Rhizobial bacteria are known for their ability to fix nitrogen for leguminous plants and their essential function for sustainable agriculture. This study characterizes the taxonomic status and functional potential of the Bradyrhizobium B64 isolate using integrated genomic and molecular approaches. The whole genome of the B64 isolate was sequenced via Illumina paired-end technology. Species delimitation was performed using average nucleotide identity (ANI) and digital DNA-DNA Hybridization (dDDH). The NodD1 protein structure was modeled using AlphaFold3 and validated by Ramachandran plot analysis. Molecular docking was then conducted to evaluate interactions between NodD1 and four signaling flavonoids: Apigenin, Daidzein, Genistein, and Naringenin. Genomic analysis revealed a maximum ANI of 94.4

The aromatic rice cultivar Rojolele (Oryza sativa L. cv. Rojolele), prized for its superior organoleptic qualities, is highly susceptible to yellow stem borer (Scirpophaga incertulas), a pest causing significant yield losses in Asia. To address this vulnerability, we developed marker-free transgenic Rojolele lines expressing the cry1Ab gene using a double T-DNA vector system, eliminating reliance on antibiotic resistance markers. Agrobacterium-mediated transformation yielded 21 independent T0 lines, with PCR and Southern blot analysis confirming stable integration of cry1Ab in seven lines by the T3 generation. Immunostrip assays verified functional Cry1Ab protein expression, while bioassays demonstrated complete resistance in lines I.AR.4 and III.AR.5.3. Susceptible lines (I.AR.2, III.AR.5.2) exhibited variable transgene expressions, highlighting the importance of event selection. The marker-free strategy aligns with biosafety regulations, and the retained agronomic traits ensure compatibility with commercial cultivation. This study provides a sustainable solution to protect high-value aromatic rice, combining insect resistance with consumer-preferred qualities. Field trials and resistance management strategies, such as gene pyramiding, are recommended for future deployment.

Fusarium wilt poses a significant challenge to the cultivation of Vanilla planifolia, resulting in severe plant decline and yield loss. The aim of this study was to identify the causal pathogen of Fusarium wilt in vanilla and to evaluate the biocontrol potential of Trichoderma asperellum using an integrated approach combining morphology, molecular techniques and functional analysis. The pathogen isolate obtained from diseased vanilla plants was identified as Fusarium sp. strain EF4 based on morphological characteristics and phylogenetic analysis. The antagonist isolate was identified as T. asperellum and exhibited rapid growth and strong colonisation capacity. An in vitro antagonistic test demonstrated that T. asperellum effectively inhibited the growth of Fusarium sp. strain EF4, achieving a pathogen growth inhibition value of 60.27% at seven days post-inoculation. Microscopic and Field Emission Scanning Electron Microscopy (FESEM) observations revealed clear mycoparasitic interactions, including hyphal attachment, coiling and structural degradation of the pathogen. Metabolite profiling showed that T. asperellum produces a diverse array of antimicrobial secondary metabolites, dominated by long-chain hydrocarbons and ether derivatives, such as tetracosane and hexacosyl nonyl ether. This indicates synergistic antifungal activity. In planta assays further confirmed the effectiveness of T. asperellum, significantly reducing both stem infection progression (F = 50.56, p < 0.01) and leaf fall percentage (F = 4.36, p < 0.05). Overall, T. asperellum represents a promising, sustainable biocontrol agent for managing Fusarium wilt in vanilla cultivation.

