added as external N source, with four dosages (N0 = 0 kg N ha⁻² y⁻¹, N1 = 50 kg N ha⁻² y⁻¹, N2 = 100 kg N ha⁻² y⁻¹, N3 = 150 kg N ha⁻² y⁻¹). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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8 pages, 1142 KiB

Open AccessCommunication

Long-Term Exposure to Azo Dyes from Textile Wastewater Causes the Abundance of Saccharibacteria Population

by Ramasamy Krishnamoorthy, Aritra Roy Choudhury, Polpass Arul Jose, Kathirvel Suganya, Murugaiyan Senthilkumar, James Prabhakaran, Nellaiappan Olaganathan Gopal, Jeongyun Choi, Kiyoon Kim, Rangasamy Anandham and Tongmin Sa

Appl. Sci. 2021, 11(1), 379; https://doi.org/10.3390/app11010379 - 2 Jan 2021

Cited by 19 | Viewed by 3810

Abstract

Discharge of untreated wastewater is one of the major problems in various countries. The use of azo dyes in textile industries are one of the key xenobiotic compounds which effect both soil and water ecosystems and result in drastic effect on the microbial communities. Orathupalayam dam, which is constructed over Noyyal river in Tamil Nadu, India has become a sink of wastewater from the nearby textile industries. The present study had aimed to characterize the bacterial diversity and community profiles of soil collected from the vicinity of the dam (DS) and allied agricultural field (ALS) nearby the catchment area. The soil dehydrogenase and cellulase activities were significantly lower in DS compared to ALS. Additionally, the long-term exposure to azo dye compounds resulted in higher relative abundance of Saccharibacteria (36.4%) which are important for degradation of azo dyes. On the other hand, the relative abundance of Proteobacteria (25.4%) were higher in ALS. Interestingly, the abundance of Saccharibacteria (15.2%) were also prominent in ALS suggesting that the azo compounds might have deposited in the agricultural field through irrigation. Hence, this study revealed the potential bacterial phyla which can be key drivers for designing viable technologies for degradation of xenobiotic dyes. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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18 pages, 3390 KiB

Open AccessArticle

Identification of Bacterial and Fungal Communities in the Roots of Orchids and Surrounding Soil in Heavy Metal Contaminated Area of Mining Heaps

by Miroslav Böhmer, Daniel Ozdín, Matúš Račko, Michal Lichvár, Jaroslav Budiš and Tomáš Szemes

Appl. Sci. 2020, 10(20), 7367; https://doi.org/10.3390/app10207367 - 21 Oct 2020

Cited by 15 | Viewed by 3653

Abstract

Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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18 pages, 5533 KiB

Open AccessArticle

Structure of Bacterial Communities in Phosphorus-Enriched Rhizosphere Soils

by Yuwei Hu, Changqun Duan, Denggao Fu, Xiaoni Wu, Kai Yan, Eustace Fernando, Samantha C. Karunarathna, Itthayakorn Promputtha, Peter E. Mortimer and Jianchu Xu

Appl. Sci. 2020, 10(18), 6387; https://doi.org/10.3390/app10186387 - 14 Sep 2020

Cited by 8 | Viewed by 3017

Abstract

Although phytoremediation is the main method for P-removal and maintaining ecosystem balance in geological phosphorus-enriched soils (PES), little is known about the structure and function of microbial communities in PES. Interactions between plants and soil microorganisms mainly occur in the rhizosphere. The aim of this work was to investigate the composition and diversity of bacterial communities found in rhizosphere soils associated with the following three dominant plant species: Erianthus rufipilus, Coriaria nepalensis, and Pinus yunnanensis. In addition, we compared these rhizosphere bacterial communities with those derived from bulk soils and grassland plots in PES from the Dianchi Lake basin of southwestern China. The Illumina MiSeq platform for high-throughput sequencing of 16S rRNA was used for the taxonomy and the analysis of soil bacterial communities. The results showed higher bacterial diversity and nutrient content in rhizosphere soils as compared with bulk soils. Rhizosphere bacteria were predominantly comprised of Proteobacteria (24.43%) and Acidobacteria (21.09%), followed by Verrucomicrobia (19.48%) and Planctomycetes (9.20%). A comparison of rhizosphere soils of the selected plant species in our study and the grassland plots showed that Acidobacteria were the most abundant in the rhizosphere soil of E. rufipilus; Bradyrhizobiaceae and Rhizobiaceae in the order Rhizobiales from C. nepalensis were found to have the greatest abundance; and Verrucomicrobia and Planctomycetes were in higher abundance in P. yunnanensis rhizosphere soils and in grassland plots. A redundancy analysis revealed that bacterial abundance and diversity were mainly influenced by soil water content, soil organic matter, and total nitrogen. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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16 pages, 2665 KiB

