SUBHAJIT BASU

Scopus Publications

Culturable rhizospheric microbiota of Lactuca sativa cultivars during nutrient-film farming reveals potential biocontrol and plant-growth promoting traits against commonly infesting fungal pathogens
Siya Sharma, Bipin Sati, Durgesh Pant, Subhajit Basu
Archives of Microbiology, 2026
Comparative assessment of microbial arsenite oxidation: Mechanisms, oxidation rates, challenges, and bioremediation potentials
Saif Ali, Rajesh Singh, Subhajit Basu
Journal of Water Process Engineering, 2026
Rhizosphere Microbiome Dynamics in Hydroponics: Core Taxa, Fungal Pathogen Infestations and Probiotic-Based Management
Siya Sharma, Bipin Sati, Durgesh Pant, Shakti Kumar, Subhajit Basu
Plant Pathology, 2026
Hydroponics is emerging as a promising method of controlled‐environment agriculture (CEA), known for its high yields and efficient use of water through continuous recycling within the channels. In hydroponic systems, commercially grown crops in soilless substrates can be cultivated year‐round with optimised nutrient delivery under CEA conditions. Despite these advantages, the structure and function of rhizospheric microbiomes in hydroponics remain inadequately characterised, particularly regarding their roles in plant health and disease resistance. This review critically examines the development and composition of the hydroponic rhizosphere microbiome based on current literature, with a specific focus on the challenges posed by fungal phytopathogens. A meta‐analysis of rhizospheric microbiomes associated with hydroponically grown Lactuca sativa (lettuce), Solanum lycopersicum (tomato) and Allium schoenoprasum (chive) across various cultivation systems identified 99 distinct bacterial genera. These taxa were primarily affiliated with the phyla Pseudomonadota, Bacteroidota, Actinobacteriota and Verrucomicrobiota. Importantly, the core microbiome genera are significantly fewer compared to system‐specific genera. Microbiome composition is strongly influenced by crop species, hydroponic system architecture, fertigation regimes, substrate type and greenhouse environmental conditions. Pathogen intrusion, particularly by opportunistic fungi such as Fusarium spp. and oomycetes such as Pythium and Phytophthora spp., was frequently associated with major disruptions to native microbiota, occasionally resulting in increased alpha‐diversity. This paradox suggests a transition towards rhizosphere dysbiosis rather than a stable microbial equilibrium. These observations underscore the need for targeted microbiome management strategies that account for ecological specificity and functional redundancy.
Insights into drug resistance in Leishmania: Mechanisms, therapeutics, and clinical case studies
Gajala Deethamvali Ghousepeer, Mansi Rani, Aman Kumar, Shubhankar Kumar Singh, Anjali Priyadarshini, et al.
Admet and Dmpk, 2026
Background and purpose: Leishmaniasis, a neglected tropical disease caused by the protozoan parasite Leishmania, remains a significant public health concern in endemic regions. The disease manifests in various forms, including cutaneous, mucocutaneous, and visceral leishmaniasis, each associated with specific Leishmania species and influenced by host immune responses. Over the past few decades, treatment for leishmaniasis has relied on a limited range of drugs, including pentavalent antimonials, amphotericin B formulations, miltefosine, and paromomycin. However, widespread drug resistance, particularly in visceral leishmaniasis, has severely compromised treatment efficacy, leading to rising cases of treatment failure. This review aims to provide a comprehensive understanding of the mechanisms underlying drug resistance in leishmaniasis and to highlight the factors that contribute to its development. Experimental approach: The study synthesizes existing literature on resistance mechanisms among anti-leishmanial drugs, focusing on changes in parasite uptake and efflux, intracellular sequestration, and modulation of stress responses. It also examines the impact of environmental factors, such as arsenic exposure in endemic regions, and reviews recent molecular and genomic studies that have identified resistance-associated markers. Conclusion: The review underscores the urgent need for innovative therapeutic strategies and highlights the importance of an integrated approach to combat drug resistance through enhanced surveillance, molecular insights, and global collaboration.
Costs of Dust Collection by Trichodesmium: Effect on Buoyancy and Toxic Metal Release
Siyuan Wang, Futing Zhang, Coco Koedooder, Odeta Qafoku, Subhajit Basu, et al.