Soil salinity, intensified by climate change, presents a major challenge to crop productivity. This study investigated the potential of plant growth-promoting bacteria (PGPB) to enhance salinity tolerance in Allium cepa L. var. aggregatum through modulation of the rhizosphere. Experimental treatments included PGPB inoculation, chemical fertilizer application, their combination, and co-inoculation of PGPB with vesicular-arbuscular mycorrhiza (VAM), each tested under control, moderate (4 dS m⁻¹), and severe (8 dS m⁻¹) salinity levels. Analyses focused on plant growth performance, Aquaporin (aqp1) gene expression, and rhizosphere metagenomics. PGPB application increased rhizosphere microbial diversity under saline conditions, with the combination of PGPB and half-dose chemical fertilizer proving most effective. Elevated salinity reshaped the bacterial community, favoring Proteobacteria, Bacteroidota, and Firmicutes, while reducing Actinobacteria compared to the untreated control. The combined treatment helped preserve Actinobacteria populations, enhance soluble phosphate availability, and improve plant growth, as reflected in leaf number, tiller formation, and bulb development. It also elicited the highest aqp1 expression at moderate salinity (4 dS m⁻¹), suggesting a role in strengthening physiological stress responses and preparing plants to better withstand severe salinity. These findings highlight a promising, sustainable approach to improving salinity resilience in Allium cepa L. var. aggregatum cultivation while minimizing reliance on chemical fertilizers.

Abstract Endophytic bacteria have been extensively researched for their ability to produce phytohormones and provide essential nutrients for plant growth. However, there have been a few explorations of endophytic bacteria from the Toba Frankincense plant (Styrax paralleloneurus), the primary benzoin resin source in Sumatra, Indonesia. This research aims to identify endophytic bacteria with the ability to produce IAA from S. paralleloneurus stems. This study isolated, characterized, and molecularly identified bacteria from tapped and untapped S. paralleloneurus stems. Tests were conducted to assess their potential as plant growth promoters, including IAA production. Our research successfully identified Micrococcus aloeverae and Bacillus aerius as potential plant growth-promoting bacteria, capable of producing 15.63 and 3.96 ppm of IAA, respectively. Thus, this study will also serve as a reference for understanding how tapping the frankincense sap affects the ability of endophytic bacteria to produce IAA and dissolve phosphate.

Rubber, a global industrial commodity, continues to increase in demand on the world market. However, the rubber industry faces significant challenges due to pathogen attacks, particularly in the roots and leaves of the rubber tree, leading to reduced productivity and affecting the supply of raw rubber materials. Several types of pathogenic fungi have been studied as causes of disease in rubber plants. This research presents the first report of pestalotioid fungus Truncatella angustata causing leaf fall disease on rubber plants in Indonesia and the inhibition of the fungus by Trichoderma spp. in vitro. In this study, T. angustata was isolated from symptomatic leaves suspected of leaf fall disease on rubber plantations in Jambi Province, Indonesia. This research also investigated the characteristics and mechanisms of inhibition of T. angustata by Trichoderma asperellum isolated from soil at the exact rubber plantation location. As a comparison, Trichoderma koningiopsis from our laboratory collection was used. The investigation results show that the inhibition mechanism is through entanglement. Hence, T. asperellum showed an inhibitory ability of 76.61 %, while T. koningiopsis showed 59.65 %.

Styrax paralleloneurus is a resin-producing tree native to Sumatra, Indonesia. This study investigated the effects of tapping, bark wounding and forest type on bacterial biota in the stem of styrax in natural and community forests. Amplicon metagenomic sequencing of the 16S rRNA region was deployed to identify the bacterial communities associated with tapped and untapped trees across various environmental and experimental conditions. The results of the study showed that tapped trees had lower abundance and diversity of Pseudomonas compared to untapped trees, largely due to their increased exposure to external microbe communities and environmental elements. Serratia and Pantoea were more abundant in natural forest than community forest, while Bradyrhizobium lablabi was found abundantly in untapped trees. Additionally, the taxonomic analysis revealed distinct responses of bacterial genera to tapping and forest type, indicating that community forests could play a significant role in promoting biodiversity in forest ecosystems. This finding underscores the importance of community forests in biodiversity conservation. These insights can inform future conservation and management strategies to enhance biodiversity and underscore the need for sustainable forest management practices to maintain forest health and productivity.

