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Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario

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A special issue of Sustainability (ISSN 2071-1050).

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 32142

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Prof. Dr. R. Z. Sayyed

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Guest Editor

Department of Microbiology, PSGVPM’s Arts, Science and Commerce College SHAHADA 425409 (KBC North Maharashtra University, Jalgaon) Maharashtra, 425409, India
Interests: plant-growth-promoting rhizobacteria; microbial siderophores; microbial biopolymers
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Dr. Noshin Ilyas

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Guest Editor

Department of Botany, PMAS Arid Agriculture University Rawalpindi, Rawalpindi 46300, Pakistan
Interests: plant–microbe interaction; stress physiology; environmental remediation
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Prof. Dr. Hesham Ali El Enshasy

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Guest Editor

Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru 81310, Malaysia
Interests: probiotics; prebiotics industry; microbiome; microbial bioprocess; microbial bioactive metabolites
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Sustainable food production is one of the greatest global challenges, particularly in the context of ever-increasing human population and climate change due to various anthropogenic activities. Improving crop yield using traditional ways of adding agrochemicals in soil negatively impacts the health of soil, the environment, and agroecosystems and causes groundwater and crop food contamination, etc. Moreover, the extensive and non-targeted use of various agrochemicals results in pesticide resistance.

The crop microbiome and plant-growth-promoting rhizobacteria (PGPR) have been regarded as among the most suitable strategies for sustaining the health of the soil, crop, and agroecosystem. PGPR plays a strategic role in the improvement of crop production under a changing climate, antioxidant defense and nutrient uptake in plants, sustainable management of plant disease (biocontrol), and seed priming. The crop microbiome plays a crucial role in the immunity of plants and their tolerance to various types of abiotic (drought, salinity, metal toxicity, pesticide residues) and biotic (pathogens, insects, pests, etc.) stresses. The crop microbiome and endophytic microbiome thus offer new opportunities for further research and development in plant growth and health.

Currently, the scientific world is experiencing a reinvigoration of microbial biotechnologies which can be used to improve agroecosystem functioning, utilizing the potential of the crop microbiome and PGPR for enhanced soil health, crop vigor, protection from abiotic and biotic stresses, development of resistance in plants, and removal of toxic substances from the soil. Thus, the increased awareness of the importance of microorganisms for plant and soil health has fueled a boom in research on PGPR.

This Special Issue on “Crop Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario” aims to gather contributions from scientists working in diverse disciplines related to:

The crop microbiome in plant health, plant immunity, plant defense, and plant growth promotion;
The crop microbiome in plant defense mechanisms;
Crop microbiome evolution;
Understanding the structure and function of the crop microbiome;
Resilience of the agricultural microbiome to climatic changes;
Plant-growth-promoting rhizobacteria (PGPR) for the improvement of crop production;
PGPR in the mitigation of abiotic stresses such as drought, salinity, heat, metal ions, and pesticide residues;
PGPR in the mitigation of biotic stresses such as pathogens (bacterial, fungal, viral, etc.), insects, pests, etc.;
PGPR in antioxidant defense mechanisms;
PGPR in nutrient mineralization and nutrient uptake;
PGPR in plant growth promotion;
PGPR—biofertilizer formulations;
PGPR—biocontrol agent formulations.

Prof. Dr. R. Z. Sayyed
Dr. Noshin Ilyas
Prof. Dr. Hesham Ali El Enshasy
Guest Editors

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Keywords

crop microbiome
PGPR
plant immunity
plant health
plant growth promotion
biocontrol
abiotic stress
biotic stress
antioxidant defense mechanisms
bioactive metabolites of PGPR
crop microbiome evolution
climate-resilient microbiome
PGPR in nutrient mineralization and nutrient uptake
PGPR—biofertilizer formulations
PGPR—biocontrol agent formulations

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Published Papers (9 papers)

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Research

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18 pages, 2323 KiB

Open AccessArticle

Seed-Borne Probiotic Yeasts Foster Plant Growth and Elicit Health Protection in Black Gram (Vigna mungo L.)