Journal of Geophysical Research Biogeosciences, 2024
The marine cyanobacterium Trichodesmium has the remarkable ability to interact with and utilize air‐borne dust as a nutrient source. However, dust may adversely affect Trichodesmium through buoyancy loss and exposure to toxic metals. Our study explored the effect of desert dust on buoyancy and mortality of natural Red Sea puff‐shaped Trichodesmium thiebautii. Sinking velocities and ability of individual colonies to stay afloat with increasing dust loads were studied in sedimentation chambers. Low dust loads of up to ∼400 ng per colony did not impact initial sinking velocity and colonies remained afloat in the chamber. Above this threshold, sinking velocity increased linearly with the colony dust load at a slope matching prediction based on Stoke's law. The potential toxicity of dust was assessed with regards to metal dissolution kinetics, differentiating between rapidly released metals, which may impact surface blooms, and gradually released metals that may impact dust‐centering colonies. Incubations with increasing dust concentrations revealed colony death, but the observed lethal dose far exceeded dust concentrations measured in coastal and open ocean systems. Removal of toxic particles as a mechanism to reduce toxicity was explored using SEM‐EDX imaging of colonies incubated with Cu‐minerals, yet observations did not support this pathway. Combining our current and former experiments, we suggest that in natural settings the nutritional benefits gained by Trichodesmium via dust collection outweigh the risks of buoyancy loss and toxicity. Our data and concepts feed into the growing recognition of the significance of dust for Trichodesmium's ecology and subsequently to ocean productivity.
Reactive oxygen species affect the potential for mineralization processes in permeable intertidal flats
Marit R. van Erk, Olivia M. Bourceau, Chyrene Moncada, Subhajit Basu, Colleen M. Hansel, et al.
Nature Communications, 2023
Intertidal permeable sediments are crucial sites of organic matter remineralization. These sediments likely have a large capacity to produce reactive oxygen species (ROS) because of shifting oxic-anoxic interfaces and intense iron-sulfur cycling. Here, we show that high concentrations of the ROS hydrogen peroxide are present in intertidal sediments using microsensors, and chemiluminescent analysis on extracted porewater. We furthermore investigate the effect of ROS on potential rates of microbial degradation processes in intertidal surface sediments after transient oxygenation, using slurries that transitioned from oxic to anoxic conditions. Enzymatic removal of ROS strongly increases rates of aerobic respiration, sulfate reduction and hydrogen accumulation. We conclude that ROS are formed in sediments, and subsequently moderate microbial mineralization process rates. Although sulfate reduction is completely inhibited in the oxic period, it resumes immediately upon anoxia. This study demonstrates the strong effects of ROS and transient oxygenation on the biogeochemistry of intertidal sediments.
Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia
Coco Koedooder, Futing Zhang, Siyuan Wang, Subhajit Basu, Sheean T. Haley, et al.
Msystems, 2023
The photosynthetic and diazotrophic cyanobacterium Trichodesmium is a key contributor to marine biogeochemical cycles in the subtropical-oligotrophic oceans. Trichodesmium form colonies that harbor a distinct microbial community in comparison to the surrounding seawater. The presence of their associated bacteria can expand Trichodesmium ’s functional potential and is predicted to influence the cycling of carbon, nitrogen, phosphorus, and iron (C, N, P, and Fe). To link the bacteria associated with Trichodesmium to key functional traits and elucidate how community structure can influence nutrient cycling, we characterized Red Sea Trichodesmium colonies using metagenomics and metaproteomics. Colonies harbored bacteria that typically associate with algae and particles, such as the ubiquitous Alteromonas macleodii, but also lineages specific to Trichodesmium , such as members from the order Balneolales. The majority of associated bacteria were auxotrophic for different vitamins, indicating their dependency on vitamin production by Trichodesmium . The associated bacteria carry functional traits including siderophore biosynthesis, reduced phosphorus metabolism, and denitrification pathways. The analysis supports Trichodesmium as an active hotspot for C, N, P, Fe, and vitamin exchange. In turn, Trichodesmium may rely on associated bacteria to meet its high Fe demand as several lineages synthesize photolabile siderophores (e.g., vibrioferrin, rhizoferrin, petrobactin) which can enhance the bioavailability of particulate Fe to the entire consortium. Collectively, the results indicate that Trichodesmium colonies provide a structure where these interactions can take place. While further studies are required to clarify the exact nature of these interactions, Trichodesmium ’s reliance on particle and algae-associated bacteria and the observed redundancy of key functional traits likely underpins the resilience of Trichodesmium within an ever-changing global environment. IMPORTANCE Colonies of the cyanobacteria Trichodesmium act as a biological hotspot for the usage and recycling of key resources such as C, N, P, and Fe within an otherwise oligotrophic environment. While Trichodesmium colonies are known to interact and support a unique community of algae and particle-associated microbes, our understanding of the taxa that populate these colonies and the gene functions they encode is still limited. Characterizing the taxa and adaptive strategies that influence consortium physiology and its concomitant biogeochemistry is critical in a future ocean predicted to have increasingly resource-depleted regions.
