Malek Marian

Scopus Publications

Cold-Tolerant Bacteria Isolated from Alpine Plants Can Promote Growth and Mitigate Cold Stress in Tomato Seedlings by Complex Transcriptional Reprogramming of Stress-Related Genes
Irma Milanese, Aureliano Bombarely, Malek Marian, Michele Perazzolli
Plants, 2025
Cold stress adversely affects crop growth, and climate change is increasing its severity and frequency in many agricultural regions. Tomato plants are sensitive to low temperatures, although they activate some stress response mechanisms. Beneficial microorganisms can enhance cold-stress acclimation in tomato plants, but the transcriptional regulation underlying this process remains poorly understood. This study aimed to investigate the transcriptional processes activated by cold stress in tomato plants following inoculation with cold-tolerant bacteria isolated from alpine plants to identify genes potentially involved in cold stress acclimation. Among 41 cold-tolerant bacterial isolates tested, Chryseobacterium sp. GRCS301 and Pseudomonas sp. GRCS202 inoculation in sterilized soil promoted tomato growth under controlled non-stress (25 ± 2 °C) and cold-stress (10 ± 2 °C) conditions. Bacterial inoculations lowered H2O2 content and affected the transcriptional regulations activated in tomato shoots after one day and 14 days of incubation under cold-stress conditions. In mock-inoculated plants, cold stress downregulated genes related to energy generation, photosynthesis, and reproductive processes, highlighting its detrimental effects. Conversely, plants inoculated with Chryseobacterium and Pseudomonas upregulated genes involved in DNA replication, galactose metabolism, polysaccharide metabolism, photosynthesis, and protein metabolism in response to cold stress. Bacterial inoculation induced the expression of genes involved in reactive oxygen species homeostasis, cold-stress response, and hormonal signaling, suggesting that cold-tolerant bacteria trigger key transcriptional changes in tomato plants and enhance cold-stress acclimation.
Amplicon sequencing and culture-dependent approaches reveal core bacterial endophytes aiding freezing stress tolerance in alpine Rosaceae plants
Malek Marian, Livio Antonielli, Ilaria Pertot, Michele Perazzolli
Mbio, 2025
Wild plants growing in alpine regions are associated with endophytic microbial communities that may support plant growth and survival under cold conditions. The structure and function of endophytic bacterial communities were characterized in flowers, leaves, and roots of three alpine Rosaceae plants in Alpine areas using a combined amplicon sequencing and culture-dependent approaches to determine the role of core taxa on plant freezing stress tolerance. Amplicon sequencing analysis revealed that plant tissue, collection site, and host plant are the main factors affecting the richness, diversity, and taxonomic structure of endophytic bacterial communities in alpine Rosaceae plants. Core endophytic bacterial taxa were identified as 31 amplicon sequence variants highly prevalent across all plant tissues. Psychrotolerant bacterial endophytes belonging to the core taxa of Duganella , Erwinia , Pseudomonas , and Rhizobium genera mitigated freezing stress in strawberry plants, demonstrating the beneficial role of endophytic bacterial communities and their potential use for cold stress mitigation in agriculture. IMPORTANCE Freezing stress is one of the major abiotic stresses affecting fruit production in Rosaceae crops. Current strategies to reduce freezing damage include physical and chemical methods, which have several limitations in terms of costs, efficacy, feasibility, and environmental impacts. The use or manipulation of plant-associated microbial communities was proposed as a promising sustainable approach to alleviate cold stress in crops, but no information is available on the possible mitigation of freezing stress in Rosaceae plants. A combination of amplicon sequencing, culture-dependent, and plant bioassay approaches revealed the beneficial role of the endophytic bacterial communities in alpine Rosaceae plants. In particular, we showed that culturable psychrotolerant bacterial endophytes belonging to the core taxa of Duganella , Erwinia , Pseudomonas , and Rhizobium genera can mitigate freezing stress on strawberry seedlings. Overall, this study demonstrates the potential use of psychrotolerant bacterial endophytes for the development of biostimulants for cold stress mitigation in agriculture.
Community standards and future opportunities for synthetic communities in plant–microbiota research
Trent R. Northen, Manuel Kleiner, Marta Torres, Ákos T. Kovács, Mette Haubjerg Nicolaisen, et al.
Nature Microbiology, 2024
Biocontrol of Pythium root rot on lisianthus using a new dark septate endophytic fungus Hyaloscypha variabilis J1PC1
Malek Marian, Yusuke Takashima, Wiwiek Harsonowati, Haruhiko Murota, Kazuhiko Narisawa
European Journal of Plant Pathology, 2022
Ecology and potential functions of plant-associated microbial communities in cold environments
Malek Marian, Giorgio Licciardello, Bianca Vicelli, Ilaria Pertot, Michele Perazzolli
FEMS Microbiology Ecology, 2022
Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.
Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114
Malek Marian, Takashi Fujikawa, Masafumi Shimizu
Archives of Microbiology, 2021
Mitsuaria sp. TWR114 is a biocontrol agent against tomato bacterial wilt (TBW). We aimed to gain genomic insights relevant to the biocontrol mechanisms and colonization ability of this strain. The draft genome size was found to be 5,632,523 bp, with a GC content of 69.5%, assembled into 1144 scaffolds. Genome annotation predicted a total of 4675 protein coding sequences (CDSs), 914 pseudogenes, 49 transfer RNAs, 3 noncoding RNAs, and 2 ribosomal RNAs. Genome analysis identified multiple CDSs associated with various pathways for the metabolism and transport of amino acids and carbohydrates, motility and chemotactic capacities, protection against stresses (oxidative, antibiotic, and phage), production of secondary metabolites, peptidases, quorum-quenching enzymes, and indole-3-acetic acid, as well as protein secretion systems and their related appendages. The genome resource will extend our understanding of the genomic features related to TWR114's biocontrol and colonization abilities and facilitate its development as a new biopesticide against TBW.
Lysinibacillus xylanilyticus strain gic41 as a potential plant biostimulant
Nusrat Ahsan, Malek Marian, Haruhisa Suga, Masafumi Shimizu
Microbes and Environments, 2021
To identify Lysinibacillus strains with the potential to function as plant biostimulants, we screened 10 previously isolated Lysinibacillus strains from the rhizosphere and soil for their plant growth-promoting (PGP) effects. In vitro tests showed that all strains produced indole-3-acetic acid. In primary screening, the PGP effects of these strains were assessed on spinach seedlings grown on Jiffy-7 pellets; strains GIC31, GIC41, and GIC51 markedly promoted shoot growth. In secondary screening, the PGP efficacies of these three strains were examined using spinach seedlings grown in pots under controlled conditions. Only GIC41 exerted consistent and significant PGP effects; therefore, it was selected for subsequent experiments. The results of 6-week glasshouse experiments revealed that GIC41 markedly increased shoot dry weight by ca. 12-49% over that of the control. The impact of fertilization levels on the PGP efficacy of GIC41 was investigated using pot experiments. The application of a specific level of fertilizer was required for the induction of sufficient PGP effects by this strain. The phylogenetic ana-lysis based on the 16S rDNA sequence identified GIC41 as L. xylanilyticus. Collectively, these results show the potential of strain GIC41 to function as a plant biostimulant.
The Effectiveness of a Dark Septate Endophytic Fungus, Cladophialophora chaetospira SK51, to Mitigate Strawberry Fusarium Wilt Disease and With Growth Promotion Activities
Wiwiek Harsonowati, Malek Marian, Surono, Kazuhiko Narisawa
Frontiers in Microbiology, 2020
Strawberry Fusarium wilt, caused by the virulent fungus Fusarium oxysporum formae speciales fragariae (Fof) is a devastating soil-borne disease that causes severe production losses worldwide, including Japan. Fof is one of the top 10 fungal pathogens that threaten global crop security, and a method to effectively control this pathogen has yet to be found. This study aimed to investigate the effectiveness of dark septate endophytic (DSE) fungi against Fof to develop an efficient, effective, and environmentally friendly approach to improve plant health and fitness. A total of 19 fungal isolates were assessed, out of which three (SK47, SK48, and SK51) were selected based on their effectiveness in disease suppression in controlled growth chamber conditions using a soil system. Isolates SK47, SK48, and SK51 suppressed disease severity by 85.71, 61.90, and 90.48%, respectively. Molecular identification based on highly conserved small subunit (SSU), internal transcribed spacer (ITS), and large subunit (LSU) nrRNA regions identified these isolates as DSE Exophiala sp., Exophiala pisciphila, and Cladophialophora chaetospira, respectively. The sequences were deposited under accession numbers MN811693–MN811695 in the GenBank database. Notably, our results revealed that isolate C. chaetospira SK51 possessed superior growth promotion activities as well as disease suppression by significantly increased plant growth parameters (shoot and root dry mass, chlorophyll content, flower bud initiation, and number of fruit) in comparison to control plants and other two fungal candidates. Root colonization by C. chaetospira SK51 was visualized, and it was confirmed that the symbiosis with strawberry plants occurred successfully. Our results provide new insights in the application of DSE fungus C. chaetospira SK51 as a biocontrol agent on strawberry plants could promote plant growth, flower bud initiation, and fruit formation. C. chaetospira SK51 exhibited remarkable beneficial traits for the host plant, and it can potentially be applied in the development of new, safe, and effective treatments as an alternative to chemical fertilizers and fungicides for sustainable crop protection.