Bakteri endofit adalah bakteri menguntungkan yang hidup di dalam tanaman dan dapat meningkatkan pertumbuhan tanaman inang dan ketahanan terhadap cekaman. Rendahnya produktivitas tanaman bawang merah disebabkan penggunaan pupuk kimia dalam jangka waktu lama dan dosis berlebihan akan menurunkan kualitas tanah. Penggunan pupuk hayati berbasis mikroba diharapkan dapat meningkatkan produktivitas tanaman bawang dan memperbaiki kulitas tanah. Tujuan penelitian ini adalah untuk memperoleh dan menentukan aktivitas bakteri endofit dari tanaman bawang merah sebagai pemacu pertumbuhan tanaman. Sampel tanaman bawang merah berumur 26 HST dan 45 HST diambil dari daerah Brebes, Jawa Tengah. Sebanyak 75 isolat diperoleh dari akar, bunga, daun dan umbi. Hasil karakterisasi diperoleh 2 isolat mempunyai tiga aktivitas penghasil hormon IAA, pelarut fosfat dan pemfiksasi nitrogen. Berdasarkan analisis molekuler, kedua isolat teridentifikasi sebagai Burkholderia sp. (BMD 2.4) dan Pseudomonas aeruginosa (BTBn 2.6).

More than 50% of the main crops in the world are lost to agricultural stressors, either biotic or abiotic. It has been demonstrated that using chemical approaches to boost plant yield causes other serious problems, including a decline in soil fertility and significant health problems. While advanced plant biotechnology techniques, like genetic modification, still faces ethical questions, unpredictable environmental risks, challenges in their usability and commercial viability, as well as high labour and costs. Using plant-associated microbes with 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity can be a solution to speed up plant production upon environmental stresses. They offer stress-protective responses by reducing the production of the plant stress hormone ethylene to a level that is not detrimental to plants. Furthermore, adopting ACCD-producing microbes with additional supporting traits or mixing them with other beneficial microbes in a consortium can be a promising strategy to sustain their effectiveness in practical use. This paper reviews the current research on the role of ACCD-producing microbes in increasing plant productivity under various stresses, along with their limitations and recommendations for field application.

Soil salinity poses a significant agricultural challenge exacerbated by climate change. Plant growth-promoting bacteria (PGPB) have the potential to induce systemic plant tolerance against salinity stress. This study investigated Allium cepa responses and the rhizosphere microbiome under varying salinity levels to unveil plant salinity tolerance facilitated by a bacterial consortium. The assessment of plant salinity tolerance involved multiple treatments, including co-inoculation of PGPB, chemical fertilizer application, a combination of PGPB with chemical fertilizer, and PGPB with vesicular-arbuscular mycorrhiza (VAM). The gene expression of Aquaporin (aqp1) was also examined to understand plant responses to salinity stress. Our hypothesis posited that applying PGPB would enhance Allium cepa growth, induce salinity tolerance, and reduce the dependence on chemical fertilizers. Microbiome biodiversity analyses post-PGPB application revealed increased diversity in the rhizosphere microbiome, particularly evident in the PGPB in combination with half the standard dose of chemical fertilizer under salinity conditions. Under high salinity stress, the bacterial community shaped a distinct rhizosphere microbiome composition, with dominance by Proteobacteria and Bacteroidota. At the same time, Actinobacteria and Actinobacteriota exhibited reduced prevalence compared to the control group. The joint application of PGPB with chemical fertilizer improved plant tolerance to salinity stress. This study uncovered the potential of PGPB in reducing chemical fertilizer usage and identified promising bacterial candidates for biofertilizer applications.

Abstract. Nuriyanah, Widowati T, Masnang A, Nurjanah L, Novilasari D, Lekatompessy SJR, Simarmata R. 2023. Screening and characterization of endophytic bacteria isolated from celery with the potential to promote plant growth. Biodiversitas 24: 6897-6904. Endophytic bacteria that inhabit plant tissue contribute to the enhancement of host plant growth by producing secondary metabolites. They can improve plant growth by phytohormone modulation and nutrient uptake. In addition, endophytic bacteria can increase plant health and tolerance by antibiotic and hydrolytic enzyme production. This study aims to screen and characterize endophytic bacteria of celery as plant growth promoter agents. Thirty endophytic bacteria were isolated successfully from part of the celery plant using the spread plate and plant piece method which grew at Nutrient Agar media. Based on the characterization assay, 30 isolates may produce IAA with various concentrations of 0.21-7.18 mg/L. In addition, 3 of 30 isolates had phosphate solubilizing activity, in different indexes ranging from 0.71-1.43. Twenty-one isolates were able to grow in an N-free medium, indicating the capability of isolates to fix nitrogen qualitatively. The hydrolytic enzymes assay resulted in 14 amylolytic, 17 proteolytic, and 12 cellulolytic activities. In addition, nine of 30 isolates show multi-activity in amylase, protease, and cellulase enzyme production. Based on the screening results, there are four potential isolates (SLBg 1.2; SLBg 1.5; SLAg 1.1, and SLAg 1.5) as promising plant-growth promoters and were molecularly identified as members of the Bacillus genus. These isolates can be developed as biofertilizers for supporting the cultivation of celery plants.

