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Land
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Control of Soil Microbiota on Soil Ecosystem Functioning and Plant...
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Control of Soil Microbiota on Soil Ecosystem Functioning and Plant Yields

A special issue of Land (ISSN 2073-445X). This special issue belongs to the section "Land Systems and Global Change".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 10746

Special Issue Editors

Dr. Shamina Imran Pathan

E-Mail Website
Guest Editor
Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine, 28 - 50144 Florence, Italy
Interests: soil microbial ecology; functional diversity; plant–soil–microbial interaction
Prof. Dr. Giacomo Pietramellara

E-Mail Website
Guest Editor
Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine, 28 - 50144 Florence, Italy
Interests: soil chemistry; agroecosystem functioning; extracellular DNA; microbial necromass

Special Issue Information

Dear Colleagues,

Soil constitutes one of the most diverse ecosystems on the earth. A handful of soil contains, on average, more than a thousand million cells encompassing bacteria, fungi, archaea, protists, earthworms, termites, and more—collectively known as the soil biome. Soil biodiversity, especially the soil microbiome, which mainly includes bacteria, fungi, and archaea, plays a critical role in ecosystem functions such as terrestrial biogeochemical chemical cycles and the maintenance of soil fertility, by decomposing and mineralizing organic byproducts into inorganic forms and simpler organic forms which encourage plant health and growth. Productive soil continually supports higher biomass production and can be used as a proxy of ecosystem health. Harnessing these soil processes can help us to meet the growing demand for agricultural productivity and healthy ecosystems. However, this first requires a deeper understanding of the link between soil microbiome structure and soil functions.

This Special Issue aims to bring together high-quality scientific research papers, reviews, and opinion papers highlighting links between soil microbial communities and soil functioning, in order to examine how these changes affect plant health and production in agroecosystems. Studies that cover the following topics: (i) soil management practices (organic vs. synthetic fertilizers, tillage system); (ii) environmental disturbances (e.g., drought, flooding, salinity, warming, etc.), will be given the highest priority. Different approaches ranging from traditional methods to advanced molecular (metagenomic and transcriptomic) and biochemical techniques (PLFA-SIP, proteomic) for studying soil microbiomes and their role in soil functioning are welcome. 

Interested authors should submit abstracts to the Guest Editors, Shamina Imran Pathan (shamina.pathan@unifi.it) and Giacomo Pietramellara (giacomo.pietramellara@unifi.it) for assessment and approval before submitting full manuscripts. Authors are encouraged to submit their contributions as soon as possible, with abstracts being submitted prior to 17 March 2022 and the full manuscript by 17 June 2022.      

Dr. Shamina Imran Pathan
Prof. Dr. Giacomo Pietramellara
Guest Editors

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. Land 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 2600 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

  • microbial community structure
  • functional diversity
  • soil-plant-interaction
  • ecosystem functioning
  • climate change

Published Papers (5 papers)