by Jeberlin Prabina Bright, Kumutha Karunanadham, Hemant S. Maheshwari, Eraivan Arutkani Aiyanathan Karuppiah, Sugitha Thankappan, Rajinimala Nataraj, Durga Pandian, Fuad Ameen, Peter Poczai and Riyaz Z. Sayyed

Sustainability 2022, 14(8), 4618; https://doi.org/10.3390/su14084618 - 12 Apr 2022

Cited by 15 | Viewed by 2770

Abstract

Black gram is one of the most indispensable components of the world food basket and the growth and health of the crop get influenced by biotic and abiotic factors. Beneficial phyto-microbes are one among them that influence the crop growth, more particularly the seed borne microbes are comparatively beneficial, that they pass from generation to generation and are associated with the plants from establishment to development. In the present study, twenty seed-borne yeasts were characterized and tested for growth promotion of black gram and their antagonism against black gram phytopathogens. Two yeasts, Pichia kudriavzevii POY5 and Issatchenkia terricola GRY4, produced indole acetic acid (IAA), siderophore, 1-amino cyclopropane-1-carboxylic acid deaminase (ACCD), and plant defense enzymes. They solubilized phosphate and zinc and fixed atmospheric nitrogen. Inoculation of these two yeast isolates and Rhizobium BMBS1 improved the seed germination, physiological parameters and yield of black gram. Inoculation of Rhizoctonia solani-challenged plants with plant growth-promoting yeasts, resulted in the synthesis of defense-related enzymes such as peroxidases (POD), chitinases, catalase (CAT), and polyphenol oxidases (PPO). Thus, the seed-borne yeasts, Pichia kudriavzevii POY5 and Issatchenkia terricola GRY4, could be used as plant probiotics for black gram. Full article

(This article belongs to the Special Issue Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario)

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15 pages, 1304 KiB

Open AccessArticle

Changes in Volatile Organic Compounds from Salt-Tolerant Trichoderma and the Biochemical Response and Growth Performance in Saline-Stressed Groundnut

by Eriyanto Yusnawan, Abdullah Taufiq, Andy Wijanarko, Dwi Ningsih Susilowati, Raden Heru Praptana, Maria V. Chandra-Hioe, Agus Supriyo and Alfi Inayati

Sustainability 2021, 13(23), 13226; https://doi.org/10.3390/su132313226 - 29 Nov 2021

Cited by 18 | Viewed by 2677

Abstract

Soil salinity is one of the major obstacles that is limiting the growth and yield of groundnut. This study aims to investigate the effect of growth-promoting fungi, Trichoderma, on groundnut plants that were cultivated in saline conditions. Five different Trichoderma isolates were grown in four different NaCl concentrations. Selected Trichoderma were then applied to the groundnut seeds and their growth and development were monitored during the study. Growth inhibition, volatile organic compounds, chlorophylls, carotenoids, total phenolics and flavonoids, and minerals were assessed between the Trichoderma treatments. Increasing the salt concentration from 0.25–0.75 M decreased the growth of the Trichoderma isolates. The amounts and profiles of the volatile organic compounds from the T. asperellum isolate were significantly different to those in the T. virens isolate. In the vegetative growth stage, increased chlorophyll content was recorded in both the T. asperellum and T. virens-treated groundnut. The leaves that were obtained from the groundnut that was treated with T. virens T.v4 contained significantly higher indole-3-acetic acid (420 µg IAA/g) than the same plants’ roots (113.3 µg IAA/g). Compared to the control groundnut, the T. asperellum T.a8-treated groundnut showed increased phenolics (31%) and flavonoids (43%) and increased shoots and biomass weight at the generative growth stage. This study demonstrates that Trichoderma, with their plant growth promotion ability, could potentially be used to improve the growth of groundnut growing under salinity stress. Importantly, salt-tolerant Trichoderma could be regarded as a beneficial and sustainable way to improve the survival of salt-sensitive crops. Full article

