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Soil Microbiomes in the Light of Sustainable Agriculture
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Soil Microbiomes in the Light of Sustainable Agriculture

A special issue of Sustainability (ISSN 2071-1050). This special issue belongs to the section "Sustainable Agriculture".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 10271

Special Issue Editors

Dr. Olivera Topalović

E-Mail Website
Guest Editor
Section of Terrestrial Ecology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
Interests: (phyto/soil) nematodes; plant health; plant defense; phytopathology; soil microbial ecology;
Dr. Doreen Babin

E-Mail Website
Guest Editor
Department of Epidemiology and Pathogen Diagnostics, Julius Kuehn Institute, Braunschweig, Germany
Interests: soil microbial ecology; plant-microbial interactions; farming systems; plant/soil health; molecular analyses;

Special Issue Information

Dear Colleagues,

The long-term use of agrochemicals and intensive soil management practices in agroecosystems to achieve higher yields has exhausted our land and negatively impacted beneficial soil organisms with important functions for the soil and plant health. Importantly, in recent years the focus has switched from these instant and short-term solutions to more sustainable ones, such as organic farming, minimum tillage, application of cover crops and crop rotation, and use of biological products to improve plant performance. The advances in molecular and next-generation sequencing tools have increased our understanding of the importance of soil biodiversity in this regard. For instance, it has been shown that soil and plant-associated microbiomes contribute to soil fertility, plant growth and stress tolerance. In addition, in-depth studies on host–parasite associations indicate that specific microbiomes facilitate the parasitism, suggesting that the onset of plant diseases is directly dependent on the communication between different organisms. Expanding this view to the soil, which is inhabited by a myriad of organisms, the contribution of different components of soil biodiversity to a disease onset and disease suppression adds a new dimension to the definition of plant and soil health. However, a better understanding of the complex relationships between soil, plants, and (micro)biota in current and future agro-ecosystems is needed in order to harness the natural biological potential for sustainable crop production and to mitigate risks for soil and plant health.  

In this Special Issue, the focus is to explore biological functions and biotic interactions in arable soils important for the sustainable plant growth and to strengthen them through appropriate agricultural management practices. Submitted manuscripts should report on data originating from greenhouse or field studies and should involve the analysis of microbial communities (i.e., bacteria, archaea, fungi, oomycetes, or protists). Submissions considering different microbial kingdoms or microbial interactions with higher organisms are especially encouraged.

We welcome high quality original research and review articles addressing, but not limited to, the following topics:

  • Effects of different agricultural management practices on soil biodiversity;
  • Innovative tools and approaches to study soil biodiversity;
  • Multitrophic interactions in agroecosystems;
  • Taxonomic or functional modulation of the indigenous soil or plant-associated microbiome;
  • Host–parasite/pest interactions;
  • Plant-microbial defence strategies in response to pathogens and pests;
  • Role of agriculture in the One Health concept.

Dr. Olivera Topalović
Dr. Doreen Babin
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. Sustainability is an international peer-reviewed open access semimonthly 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 2400 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

  • sustainable agriculture
  • soil management
  • soil biodiversity
  • microbiomes
  • nematodes
  • plant health
  • antibiotic resistance
  • next-generation sequencing
  • rhizosphere
  • One Health concept
  • soil health

Published Papers (4 papers)