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Research

15 pages, 2313 KiB  
Article
LABs Fermentation Side-Product Positively Influences Rhizosphere and Plant Growth in Greenhouse Lettuce and Tomatoes
by Gabriele Bellotti, Eren Taskin, Simone Sello, Cristina Sudiro, Rossella Bortolaso, Francesca Bandini, Maria Chiara Guerrieri, Pier Sandro Cocconcelli, Francesco Vuolo and Edoardo Puglisi
Land 2022, 11(9), 1544; https://doi.org/10.3390/land11091544 - 12 Sep 2022
Cited by 3 | Viewed by 2395
Abstract
New agronomical policies aim to achieve greener agricultural systems, sustainable fertilizers and fungicides, a reduction in Greenhouse gases (GHG), and an increase in circular economic models. In this context, new solutions are needed for the market, but it is necessary to carefully assess [...] Read more.
New agronomical policies aim to achieve greener agricultural systems, sustainable fertilizers and fungicides, a reduction in Greenhouse gases (GHG), and an increase in circular economic models. In this context, new solutions are needed for the market, but it is necessary to carefully assess both their efficacy and their ecological impact. Previously, we reported the biostimulatory activity on soil microbiome for a side-product from Lactic Acid Bacteria (LABs) fermentation: a concentrated post-centrifugation eluate. In the present study, we investigated whether this solution could partially substitute mineral N (N70% + N30% from eluate) in a fertigation (N100% vs. N70%) regime for tomato and lettuce under greenhouse conditions. The impact of the application was investigated through plant physiological parameters (number and weight of ripened fruits, shoots, and roots biomass) and biodiversity of the rhizosphere microbial composition of bacteria and fungi (High-Throughput Sequencing—HTS). The eluate (i) enhanced the plant canopy in lettuce; (ii) increased the shoot/root biomass ratio in both tomato and lettuce; and (iii) increased the harvest and delayed fruit ripening in tomato. Moreover, we found a strong correlation between the eluate and the enrichment for OTUs of plant-growth-promoting microbes (PGPMs) such as Sphingomonas sediminicola, Knoellia subterranean, and Funneliformis mosseae. These findings suggest that integrating the eluate was beneficial for the plant growth, performance, and yield in both tomato and lettuce, and additionally, it enriched specialized functional microbial communities in the rhizosphere. Further studies will investigate the underlying mechanisms regulating the selective activity of the eluate toward PGPMs and its biostimulatory activity towards target crops. Full article
(This article belongs to the Special Issue Control of Soil Microbiota on Soil Ecosystem Functioning and Plant Yields)
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12 pages, 1288 KiB  
Article
Effect of Soil Aggregate Size on Vineyard Bacterial Communities under Organic and Conventional Agro-Managements
by Yosef Steinberger, Tirza Doniger, Chen Sherman, Itaii Applebaum and Gil Eshel
Land 2022, 11(9), 1517; https://doi.org/10.3390/land11091517 - 08 Sep 2022
Cited by 2 | Viewed by 1471
Abstract
Soil microorganisms are an indispensable component of natural ecosystems and play an important role in agro-management ecosystems. However, the function of soil microbial communities is still a black box. The present study aimed to investigate the effect of organic and conventional agro-management practices [...] Read more.
Soil microorganisms are an indispensable component of natural ecosystems and play an important role in agro-management ecosystems. However, the function of soil microbial communities is still a black box. The present study aimed to investigate the effect of organic and conventional agro-management practices in a vineyard on the soil’s bacterial community and its composition in three different soil aggregate sizes using functional profiles derived using 16S rDNA metagenomics analysis for elucidating the metabolic capabilities of soil microbial communities. Soil samples were compared in terms of community composition and functionality. A clear distinction was found between the two managements. The soil samples contained 12 phyla and 45 orders, where Proteobacteria was the most common phylum in all treatments. Twenty-three functional profiles were obtained for both treatments and three aggregate sizes, showing similarity in their function, suggesting that functionality is due to the community’s composition and environmental conditions. The results indicate that organic farming systems have a beneficial effect on microbial diversity and encourage ecosystem multifunctionality. Full article
(This article belongs to the Special Issue Control of Soil Microbiota on Soil Ecosystem Functioning and Plant Yields)
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24 pages, 3386 KiB  
Article
Exploring Functional Diversity and Community Structure of Diazotrophic Endophytic Bacteria Associated with Pennisetum glaucum Growing under Field in a Semi-Arid Region
by Garima Gupta, Sangeeta Paul, Sachidanand Singh, Giacomo Pietramellara, Shamina Imran Pathan, Subhan Danish, Dilfuza Jabborova, Rahul Datta and Prabhat Nath Jha
Land 2022, 11(7), 991; https://doi.org/10.3390/land11070991 - 29 Jun 2022
Cited by 2 | Viewed by 1847
Abstract
Diazotrophic endophytic bacteria (DEB) are the key drivers of nitrogen fixation in rainfed soil ecosystems and, hence, can influence the growth and yield of crop plants. Therefore, the present work investigated the structure and composition of the DEB community at different growth stages [...] Read more.
