The system of rice intensification (SRI) is an agroecological approach to rice cultivation that seeks to create optimal conditions for healthy plant growth by minimizing inter-plant competition, transplanting widely spaced young single seedlings, and optimizing favorable soil conditions with organic amendments, increased soil aeration by weeding, and controlled water management. These practices improve rice plant growth with yields up to three times more than with conventional cultivation methods, and increase crop resilience under biotic and abiotic stresses. This review discusses the roles of beneficial microbes in improving rice plant growth, yield, and resilience when SRI practices are used, and how these modifications in plant, soil, water, and nutrient management affect the populations and diversity of soil microorganisms. Mechanisms whereby symbiotic microbes support rice plants' growth and performance are also discussed.
The residual activity of herbicides may be detrimental to the environment, requiring analysis of the persistent residues in the soil and water. A field study was conducted to measure the residues of Imidazolinone (IMI) in three Clearfield® rice field soils at three different locations in Malaysia. The analyses of IMI in the soil samples were carried out using a high-performance liquid chromatography (HPLC). These herbicides are widely used; however, few studies have been conducted on both residues, especially in the context of Malaysian soil. Residues of imazapic and imazapyr were found to fall within 0.03-0.58 µg/mL and 0.03-1.96 µg/mL, respectively, in three locations. IMI herbicides are persistent in the soil, and their residues remain for up to 85 days after application. A pre-harvest study was suggested for these herbicides on water, which will provide a clearer indicator on the use of IMI in Clearfield® rice fields.
Microbial-based fertilizer has been widely used as a healthier and better alternative to agrochemical products. However, the effects of biofertilizers on the rhizospheric microbiota has rarely been investigated. Thus, the aim of this study was to investigate the effects of symbiotic fungus Trichoderma asperellum SL2-based inoculant on the soil bacterial population through next generation sequencing using a metabarcoding approach. The treatment plots were treated with T. asperellum SL2 spore suspension, while the control plots were treated with sterilized distilled water. The results showed similar bacterial microbiome profiles in the soil of control and T. asperellum SL2-treated plots. In conclusion, the application of the T. asperellum SL2 inoculant had not exerted a negative impact towards the bacterial population as similar observation was reflected in control plots. Nonetheless, future research should be conducted to investigate the effects of repeated application of T. asperellum SL2 over a longer period on the rice microbiota communities.
Rats (Rattus species) are the most notorious vertebrate pests in Malaysian oil palm plantations. Although many studies have been conducted on Asian rats, little attention has been paid to their species composition and phylogenetic relationships in oil palm plantations in Peninsular Malaysia. We determined the mitochondrial cytochrome oxidase subunit I (COI) gene sequence (708 bp) for 216 individual rats collected from five oil palm plantations in Peninsular Malaysia. Phylogenetic analysis in conjunction with comparison with sequences from the nucleotide sequence database revealed five distinct lineages in the Malaysian oil plantations: Rattus tiomanicus, Rattus argentiventer, Rattus exulans, Rattus tanezumi, and a taxon corresponding to the Malayan house rat, which was most frequently observed (∼50%). The last taxon has traditionally been classified as a synonym of Rattus rattus (Rattus rattus diardii) or Rattus tanezumi, but our phylogenetic analysis placed it as an independent lineage, which is not particularly closely related to R. rattus or R. tanezumi, and which we refer to as Rattus diardii. The construction of the network showed that there is considerable genetic variation within the lineages of R. diardii and R tiomanicus, suggesting that these two species are native to the Malay Peninsula.
Drought-induced stress represents a significant challenge to agricultural production, exerting adverse effects on both plant growth and overall productivity. Therefore, the exploration of innovative long-term approaches for addressing drought stress within agriculture constitutes a crucial objective, given its vital role in enhancing food security. This article explores the potential use of Trichoderma, a well-known genus of plant growth-promoting fungi, to enhance plant tolerance to drought stress. Trichoderma species have shown remarkable potential for enhancing plant growth, inducing systemic resistance, and ameliorating the adverse impacts of drought stress on plants through the modulation of morphological, physiological, biochemical, and molecular characteristics. In conclusion, the exploitation of Trichoderma's potential as a sustainable solution to enhance plant drought tolerance is a promising avenue for addressing the challenges posed by the changing climate. The manifold advantages of Trichoderma in promoting plant growth and alleviating the effects of drought stress underscore their pivotal role in fostering sustainable agricultural practices and enhancing food security.
While previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice (Oryza sativa) is limited. In this work, we report six novel multiplex assays that use a universal protocol to detect major rice grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) traits with amplified products consisting of up to four primer pairs that can be analyzed using a standard agarose-based gel electrophoresis system. Recent studies have suggested that weedy rice has novel sources of disease resistance. However, an intensive screening of weedy biotypes has not been reported in Malaysia. Accordingly, we employed one of the developed multiplex assays to screen reported genes or quantitative trait loci (QTLs) associated with blast, sheath blight, and bacterial leaf blight diseases in 100 weedy rice biotypes collected from five local fields, with phenotyping performed to validate the genotyping results. In conclusion, our universal multiplex protocol is effective for the large-scale genotyping of rice genetic resources, and it can be employed in routine molecular laboratories with limited resources.
Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.
The system of rice intensification (SRI) is an extensively-researched and increasingly widely-utilized methodology for alleviating current constraints on rice production. Many studies have shown physiological and morphological improvements in rice plants induced by SRI management practices to be very similar to those that are associated with the presence of beneficial microbial endophytes in or around rice plants, especially their roots. With SRI methods, grain yields are increased by 25-100% compared to conventional methods, and the resulting plant phenotypes are better able to cope with biotic and abiotic stresses. SRI management practices have been shown to be associated with significant increases in the populations of certain microorganisms known to enhance soil health and plant growth, e.g., Azospirillum, Trichoderma, Glomus, and Pseudomonas. This article evaluates the effects of applying Trichoderma as a model microbe for assessing microbial growth-promotion, biological control activity, and modulation of gene expression under the conditions created by SRI practices. Information about the molecular changes and interactions associated with certain effects of SRI management suggests that these practices are enhancing rice plants' expression of their genetic potentials. More systematic studies that assess the effects of SRI methods respectively and collectively, compared with standard rice production methods, are needed to develop a more encompassing understanding of how SRI modifications of crops' growing environment elicit and contribute to more robust and more productive phenotypes of rice.
Trichoderma yunnanense strain TM10 was isolated from rhizosphere soil of rice plants cultivated under system of rice intensification (SRI) practises in West Java, Indonesia. It exhibits significant potential as a plant growth promoter and biocontrol agent in rice plants. Although this strain has shown promise in promoting plant growth and suppressing phytopathogens under in vitro and in planta conditions, there is still a lack of genomic data to elucidate the molecular mechanisms underlying its plant growth-promoting and biocontrol capabilities. This study reports the whole genome sequence of T. yunnanense strain TM10. The genome of the fungus was sequenced using the MGI DNBSEQ-G400 high-throughput sequencing platform. The assembled genome of T. yunnanense strain TM10 was approximately 36 Mbp in length, comprising 385 contigs with a GC content of 48 % and a sequencing coverage of 43.8×. This genomic data provides a foundation for harnessing the plant growth-promoting and biocontrol potential of this strain. The complete genome sequence has been deposited at the National Center for Biotechnology Information (NCBI) under Bioproject accession number PRJNA1181959, BioSample ID SAMN44575400, and genome accession number JBIYZQ000000000. These data are valuable for further research into the biotechnological potential of this strain and for exploring the molecular mechanisms underlying its plant growth-promoting and biocontrol activities.