(This article belongs to the Special Issue Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario)

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9 pages, 403 KiB

Open AccessArticle

Improving the Climate Resilience of Rice Farming in Flood-Prone Areas through Azolla Biofertilizer and Saline-Tolerant Varieties

by Tualar Simarmata, Muhamad Khais Prayoga, Mieke R. Setiawati, Kustiwa Adinata and Silke Stöber

Sustainability 2021, 13(21), 12308; https://doi.org/10.3390/su132112308 - 8 Nov 2021

Cited by 7 | Viewed by 2836

Abstract

Rice farming in coastal areas is often victim to flooding as a result of climate change. Low-cost adaptation strategies are required to increase resilience and rice productivity in these flood-prone coastal areas. In this study, enriched Azolla extract (EAE) liquid biofertilizers, combined with selected stress-tolerant rice varieties, were tested in farmers’ fields in Pangandaran, West Java from June to October 2020. This study aimed to investigate the effectiveness of EAE in increasing the yield of different rice varieties. The research was arranged as a split-plot design with five replications. The main plot was the EAE application (T1 = 3 ton ha⁻¹ compost and T2 = 3 ton ha⁻¹ compost + 10 L ha⁻¹ of EAE), and the sub-plots were stress-tolerant rice varieties (V1 = Inpari 43, V2 = Mawar, V3 = Inpari 30, V4 = Inpara 03, V5 = Mendawak). The application of EAE of 10 L ha⁻¹ significantly affected the rice grain yield, which was 37.06% higher than that of the control plot. The average grain yield of the five varieties under EAE treatment (5.51 ton ha⁻¹) was greater than the grain yield of local farmers’ fields (3.78−4.97 ton ha⁻¹). Inpari 43 had the highest grain yield with 5.90 ton ha⁻¹, but the yield was not significantly different from the Mendawak variety (4.90 ton ha⁻¹). This result suggests that EAE and selected stress-tolerant rice varieties (Inpari 43 or Mendawak) are an effective adaptation strategy to increase rice farms’ resilience and productivity in coastal areas prone to flooding. Full article

(This article belongs to the Special Issue Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario)

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14 pages, 1905 KiB

Open AccessArticle

Co-Inoculation of Bacillus spp. for Growth Promotion and Iron Fortification in Sorghum

by Mansani Manasa, Polapally Ravinder, Subramaniam Gopalakrishnan, Vadlamudi Srinivas, R. Z. Sayyed, Hesham Ali El Enshasy, Maizatulakmal Yahayu, Ali Tan Kee Zuan, Hazem S. Kassem and Bee Hameeda

Sustainability 2021, 13(21), 12091; https://doi.org/10.3390/su132112091 - 2 Nov 2021

Cited by 38 | Viewed by 3234

Abstract

Seven Bacillus spp. isolated from the marine water and the rhizosphere of the medicinal plant Coscinium fenestratum were studied to produce plant growth promotion (PGP) traits invitro. Among the seven isolates, MMRH22 and RHPR20 produced copious amounts of PGP traits. Based on the 16S rRNA sequence, the two potent bacterial isolates, RHPR20 and MMRH22, were identified as Bacillus mojavensis and Bacillus cereus, respectively. A compatibility test between the isolates RHPR20 and MMRH22 revealed they are compatible and can be used as a consortium. Both isolates were evaluated for the plant growth promotion and the biofortification of sorghum under greenhouse conditions. Treatments included the application of MMRH22, RHPR20, their consortium (RHPR20 + MMRH22), and an uninoculated control. Inoculation with bacterial cultures resulted in a significant increase in the plant height; the number of leaves; the leaf area; the root, shoot, and leaf weight; and the yield of sorghum at 30 and 60 days after sowing (DAS). The scanning electron micrograph of the sorghum plant roots revealed extensive colonization in the plants treated with the bacterial cultures compared to the uninoculated control. The sorghum grains obtained after final harvest were analyzed for their nutrient content by ICP–OES. The biofortification in sorghum grains was varied and was found to enhance the iron content up to 97%. This study revealed that treatments with microbial consortia enhance plant growth, yield, and iron content, which could combat nutrient deficiencies in plants and humans. Full article