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Research

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23 pages, 3820 KiB  
Article
Soil Properties and Bacterial Communities Associated with the Rhizosphere of the Common Bean after Using Brachiaria brizantha as a Service Crop: A 10-Year Field Experiment
by Carla L. Abán, Giovanni Larama, Antonella Ducci, Jorgelina Huidobro, Michel Abanto, Silvina Vargas-Gil and Carolina Pérez-Brandan
Sustainability 2023, 15(1), 488; https://doi.org/10.3390/su15010488 - 28 Dec 2022
Cited by 4 | Viewed by 1945
Abstract
Intensive agricultural farming practices, such as monoculture, require long bare fallow periods and the overuse of agrochemicals, which compromise soil health over time. Increasing plant diversity in agroecosystems with service crops represents a promising alternative to achieving sustainability goals. However, how specific cover [...] Read more.
Intensive agricultural farming practices, such as monoculture, require long bare fallow periods and the overuse of agrochemicals, which compromise soil health over time. Increasing plant diversity in agroecosystems with service crops represents a promising alternative to achieving sustainability goals. However, how specific cover crop species influence the abundance and structure of soil bacterial communities remains to be solved. In this study, we assessed the effects of B. brizantha in two different agricultural cycles for 10 years in a common bean monoculture system in the northwestern region of Argentina (NWA) by measuring chemical, physical, and microbiological parameters in the rhizosphere, as well as by screening the rhizobiome using 16S rRNA sequencing. The ten-year inclusion of B. brizantha had a positive impact on properties in the rhizosphere compared to the common bean monoculture. The bacterial beta-diversity was different among treatments, but not the alpha-diversity. The most abundant phyla were Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi and Myxococcota. The predicted functions related to chemoheterotrophy and aerobic chemoheterotrophy were increased under B. brizantha treatments compared to the bean monoculture. The inclusion of the pasture B. brizantha contributed to restoring soil health and minimizing soil degradation. Full article
(This article belongs to the Special Issue Soil Microbiomes in the Light of Sustainable Agriculture)
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10 pages, 514 KiB  
Article
Pochonia chlamydosporia Is the Most Prevalent Fungal Species Responsible for Meloidogyne Suppression in Sustainable Vegetable Production Systems
by Zahra Ghahremani, Nuria Escudero, Ismael Marín, Anna Sanz, Sergi García, Alejandro Expósito, Ariadna Giné and Francisco Javier Sorribas
Sustainability 2022, 14(24), 16941; https://doi.org/10.3390/su142416941 - 17 Dec 2022
Cited by 1 | Viewed by 1419
Abstract
The fluctuations in Meloidogyne densities and fungal egg parasitism were determined from February 2015 to July 2016 in four vegetable production sites conducted under organic production and two sides conducted under integrated standards. At each site, the soil nematode densities at transplanting and [...] Read more.
The fluctuations in Meloidogyne densities and fungal egg parasitism were determined from February 2015 to July 2016 in four vegetable production sites conducted under organic production and two sides conducted under integrated standards. At each site, the soil nematode densities at transplanting and at the end of the crops, the galling index, the number of eggs in roots, and the percentage of fungal egg parasitism were determined, and the fungal species were identified. In addition, two pot experiments were conducted with soil taken from each site in February 2015 and 2016 to assess the fungal egg parasitism comparing non-sterile and sterile soil from each site. In field conditions, the nematode population densities in the soil decreased along the crop rotations. The maximum number of eggs per plant was recorded in the spring–summer crops. Egg parasitism ranged from 11.2 to 55% in the organic sites and from 0.8 to 16.5% in the integrated production sites. Pochonia chlamydosporia was the only fungal species isolated in five of the six sites. In both pot experiments, the number of eggs per plant was lower in non-sterile than in sterile soils, except for the M10.45 site, where fungal egg parasites were not recovered. P. chlamydosporia was the only fungal species isolated, ranging between 11 and 74%. Therefore, P. chlamidosporia was the most prevalent fungal species related to Meloidogyne suppression. Full article
(This article belongs to the Special Issue Soil Microbiomes in the Light of Sustainable Agriculture)
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18 pages, 2963 KiB  
Article
Sea Minerals Reduce Dysbiosis, Improve Pasture Productivity and Plant Morphometrics in Pasture Dieback Affected Soils
by Maria M. Whitton, Xipeng Ren, Sung J. Yu, Andrew D. Irving, Tieneke Trotter, Yadav S. Bajagai and Dragana Stanley
Sustainability 2022, 14(22), 14873; https://doi.org/10.3390/su142214873 - 10 Nov 2022
Cited by 4 | Viewed by 2279
Abstract
Pasture dieback (PD) is a grassland deteriorating syndrome resulting in grass loss and weed expansion in Australian pastures, with current estimates indicating that over four million hectares are affected. PD creates financial losses to the industry by reducing animal carrying capacity and producing [...] Read more.
Pasture dieback (PD) is a grassland deteriorating syndrome resulting in grass loss and weed expansion in Australian pastures, with current estimates indicating that over four million hectares are affected. PD creates financial losses to the industry by reducing animal carrying capacity and producing poor-quality feed, resulting in diminished productivity. After more than a decade since PD first appeared in Australia, the causes and effective treatments are still unknown. Suggested causes include soil microbiota dysbiosis, pathogens, insects, climate change and overuse of chemical fertilisers. Sea minerals have been suggested as capable of improving plants’ yield, quality, taste, and nutritional value, but were never brought into conventional practice as an alternative to chemical fertilisers. Here, we investigated the capacity of sea minerals to improve grass health and yield of PD-affected soil. The replicate plots were treated with water or with 4 mL/m2 of commercially available sea mineral product to investigate the soil chemistry profile, plant morphometrics, pasture productivity, soil microbiota profile, and microbiota-nutrient interactions. Sea mineral application significantly increased total dry matter 20 weeks after a single application, translating to an additional 967 kg/ha; this benefit was still present at 498 kg/ha eleven months post a single application. Sea mineral application improved soil microbiota by boosting beneficial taxa while reducing genera associated with arid and toxic soils. Additionally, sea mineral application increased the number of grassroots up to eleven months post a single application. Our data suggest the benefits of sea mineral application to damaged, unproductive or exhausted soils could be further explored as a natural, affordable, and non-toxic alternative to chemical fertilisers. Full article
(This article belongs to the Special Issue Soil Microbiomes in the Light of Sustainable Agriculture)
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Review