Bakteri endofit yang terdapat dalam akar, batang, dan daun tanaman memiliki potensi sebagai agen biokontrol dan pendorong perkembangan tanaman, selain itu dalam akar tanaman juga terdapat plant growth promoting rhizobacteria (PGPR) dengan kemampuan yang sama. Konsorsium kedua bakteri tersebut akan menghasilkan senyawa Indol 3 asam asetat (IAA) yang selanjutnya dirubah menjadi auksin yang menguntungkan bagi tanaman. Penelitian bertujuan untuk mengetahui kemampuan bakteri endofit dan PGPR dari akar tumbuhan cabai merah keriting dalam memproduksi hormon auksin. Prosedur kerja penelitian meliputi peremajaan isolat bakteri, karakteristik makroskopik dan mikroskopik, mengukur kadar auksin menggunakan HPLC (High Performance Liquid Chromatography). Hasil penelitian menunjukkan bahwa dari konsorsium 6 bakteri (3 endofit dan 3 PGPR) menghasilkan konsentrasi auksin sebesar 46,122 ppm, konsorsium bakteri endofit sebesar 24,201 ppm, konsorsium bakteri PGPR sebesar 162,723 ppm, dan terakhir single bakteri endofit dan single bakteri PGPR menghasilkan auksin sebesar A 158,913 ppm; B 64,882 ppm; C 93,923 ppm; CB1 240,817 ppm; CB2 186,807 ppm; dan CMBC 11,689 ppm, sedangkan untuk kontrol 0 ppm. Kesimpulannya konsentrasi auksin tertinggi diperoleh dari hasil single bakteri PGPR CB1 240,817 ppm.

Soils support an enormous diversity of microorganisms, much of which is yet unknown. Soil microbes may colonize the rhizosphere and can be transmitted to endophytes, which live inside plant tissues. Roots exudate effect on activity, function, abundance, and composition and structure of soil microbial communities. Furthermore, bioinoculants' application can affect microbial diversity, which can vary the processes parallelly occurring in the rhizosphere, creating a unique and active niche that other influences the health and development of plants in modulating responses to both biotic and abiotic stresses. Part of the soil microbial diversity has been discovered using a variety of innovative approaches, the majority of which are based on rRNA and rDNA studies. Complex studies using molecular phylogenetics, DNA microarrays, functional genomics, and in situ activity measurements will generate a large amount of new data. The extraction of genomic, evolutionary, and practical information from bacterial artificial chromosome libraries of soil community genomes is the next stage in the era of microbial ecology (the metagenome). Identification of microbial diversity and good management of metagenome data potentially improve our knowledge to understand the structure and function of microbial soil ecosystems and the interactions with their physically close neighbors. The ability of metagenomes is necessary considering that microorganisms play essential roles in soil fertility, including nutrient cycling, organic matter formation, decomposition, soil structure formation, and promotion of plant health. This chapter will review the latest improvements in the study of microbial diversity, with an emphasis on novel tools and approaches that shed light on the link between phylogenetic and functional diversity.