(This article belongs to the Special Issue Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario)

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16 pages, 2700 KiB

Open AccessArticle

The Synergistic Action of Three Piper Plant Extracts and Biofertilizer for Growth Promotion and Biocontrol of Blast Disease in Red Rice

by Ni Luh Suriani, Dewa Ngurah Suprapta, Agung Wiwiek Indrayani, Susila Herlambang, Ni Made Delly Resiani, Hind A. AL-Shwaiman, Manal M. Al Khulaifi, Abdallah M. Elgorban, Rahul Datta, Sri Gunawan and Ali Tan Kee Zuan

Sustainability 2021, 13(18), 10412; https://doi.org/10.3390/su131810412 - 18 Sep 2021

Cited by 6 | Viewed by 2677

Abstract

Bali is a world tourist destination and has many natural resources that need to be developed to support the tourism sector. One of the local Bali resources that has the potential to be developed to support tourism and food is the local red Bali rice. This local Balinese rice is a characteristic of the ecotourism area of the Jatiluwih village of Tabanan, Bali. Balinese rice is grown with inorganic pesticides and there is an urgent need to develop organic pesticides as a sustainable approach to rice farming. In this regard, extracts of piper plants can serve as the best and greenest biopesticides as plant growth-promoting rhizobacteria (PGPR), and compost functions as organic fertilizer. The present research aimed to evaluate PGPR, compost, and the synergistic biopesticidal effects of extracts of three piper plants, namely Piper caninum, Piper betle var. Nigra, and Piper betle, against blast disease in Bali red rice plants. The results showed that the synergistic action of PGPR, compost, and crude extract of piper plant provided an inhibitory activity against blast disease in rice plants where the greatest inhibition was found in a mixture of the three extracts with an inhibition of 50 cm. This shows that the mixed compounds of the three piper extracts work synergistically in suppressing blast disease; in addition, PGPR also exhibited a positive impact on the growth of red rice because PGPR produce growth hormones and various antifungal metabolites that help the plant growth and induce systemic resistance against phytopathogens. The active principles were identified as citronella, trans-geraniol, and 4.6-dipropyl-nonan-5-one. A combination of these extracts with compost and PGPR showed potential antifungal activity against blast disease at a concentration of 2%. This application also promoted the growth of Bali red rice. There is a significant increase in the number of leaves and the number of tillers, where the height is inversely proportional to the higher the extract up to 2%, as the height of the red Bali rice plant decreases. This is good because it reduces the red Bali rice stalks’ possibility of falling during small production. The piper extract mixture at a concentration of 2% had the highest effect on grain production/tonne (6.59 tonne/ha) compared to the control at only 3.21–3.41 tonnes/ ha. The 2% concentration of the extracts from the mixture of the three pipers has the highest effect on growth and red Bali rice production, and provides the greatest obstacle to the intensity of blast disease in red Bali rice. Full article

(This article belongs to the Special Issue Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario)

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8 pages, 1352 KiB

Open AccessCommunication

Inoculation of ACC Deaminase-Producing Brevibacterium linens RS16 Enhances Tolerance against Combined UV-B Radiation and Heat Stresses in Rice (Oryza sativa L.)

by Jeongyun Choi, Aritra Roy Choudhury, Song-Yi Park, Myung-Min Oh and Tongmin Sa

Sustainability 2021, 13(18), 10013; https://doi.org/10.3390/su131810013 - 7 Sep 2021