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15 pages, 528 KiB  
Review
Ditching Phosphatic Fertilizers for Phosphate-Solubilizing Biofertilizers: A Step towards Sustainable Agriculture and Environmental Health
by Adishiwot Wendimu, Tarekegn Yoseph and Tewodros Ayalew
Sustainability 2023, 15(2), 1713; https://doi.org/10.3390/su15021713 - 16 Jan 2023
Cited by 7 | Viewed by 2786
Abstract
Chemical phosphatic fertilizers are mainly produced from phosphate rocks, a natural reserve that is depleting rapidly. These chemical phosphatic fertilizers are polluting the environment at an alarming rate as a result of injudicious application to farmlands. On the other hand, phosphate-solubilizing biofertilizers (PSBs) [...] Read more.
Chemical phosphatic fertilizers are mainly produced from phosphate rocks, a natural reserve that is depleting rapidly. These chemical phosphatic fertilizers are polluting the environment at an alarming rate as a result of injudicious application to farmlands. On the other hand, phosphate-solubilizing biofertilizers (PSBs) are often considered better alternatives to industrial phosphatic fertilizers in many ways. PSBs are microorganisms capable of solubilizing insoluble forms of phosphate into soluble plant-usable forms. This paper is written with the objective of discussing the impacts of phosphatic fertilizers and making the case for why we should shift to PSBs instead. Phosphatic fertilizers have numerous impacts on the environment (water bodies, land resources, and air), and micro- and macro-organisms, including humans. Chemical fertilizers also tend to be more expensive, especially for farmers in developing countries. On the contrary, PSBs tend to be safer and way more beneficial than their chemical counterparts in that they are environmentally friendly and cheaper options of availing plant-usable phosphorus. PSBs are also involved in other beneficial roles such as the production of phytohormones and secretion of anti-phytopathogenic metabolites. The phytohormones enhance plant growth and the metabolites render crops immunity against phytopathogens. Hence, it is vital to replace chemical phosphatic fertilizers with PSB inoculants both to prevent the irreversible impacts of chemical fertilizers and to take advantage of the numerous benefits of PSBs. Moreover, it does not seem as if there is an option given the fact that the global phosphate reserve is depleting and the impact of fertilizer on the environment is worsening as time goes by. Full article
(This article belongs to the Special Issue Soil Microbiomes in the Light of Sustainable Agriculture)
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