The microbial community plays an important role in A. cepa productivity and soil fertility. In this study, we applied chemical (A2) and endophyte-based fertilizer (B) to A. cepa; where the use of B successfully improved productivity by the number of tubers and chlorophyll content compared to control (A1) and A2. We aimed to investigate how those fertilizers manipulate the rhizosphere bacterial community in A. cepa. The 16S-metagenomic analysis was conducted to investigate the bacterial community of the samples by amplifying the V3-V4 region. The application of A2 and B potentially enhanced the abundance of rhizosphere bacteria compared to the A1, possibly due to the increase in nutrient availability. Beta-diversity analysis showed that the B fertilizer did not highly change the bacterial community of indigenous rhizosphere bacteria, whereas the A2 fertilizer did. The endophytes themselves did not also greatly affect the original rhizosphere bacteria because they may enter the plant tissue and release the metabolites inside the plant host. The NGS data showed that the genus Aquicella was the most abundant in the rhizosphere treated with B and A1. Aquicella was discovered to boost plant resilience to contaminants by enhancing plant nutrition availability and encouraging plant root growth. Interestingly, Acidobacteria and Gemmatimonadetes decreased their population in the treatments of A2 or B. Overall, the use of B has a higher impact on plant productivity and soil properties without highly changing the composition of the bacterial community in the rhizosphere. Yet our metagenomic data support the hypothesis of phylogenetical conservation of bacterial communities concerning particular ecological conditions.

Fifty-nine endophytic bacterial isolates from rat taro have been obtained; thirty-four bacterial isolates from rat taro type 3 (TF3) and twenty-five bacterial isolates were from type 4 (TF4). The extracellular enzyme activity was observed qualitatively from rat taro endophytic bacterial isolates. The amylase activity test used starch as substrate, whereas the protease test used gelatin. A cellulose activity test was carried out using Carboxy Methyl Cellulase (CMC) media. The results showed that twenty-seven endophytic bacterial isolates of rat taro TF3 and TF4 showed extracellular enzyme activity. Endophytic bacterial isolate TF3Bt4 had the highest protease activity, indicated by its lytic index of about 11.304 mm in the gelatin-containing medium. The highest amylase activity was produced by isolate TF3U3, where the lytic index was 23.875 mm in the starch containing medium. Bacterial isolate TF3A4 showed a lytic index of about 6.9653 mm in the CMC medium, indicating the highest cellulase activity. The endophytic bacteria with protease activity are potentially utilized in the food industry, whereas endophytic bacteria with cellulase activity can be used in the textile industry.

Plant growth promoting bacteria with dual activity, 1-aminocyclopropane-1-carboxylic-acid deaminase (ACCD) and nitrogenase, is more effective in supporting plant growth under stress condition. Previously, we were obtained several endophytic bacterial strains that exhibited dual activity, one of which was Raoultella terrigena PCM8. This study aimed to characterize the ACCD and nitrogenase genes of PCM8 strain. The acdS gene was obtained from the results of Whole Genomic Sequencing analyis, while the nifH gene was obtained by PCR. The characterization of both of the genes was carried out by means of in-silico analysis. WGS annotation analysis, showed that the acdS gene of PCM8 was located at the locus 19090 of genomic DNA and contains 978 nucleotides. In silico analysis of both acdS and nifH gene products showed that the ACCD enzyme of PCM8 had 325 amino acids, with molecular weight of 34.95 kDa, while nitrogenase as represented by nifH subunit product consist of 96 amino acids with molecular weight of 93.98 kDa, respectively. The ACCD had pI value of 5.06, and catalytic residues of Lys51, Ser78, Tyr287, and Thr288, while nifH gene product had the pI value of 11.77. The results suggested that R. terrigena PCM8 potentially produce double activity of ACCD and nitrogenase and therefore it can be a good candidate as plant growth promoting under stress condition. Keywords: acdS gene, 1-aminocyclopropane-1-carboxylic acid deaminase, endophytic bacteria, nifH gene, nitrogenase Raoultella terrigena

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Tiwit Widowati, Nuriyanah, Liseu Nurjanah, Sylvia J. R. Lekatompessy, Rumella Simarmata; Bioproduction of indole acetic acid by endophytic bacteria of Bacillus strains isolated from chili (Capsicum annuum L.) and its potential for supporting the chili seedlings. AIP Conf. Proc. 4 January 2023; 2606 (1): 020018. https://doi.org/10.1063/5.0118396 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search