Trichoderma species : our best fungal allies in the biocontrol of plant diseases : a review

Biocontrol agents (BCA) have been an important tool in agriculture to prevent crop losses due to plant pathogens infections and to increase plant food production globally, diminishing the necessity for chemical pesticides and fertilizers and offering a more sustainable and environmentally friendly option. Fungi from the genus Trichoderma are among the most used and studied microorganisms as BCA due to the variety of biocontrol traits, such as parasitism, antibiosis, secondary metabolites (SM) production, and plant defense system induction. Several Trichoderma species are well-known mycoparasites. However, some of those species can antagonize other organisms such as nematodes and plant pests, making this fungus a very versatile BCA. Trichoderma has been used in agriculture as part of innovative bioformulations, either just Trichoderma species or in combination with other plant-beneficial microbes, such as plant growth-promoting bacteria (PGPB). Here, we review the most recent literature regarding the biocontrol studies about six of the most used Trichoderma species, T. atroviride, T. harzianum, T. asperellum, T. virens, T. longibrachiatum, and T. viride, highlighting their biocontrol traits and the use of these fungal genera in Trichoderma-based formulations to control or prevent plant diseases, and their importance as a substitute for chemical pesticides and fertilizers

Editorial: plant-microbial symbiosis toward sustainable food security

The use of plant-associated microorganisms is increasingly being investigated as a key tool for mitigating the impact of biotic and abiotic threats to crops and facilitating migration to sustainable agricultural practices. The microbiome is responsible for several functions in agroecosystems, such as the transformation of organic matter, nutrient cycling, and plant/pathogen growth regulation. As climate change and global warming are altering the dynamics of plant-microbial interactions in the ecosystem, it has become essential to perform comprehensive studies to decipher current and future microbial interactions, as their useful symbiotic mechanisms could be better exploited to achieve sustainable agriculture. This will allow for the development of effective microbial inoculants that facilitate nutrient supply for the plant at its minimal energy expense, thus increasing its resilience to biotic and abiotic stresses. This article collection aims to compile state-of-the-art research focused on the elucidation and optimization of symbiotic relationships between crops and their associated microbes. The information presented here will contribute to the development of next-generation microbial inoculants for achieving a more sustainable agriculture

Complete genome sequencing of Bacillus cabrialesii TE3T: A plant growth-promoting and biological control agent isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley

Bacillus cabrialesii TE3T is a strictly aerobic and Gram-stain-positive plant growth-promoting bacterium, motile and catalase-positive. In addition, strain TE3T was also recently described as a biological control agent. Here, we present the complete circularized genome of this type strain, as well as a whole genome analysis identifying genes of agricultural interest. Thus, a hybrid assembly method was performed using short-read sequencing through the Illumina MiSeq platform, and long-read sequencing through the MinION sequencing technology by Oxford Nanopore Technology (ONT). This assembly method showed a closed circular chromosome of 4,125,766 bp and 44.2% G + C content. The strain TE3T genome annotation, based on the RAST platform, presented 4,282 Coding DNA sequences (CDS) distributed in 335 subsystems, from which 4 CDS are related to the promotion of plant growth and 28 CDS to biological control. Also, Prokka (Rapid Prokaryotic Genome Annotation) predicted a total of 119 RNAs composed of 87 tRNAs, 31 rRNA, and 1 tmRNA; and the PGAP (Prokaryotic Genome Annotation Pipeline) predicted a total of 4,212 genes (3,991 CDS). Additionally, seven putative biosynthetic gene clusters were identified by antiSMASH, such as Fengycin, Bacilysin, Subtilosin A, Bacillibactin, Bacillaene, Surfactin, and Rizocticin A, which are related to antimicrobial and antifungal properties, whose gene presence was further supported by the Prokaryotic Genome Annotation Pipeline (PGAP) annotation. Thus, the complete genome of Bacillus cabrialesii TE3T showed promising bioactivities for the use of this type strain to bioformulate bacterial inoculants for sustainable agriculture

Bacillus cabrialesii subsp. cabrialesii subsp. nov. and Bacillus cabrialesii subsp. tritici subsp. nov., plant growth-promoting bacteria and biological control agents isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico

   Strain TSO2T, a plant growth-promoting rhizobacteria and biological control agent, was isolated from wheat rhizosphere sampled from the Yaqui Valley in Mexico. The strain was identified using a polyphasic approach. Based on its analysis of the full-length 16S rRNA gene, strain TSO2T was assigned to the genus Bacillus, which was supported by morphological and metabolic traits, such as Gram-positive staining, rod shape, spore formation, strictly aerobic metabolism, catalase-positive activity, starch, and casein hydrolysis, reduction of nitrate to nitrite, growth in presence of lysozyme and 2% NaCl, citrate utilization, growth at pH 6.0, acid production from glucose and indole production from tryptophan. Additionally, strain TSO2T possesses swarming motility, presenting a featureless mat pattern that can cover the whole petri dish. The whole-genome phylogenetic relationship analysis elucidated that strain TSO2T is closely related to Bacillus cabrialesii TE3T. The maximum values for average nucleotide identity (ANI) and in silico DNA–DNA hybridization from the genome-to-genome distance calculator (GGDC) were 97% and 73.4%, respectively, related to Bacillus cabrialesii TE3T, where both ANI and GGDC values were barely above the species delimitation threshold, but below the subspecies limit. Also, strain TSO2T showed the ability to produce a fatty acid (C18:0) that is not present in closely related Bacillus species. These results provide evidence that strain TSO2T is a novel subspecies of the species Bacillus cabrialesii, for which the name Bacillus cabrialesii subsp. tritici subsp. nov. is proposed. The type strain of Bacillus cabrialesii subsp. tritici subsp. nov. is TSO2T (CM-CNRG TB52T = LBPCV TSO2T). The description of this novel subspecies automatically creates the subspecies Bacillus cabrialesii subsp. cabrialesii subsp. nov. for which the type strain is TE3T (CM-CNRG TB54T= CCStamb A1T).</p