Cited by 12 | Viewed by 2015

Abstract

UV-B radiation and high temperature have detrimental effects on plant physiological and biochemical processes. The use of bacterial inoculants for stress alleviation has been regarded as a sustainable and eco-friendly approach. Hence, this study was conducted to evaluate the ability of 1-aminocyclopropane-1-caboxylate (ACC) deaminase-producing Brevibacterium linens RS16 in enhancing stress tolerance in rice against combined UV-B radiation and heat stresses. A combination of 0.5 Wm⁻² UV-B radiation and 40 °C of temperature were imposed on rice plants for 5 days. The plants imposed with combined stress had shown significantly higher ethylene emissions compared to the plants grown under normal conditions. In addition, the stress imposition had shown negative effects on the photosynthetic traits, biomass, and genetic material of rice plants. The inoculation of bacteria had shown a 26.5% and 31.8% decrease in ethylene emissions at 3 and 4 days of stress imposition compared to the non-inoculated plants. Additionally, bacterial inoculation had also enhanced plant biomass and photosynthetic traits, and had proved to be effective in restricting DNA damage under stress conditions. Taken together, the current study has shown the effective strategy of enhancing stress tolerance against the interactive effects of UV-B radiation and heat stresses by regulation of ethylene emissions through inoculating ACC deaminase-producing bacteria. Full article

(This article belongs to the Special Issue Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario)

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14 pages, 1616 KiB

Open AccessArticle

Halotolerant Microbial Consortia for Sustainable Mitigation of Salinity Stress, Growth Promotion, and Mineral Uptake in Tomato Plants and Soil Nutrient Enrichment

by Chintan Kapadia, R. Z. Sayyed, Hesham Ali El Enshasy, Harihar Vaidya, Deepshika Sharma, Nafisa Patel, Roslinda Abd Malek, Asad Syed, Abdallah M. Elgorban, Khurshid Ahmad and Ali Tan Kee Zuan

Sustainability 2021, 13(15), 8369; https://doi.org/10.3390/su13158369 - 27 Jul 2021

Cited by 64 | Viewed by 3752

Abstract

Salinity significantly impacts the growth, development, and reproductive biology of various crops such as vegetables. The cultivable area is reduced due to the accumulation of salts and chemicals currently in use and is not amenable to a large extent to avoid such abiotic stress factors. The addition of microbes enriches the soil without any adverse effects. The effects of microbial consortia comprising Bacillus sp., Delftia sp., Enterobacter sp., Achromobacter sp., was evaluated on the growth and mineral uptake in tomatoes (Solanum Lycopersicum L.) under salt stress and normal soil conditions. Salinity treatments comprising Ec 0, 2, 5, and 8 dS/m were established by mixing soil with seawater until the desired Ec was achieved. The seedlings were transplanted in the pots of the respective pH and were inoculated with microbial consortia. After sufficient growth, these seedlings were transplanted in soil seedling trays. The measurement of soil minerals such as Na, K, Ca, Mg, Cu, Mn, and pH and the Ec were evaluated and compared with the control 0 days, 15 days, and 35 days after inoculation. The results were found to be non-significant for the soil parameters. In the uninoculated seedlings’ (control) seedling trays, salt treatment significantly affected leaf, shoot, root dry weight, shoot height, number of secondary roots, chlorophyll, and mineral contents. While bacterized seedlings sown under saline soil significantly increased leaf (105.17%), shoot (105.62%), root (109.06%) dry weight, leaf number (75.68%), shoot length (92.95%), root length (146.14%), secondary roots (91.23%), and chlorophyll content (−61.49%) as compared to the control (without consortia). The Na and K intake were higher even in the presence of the microbes, but the beneficial effect of the microbe helps plants sustain in the saline environment. The inoculation of microbial consortia produced more secondary roots, which accumulate more minerals and transport substances to the different parts of the plant; thus, it produced higher biomass and growth. Results of the present study revealed that the treatment with microbial consortia could alleviate the deleterious effects of salinity stress and improve the growth of tomato plants under salinity stress. Microbial consortia appear to be the best alternative and cost-effective and sustainable approach for managing soil salinity and improving plant growth under salt stress conditions. Full article