Open AccessArticle

Plant Species-Dependent Effects of Liming and Plant Residue Incorporation on Soil Bacterial Community and Activity in an Acidic Orchard Soil

by Xiaodi Liu, Zengwei Feng, Yang Zhou, Honghui Zhu and Qing Yao

Appl. Sci. 2020, 10(16), 5681; https://doi.org/10.3390/app10165681 - 15 Aug 2020

Cited by 2 | Viewed by 2476

Abstract

Both liming and plant residue incorporation are widely used practices for the amelioration of acidic soils—however, the difference in their effects is still not fully understood, especially regarding the microbial community. In this study, we took the acidic soils from a subtropical orchard as target soils, and implemented liming and plant residue incorporation with a leguminous and a gramineous cover crop as test plants. After six months of growth, soil pH, total organic carbon (TOC), dissolved organic carbon (DOC) and nutrient contents were determined, soil enzymes involving C, N, P cycling were assayed, and microbial communities were also analyzed using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). Results showed that liming was more effective in elevating soil pH, while plant residue incorporation exerted a more comprehensive influence—not only on soil pH, but also on soil enzyme activity and microbial community. PCR-DGGE analysis revealed that liming changed the microbial community structure more greatly than plant residue incorporation, while plant residue incorporation altered the microbial community composition much more than liming. The growth responses of test plants to liming and plant residue incorporation depended on plant species, indicating the necessity to select appropriate practice for a particular crop. A further, detailed investigation into the microbial community composition, and the respective functions using metagenomic approach, is also suggested. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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17 pages, 3498 KiB

Open AccessArticle

Effect of Arbuscular Mycorrhizal Fungi (AMF) and Plant Growth-Promoting Bacteria (PGPR) Inoculations on Elaeagnus angustifolia L. in Saline Soil

by Jing Pan, Cuihua Huang, Fei Peng, Wenjuan Zhang, Jun Luo, Shaoxiu Ma and Xian Xue

Appl. Sci. 2020, 10(3), 945; https://doi.org/10.3390/app10030945 - 1 Feb 2020

Cited by 54 | Viewed by 6960

Abstract

Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) are considered highly-efficient agents for conferring salt tolerance in host plants and improving soil fertility in rhizosphere. However, information about the inoculation of beneficial microbes on halophytes in arid and semi-arid regions remains inadequate. The objective of this study was to evaluate the influence of AMF (Glomus mosseae) inoculation, alone or in combination with PGPR (Bacillus amyloliquefaciens), on biomass accumulation, morphological characteristics, photosynthetic capacity, and rhizospheric soil enzyme activities of Elaeagnus angustifolia L., a typical halophyte in the northwest of China. The results indicate that, for one-year-old seedlings of Elaeagnus angustifolia L., AMF significantly promoted biomass accumulation in aboveground organs, increased the numbers of leaves and branches, and improved the leaf areas, stem diameters and plant height. AMF-mediated morphological characteristics of aboveground organs favored light interception and absorption and maximized the capacities for photosynthesis, transpiration, carbon dioxide assimilation and gas exchange of Elaeagnus angustifolia L. seedlings in saline soil. AMF also promoted root growth, modified root architecture, and enhanced soil enzyme activities. Elaeagnus angustifolia L. was more responsive to specific inoculation by AMF than by a combination of AMF and PGPR or by solely PGPR in saline soils. Therefore, we suggest that G. mosseae can be used in saline soil to enhance Elaeagnus angustifolia L. seedlings growth and improve soil nutrient uptake. This represents a biological technique to aid in restoration of saline-degraded areas. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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Review

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11 pages, 597 KiB

Open AccessFeature PaperReview

Soil Is Still an Unknown Biological System

by Paolo Nannipieri

Appl. Sci. 2020, 10(11), 3717; https://doi.org/10.3390/app10113717 - 27 May 2020

Cited by 18 | Viewed by 4287

Abstract

More than a thousand million cells encompassing bacteria, fungi, archaea, and protists inhabit a handful of soil. The bacterial and fungal biomass can account for 1–2 and 2–5 tha⁻¹ in temperate grassland soils, respectively. Despite this huge microbial biomass, the volume occupied by microorganisms is less than 1% of the available soil volume because most micro-niches are hostile environments. Soil microorganisms and fauna play a crucial role in soil ecosystem services, and functional redundancy is a peculiar characteristic of soil as a biological system. Complex interactions are often mediated by molecular signals that occur between microbes, microbes and plants, and microbes and animals. Several microbial species have been detected in soil using molecular techniques, particularly amplicon sequencing and metagenomics. However, their activities in situ are still poorly known because the use of soil metatranscriptomics and, in particular, soil proteomics is still a technical challenge. A holistic approach with the use of labelled compounds can give quantitative information on nutrient dynamics in the soil-plant system. Despite the remarkable technical progresses and the use of imaginative approaches, there are many knowledge gaps about soil as a biological system. These gaps are discussed from a historic perspective, starting from the seven grand questions proposed by Selman A. Waksman in 1927. Full article

(This article belongs to the Special Issue Environmental Factors Shaping the Soil Microbiome)

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