A novel strain of endophytic Streptomyces for the biocontrol of strawberry anthracnose caused by Glomerella cingulata
Malek Marian, Teppei Ohno, Hirofumi Suzuki, Hatsuyoshi Kitamura, Katsutoshi Kuroda, et al.
Microbiological Research, 2020
Anthracnose caused by Glomerella cingulata is one of the most devastating diseases of strawberry in Japan, particularly during its nursery period in the summer. In this study, we aimed to isolate and screen endophytic actinobacteria, to identify potential biocontrol agents capable of suppressing strawberry anthracnose. A total of 226 actinobacteria were successfully isolated from surface-sterilized strawberry tissues. In the first screening, 217 out of 226 actinobacteria isolates were studied for their suppression effect on strawberry anthracnose using a detached leaflet assay. It was discovered that isolates MBFA-172 and MBFA-227 markedly suppressed the development of anthracnose lesions. The efficacy of both isolates was then tested on two-month-old strawberry plug seedlings in a controlled environmental chamber. It was found that isolate MBFA-172 provided consistent disease suppression and was thus selected as a final candidate for further evaluation in a glasshouse experiment. Results showed that the severity as well as incidence rate of strawberry anthracnose was significantly reduced by treatment with isolate MBFA-172 compared with that of untreated control. Accordingly, the disease control efficacy provided by MBFA-172 was statistically comparable to the chemical fungicide propineb. A re-isolation experiment using a spontaneous thiostrepton-resistant mutated strain of isolate MBFA-172 revealed that it efficiently colonized the above-ground tissues of strawberry plants for at least three weeks after spray treatment. Using cultural, morphological, and physiological tests combined with 16S rRNA-based molecular analysis, MBFA-172 was identified as a moderately thermophilic Streptomyces thermocarboxydus-related species. Upon review, our results strongly indicated that MBFA-172 is a promising biocontrol agent for strawberry anthracnose.
Potential use of L-arabinose for the control of tomato bacterial wilt
Hui-Zhen Fu, Malek Marian, Takuo Enomoto, Haruhisa Suga, Masafumi Shimizu
Microbes and Environments, 2020
The present study aimed to investigate the potential of simple sugars for use as protection agents in the control of tomato bacterial wilt caused by Ralstonia pseudosolanacearum. Based on the sugar assimilation patterns of the pathogen, four unassimilable sugars (L-arabinose, maltose, D-raffinose, and D-ribose) were selected from 10 representative sugars present in tomato root exudates. These sugars were evaluated for their effects on bacterial wilt using a tomato seedling bioassay. The application of 0.25% L-arabinose significantly reduced disease severity and was, thus, selected as a candidate for further evaluations in a pot experiment under glasshouse conditions. The results obtained showed that the disease suppressive effects of L-arabinose slightly increased at higher concentrations; drench treatments at 0.1, 0.25, and 0.5% reduced disease severity by ca. 48, 70, and 87%, respectively. The drench treatment with 0.5% L-arabinose significantly reduced the pathogen population in the rhizosphere and stem tissues of tomato plants without any antibacterial activity. Real-time reverse-transcription PCR revealed that the expression of salicylic acid-dependent and ethylene-dependent defense genes was significantly enhanced in the stem tissues of L-arabinose-treated tomato plants following the pathogen inoculation. These results suggest that soil drenching with L-arabinose effectively suppresses tomato bacterial wilt by preventing pathogen proliferation in the rhizosphere and stem tissues of tomato plants. This is the first study to report the potential of L-arabinose as a safe, eco-friendly, and cost-effective plant protection agent for the control of tomato bacterial wilt.
Biocontrol of tomato bacterial wilt by foliar spray application of a novel strain of endophytic bacillus sp.
Hui-Zhen Fu, Malek Marian, Takuo Enomoto, Ayaka Hieno, Hidemasa Ina, et al.
Microbes and Environments, 2020
Microbial basis of Fusarium wilt suppression by Allium cultivation
Tomoki Nishioka, Malek Marian, Issei Kobayashi, Yuhko Kobayashi, Kyosuke Yamamoto, et al.
Scientific Reports, 2019
Improving performance of microbial biocontrol agents against plant diseases
Malek Marian, Masafumi Shimizu
Journal of General Plant Pathology, 2019
Enhanced biocontrol of tomato bacterial wilt using the combined application of Mitsuaria sp. TWR114 and nonpathogenic Ralstonia sp. TCR112
Malek Marian, Akio Morita, Hiroyuki Koyama, Haruhisa Suga, Masafumi Shimizu
Journal of General Plant Pathology, 2019
Biocontrol potential of Ralstonia sp. TCR112 and Mitsuaria sp. TWR114 against tomato bacterial wilt
Malek Marian, Tomoki Nishioka, Hiroyuki Koyama, Haruhisa Suga, Masafumi Shimizu
Applied Soil Ecology, 2018