(This article belongs to the Special Issue Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario)

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15 pages, 3505 KiB

Open AccessArticle

Biocontrol Activity of Aureubasidium pullulans and Candida orthopsilosis Isolated from Tectona grandis L. Phylloplane against Aspergillus sp. in Post-Harvested Citrus Fruit

by Dalia Sukmawati, Nurul Family, Iman Hidayat, R. Z. Sayyed, Elsayed A. Elsayed, Daniel Joe Dailin, Siti Zulaiha Hanapi, Mohammad A. Wadaan and Hesham El Enshasy

Sustainability 2021, 13(13), 7479; https://doi.org/10.3390/su13137479 - 5 Jul 2021

Cited by 34 | Viewed by 3916

Abstract

This study aimed to isolate and identify moulds from rotten Citrus sinensis post-harvests and to investigate the activity of antagonist and biocontrol activity moulds that cause citrus fruit rotting. A total of 12 mould isolates were obtained. Following the pathogenicity test, two representative mould isolates were selected and identified based on the sequence analyses of internal transcribed spacer (ITS) regions of the rDNA. Methods used in this study include isolation of fungal postharvest diseases, pathogenicity assay, antagonism assay, growth curve analysis, in vitro biocontrol assay, and molecular phylogenetic analysis. Two isolates of fungal postharvest diseases were determined as the most destructive pathogens. The biocontrol assay showed that isolates of Y1 and Y10 were capable to reduce the growth of fungal isolates K6 and K9 and mitigate up to 100% of the damage of sweet citrus fruits after 7 days of incubation. The moulds were identified as K6 (Aspergillus flavus sensu lato) and K9 (Aspergillus niger sensu lato). Phylogenetic analysis showed that the Y10 yeast isolate was identified as Candida orthopsilosis, whereas the Y1 isolate had a close genetic relationship with Aureobasidium pullulans and possibly belongs to a new species. Further analysis is necessary to confirm this finding. Full article

(This article belongs to the Special Issue Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario)

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Review

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26 pages, 1713 KiB

Open AccessReview

Halotolerant Rhizobacteria for Salinity-Stress Mitigation: Diversity, Mechanisms and Molecular Approaches

by Alka Sagar, Shalini Rai, Noshin Ilyas, R. Z. Sayyed, Ahmad I. Al-Turki, Hesham Ali El Enshasy and Tualar Simarmata

Sustainability 2022, 14(1), 490; https://doi.org/10.3390/su14010490 - 3 Jan 2022

Cited by 52 | Viewed by 5596

Abstract

Agriculture is the best foundation for human livelihoods, and, in this respect, crop production has been forced to adopt sustainable farming practices. However, soil salinity severely affects crop growth, the degradation of soil quality, and fertility in many countries of the world. This results in the loss of profitability, the growth of agricultural yields, and the step-by-step decline of the soil nutrient content. Thus, researchers have focused on searching for halotolerant and plant growth-promoting bacteria (PGPB) to increase soil fertility and productivity. The beneficial bacteria are frequently connected with the plant rhizosphere and can alleviate plant growth under salinity stress through direct or indirect mechanisms. In this context, PGPB have attained a unique position. The responses include an increased rate of photosynthesis, high production of antioxidants, osmolyte accumulation, decreased Na⁺ ions, maintenance of the water balance, a high germination rate, and well-developed root and shoot elongation under salt-stress conditions. Therefore, the use of PGPB as bioformulations under salinity stress has been an emerging research avenue for the last few years, and applications of biopesticides and biofertilizers are being considered as alternative tools for sustainable agriculture, as they are ecofriendly and minimize all kinds of stresses. Halotolerant PGPB possess greater potential for use in salinity-affected soil as sustainable bioinoculants and for the bioremediation of salt-affected soil. Full article

(This article belongs to the Special Issue Rhizo-Microbiome for the Sustenance of Agro-Ecosystems in the Changing Climate Scenario)

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