Draft Genome Sequence of <em>Priestia</em> sp. Strain TSO9, a Plant Growth-Promoting Bacterium Associated with Wheat <em>(Triticum turgidum</em> subsp. <em>durum)</em> in the Yaqui Valley, Mexico

Strain TSO9 was isolated from a commercial field of wheat (Triticum turgidum L. subsp. durum) located in the Yaqui, Valley, Mexico. Here, the genome of this strain was sequenced, obtaining a total of 5,248,515 bp; 38.0% G + C content; 1,186,514 bp N50; and 2 L50. Based on the 16S rRNA gene sequencing, strain TSO9 was affiliated with the genus Priestia. The genome annotation of Priestia sp. TSO9 contains a total of 147 RNAs, 128 tRNAs, 1 tmRNA, and 5512 coding DNA sequences (CDS) distributed into 332 subsystems, where CDS associated with agricultural purposes were identified, such as (i) virulence, disease, and defense (57 CDS) (i.e., resistance to antibiotics and toxic compounds (34 CDS), invasion and intracellular resistance (12 CDS), and bacteriocins and ribosomally synthesized antibacterial peptides (10 CDS)), (ii) iron acquisition and metabolism (36 CDS), and (iii) secondary metabolism (4 CDS), i.e., auxin biosynthesis. In addition, subsystems related to the viability of an active ingredient for agricultural bioproducts were identified, such as (i) stress response (65 CDS). These genomic traits are correlated with the metabolic background of this strain, and its positive effects on wheat growth regulation reported in this work. Thus, further investigations of Priestia sp. TSO9 are necessary to complement findings regarding its application in agroecosystems to increase wheat yield sustainably

Effect on production parameters measured in <i>A. cruentus</i> plants inoculated with different PGPR.

<p>(<b>A</b>) Seed yield, (<b>B</b>) harvest index and (<b>C</b>) weight of 100 seeds were determined in <i>A. cruentus</i> plants inoculated with two strains of <i>Burkholderia</i> (<i>B. ambifaria</i> Mex5 or <i>B. caribensis</i> XV) and grown to maturity in a rich substrate. Inoculated plants ± chemical fertilization (CF) were compared with un-inoculated plants ± CF. Mean values ± SE are presented. Different letters over the bars represent statistically different values at <i>P</i>≤0.05. The results of a representative experiment that was performed in duplicate are shown.</p

Growth promoting effect of PGPR inoculation on grain amaranth plants maintained in a low-fertility soil.

<p>The effect on different growth parameters were determined in <i>A. cruentus</i> plants grown in a low fertility soil and inoculated with two strains of <i>Burkholderia</i> (<i>B. ambifaria</i> Mex5 and <i>B. caribensis</i> XV). The parameters measured 7 weeks after inoculation were the following: <b>A</b>) plant height and stem diameter; <b>B</b>) leaf area; <b>C</b> and <b>D</b>) total biomass in fresh and dry weight basis, respectively, and <b>F</b> and <b>G</b>) total leaf, stem and root biomass in a FW and DW basis, respectively. Differences in plant height and leaf area between controls and plants inoculated with <i>B. caribensis XV</i> or <i>B. ambifaria</i> Mex5 are shown in (<b>E</b>). The effect on total nitrogen levels in leaves, stems and roots produced in plants inoculated with <i>B. caribensis</i> XV is shown in (<b>H</b>). Mean values ± SE are presented. Asterisks over the bars and lines represent statistically different values at <i>P</i>≤0.05. Experiments were performed twice, and representative results are shown.</p

Real-time PCR analysis of gene expression in different tissues of PGPR-inoculated <i>A. cruentus</i> plants.

<p>The expression levels of a battery of genes involved in C and N metabolism and transport were measured in roots (<b>A</b>), and leaves (<b>B</b>), of <i>A. cruentus</i> plants inoculated with <i>Burkholderia caribensis</i> XV. The relative expression levels were determined by qPCR at 3, 5 and 7 weeks after seed inoculation, using the 2^−ΔΔCt method, as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088094#pone.0088094-Livak1" target="_blank">[94]</a>. The bars represent mean values ± SE. Dashed lines indicate upper and lower limits beyond which genes were considered to be up- and down-regulated, respectively. Experiments were performed thrice, and results from a representative experiment are shown.</p

Time-course changes in non-structural carbohydrate levels in different tissues of PGPR-inoculated <i>A. cruentus</i> plants.

1<p> = Burkholderia caribensis XV and B. ambifaria Mex5;</p><p>ND = Not determined;</p>*<p> = Significant difference with controls at <i>P</i><0.05.</p