Diazotrophic endophytic bacteria (DEB) are the key drivers of nitrogen fixation in rainfed soil ecosystems and, hence, can influence the growth and yield of crop plants. Therefore, the present work investigated the structure and composition of the DEB community at different growth stages of field-grown pearl millet plants, employing the cultivation-dependent method. Diazotrophy of the bacterial isolates was confirmed by acetylene reduction assay and amplification of the nifH gene. ERIC-PCR-based DNA fingerprinting, followed by 16S rRNA gene analysis of isolates recovered at different time intervals, demonstrated the highest bacterial diversity during early (up to 28 DAS (Days after sowing)) and late (63 DAS onwards) stages, as compared to the vegetative growth stage (28–56 DAS). Among all species, Pseudomonas aeruginosa was the most dominant endophyte. Assuming modulation of the immune response as one of the tactics for successful colonization of P. aeruginosa PM389, we studied the expression of the profile of defense genes of wheat, used as a host plant, in response to P. aeruginosa inoculation. Most of the pathogenesis-related PR genes were induced initially (at 6 h after infection (HAI)), followed by their downregulation at 12 HAI. The trend of bacterial colonization was quantified by qPCR of 16S rRNAs. The results obtained in the present study indicated an attenuated defense response in host plants towards endophytic bacteria, which is an important feature that helps endophytes establish themselves inside the endosphere of roots. Full article
(This article belongs to the Special Issue Control of Soil Microbiota on Soil Ecosystem Functioning and Plant Yields)
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21 pages, 4483 KiB  
Article
Soil Slope Exposure Affects Physico-Chemical and Microbiological Properties in Soil Aggregate Size Fractions
by Tommaso Bardelli, Shamina Imran Pathan, Paola Arfaioli, Nadia Vignozzi, Sergio Pellegrini, Flavio Fornasier, Markus Egli, María Gómez-Brandón, Heribert Insam, Giacomo Pietramellara and Judith Ascher-Jenull
Land 2022, 11(5), 750; https://doi.org/10.3390/land11050750 - 19 May 2022
Cited by 2 | Viewed by 1786
Abstract
Slope exposure is known to affect soil biogeochemical processes in mountainous forest ecosystems, but little attention has yet been paid to its influence at a soil aggregate scale. Therefore, we evaluated the effects of slope exposure (north- vs south-facing slope) on the physico-chemical [...] Read more.
Slope exposure is known to affect soil biogeochemical processes in mountainous forest ecosystems, but little attention has yet been paid to its influence at a soil aggregate scale. Therefore, we evaluated the effects of slope exposure (north- vs south-facing slope) on the physico-chemical and microbiological properties of bulk soil and dry-sieved and water-stable aggregate size fractions in both organic (OF) and mineral (AE) horizons in an Italian alpine forest. The changes in organic carbon (OC) and nitrogen (ON) fractions were assessed together with a battery of thirteen enzyme activities involved in the main nutrient cycles. In addition, soil biological properties including microbial biomass (estimated as double-stranded DNA content), and microbial activity (assessed as the ratio between the extra-(exDNA) and intracellular (iDNA) fractions of the total soil DNA pool) were determined. The OF horizon at the north-facing slope was enriched in recalcitrant and insoluble OC and ON fractions and characterized by a lower microbial activity, as indicated by the higher exDNA/iDNA ratio with respect to the south-facing slope. On the contrary, exDNA and iDNA contents, microbial biomass, as well as most of the enzyme activities, reached higher levels at the southern exposure in the AE horizon. These exposure-effects were bulk soil- and aggregate size fraction-specific. Overall, lower values of the chemical and microbiological parameters were found in the water-stable fraction. Our findings indicate that slope exposure (and thus topography), soil horizon, and aggregate size distinctly influence soil OC dynamics in mountain ecosystems. Full article
(This article belongs to the Special Issue Control of Soil Microbiota on Soil Ecosystem Functioning and Plant Yields)
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20 pages, 7526 KiB  
Article
Bio-Priming with Compatible Rhizospheric Microbes Enhances Growth and Micronutrient Uptake of Red Cabbage
by Deepranjan Sarkar, Amitava Rakshit, Hanuman Prasad Parewa, Subhan Danish, Saleh Alfarraj and Rahul Datta
Land 2022, 11(4), 536; https://doi.org/10.3390/land11040536 - 07 Apr 2022
Cited by 12 | Viewed by 1812
Abstract
Red cabbage is known as the millennium’s functional food, which has a lot of importance in our diet because of the health-promoting ingredients present in it. The current study investigated the synergistic relationship of rhizospheric-competent microbial agents (Trichoderma harzianum, Pseudomonas fluorescens [...] Read more.
Red cabbage is known as the millennium’s functional food, which has a lot of importance in our diet because of the health-promoting ingredients present in it. The current study investigated the synergistic relationship of rhizospheric-competent microbial agents (Trichoderma harzianum, Pseudomonas fluorescens, and Bacillus subtilis) in modulating the performance of red cabbage under the field conditions of Middle Gangetic Plains, India. Growth parameters were studied at three developmental stages, viz., pre-cupping, early head formation, and maturity. Our results suggested that the dual application of T. harzianum + P. fluorescens along with the 75% recommended dose of fertilizers (RDF) increased the number of leaves (24.6), leaf area (537.2 cm2), root length (19.8 cm), and micronutrient uptake (Fe, Mn, and Cu) by head of the crop, whereas the co-inoculation of P. fluorescens and B. subtilis along with 75% RDF enhanced plant spread (39.0 cm), earliness (95.2 days), and Zn uptake. Maximum plant height (28.7 cm) and chlorophyll (SPAD, 77.3) were recorded in 100% RDF (120:60:60 kg ha−1) and the combination of T. harzianum + B. subtilis along with 75% RDF, respectively. Interestingly, consortium (T. harzianum + P. fluorescens) bio-primed plants recorded about 14% higher root length in comparison to plants receiving sole fertilizers. The regression analysis revealed a significant relationship of Fe and Mn uptake with chlorophyll (SPAD) and between Zn uptake and the earliness of the crop. The present study indicated that seedling bio-priming with the dual consortium of efficient bio-agents is a viable strategy to lessen our dependence on chemical fertilizers for improving red cabbage production. Full article
(This article belongs to the Special Issue Control of Soil Microbiota on Soil Ecosystem Functioning and Plant Yields)
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