Co-acquisition of mineral-bound iron and phosphorus by natural Trichodesmium colonies
Yeala Shaked, Dirk de Beer, Siyuan Wang, Futing Zhang, Anna‐Neva Visser, et al.
Limnology and Oceanography, 2023
Low iron (Fe) and phosphorus (P) ocean regions are often home to the globally important N2‐fixing cyanobacterium Trichodesmium spp., which are physiologically adapted to Fe/P co‐limitation. Given Trichodesmium's eminent ability to capture particles and the common associations between Fe and P in sediments and aerosols, we hypothesized that mineral bio‐dissolution by Trichodesmium spp. may enable them to co‐acquire Fe and P. We present a new sensitive assay to determine P uptake from particles, utilizing 33P‐labeled ferrihydrite. To validate the method, we examined single natural Trichodesmium thiebautii colonies in a high‐resolution radiotracer ß‐imager, identifying strong colony‐mineral interactions, efficient removal of external 33P‐labeled ferrihydrite, and elevated 33P uptake in the colony core. Next, we determined bulk P uptake rates, comparing natural Red Sea colonies and P‐limited Trichodesmium erythraeum cultures. Uptake rates by natural and cultured Trichodesmium were similar to P release rates from the mineral, suggesting tight coupling between dissolution and uptake. Finally, synthesizing P‐ferrihydrite labeled with either 33P or 55Fe, we probed for Fe/P co‐extraction by common microbial mineral solubilization pathways. Dissolution rates of ferrihydrite were accelerated by exogenous superoxide and strong Fe‐chelator and subsequently enhanced 33P release and uptake by Trichodesmium. Our method and findings can facilitate further Fe/P co‐acquisition studies and highlight the importance of biological mechanisms and microenvironments in controlling bioavailability and nutrient fluxes from particles.
Metagenomes of Red Sea Subpopulations Challenge the Use of Marker Genes and Morphology to Assess Trichodesmium Diversity
Coco Koedooder, Etai Landou, Futing Zhang, Siyuan Wang, Subhajit Basu, et al.
Frontiers in Microbiology, 2022
Trichodesmium are filamentous cyanobacteria of key interest due to their ability to fix carbon and nitrogen within an oligotrophic marine environment. Their blooms consist of a dynamic assemblage of subpopulations and colony morphologies that are hypothesized to occupy unique niches. Here, we assessed the poorly studied diversity of Trichodesmium in the Red Sea, based on metagenome-assembled genomes (MAGs) and hetR gene-based phylotyping. We assembled four non-redundant MAGs from morphologically distinct Trichodesmium colonies (tufts, dense and thin puffs). Trichodesmium thiebautii (puffs) and Trichodesmium erythraeum (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both T. thiebautii and T. erythraeum, a single T. thiebautii genotype comprised both thin and dense puff morphotypes, and we hypothesize that this phenotypic variation is likely attributed to gene regulation. Additionally, we found the rare non-diazotrophic clade IV and V genotypes, related to Trichodesmium nobis and Trichodesmium miru, respectively that likely occurred as single filaments. The hetR gene phylogeny further indicated that the genotype in clade IV could represent the species Trichodesmium contortum. Importantly, we show the presence of hetR paralogs in Trichodesmium, where two copies of the hetR gene were present within T. thiebautii genomes. This may lead to the overestimation of Trichodesmium diversity as one of the copies misidentified T. thiebautii as Trichodesmium aureum. Taken together, our results highlight the importance of re-assessing Trichodesmium taxonomy while showing the ability of genomics to capture the complex diversity and distribution of Trichodesmium populations.
Mineral iron dissolution in Trichodesmium colonies: The role of O2 and pH microenvironments
Meri Eichner, Subhajit Basu, Siyuan Wang, Dirk de Beer, Yeala Shaked
Limnology and Oceanography, 2020
Colonies of the N2‐fixing cyanobacterium Trichodesmium can harbor distinct chemical microenvironments that may assist the colonies in acquiring mineral iron from dust. Here, we characterized O2 and pH gradients in and around Trichodesmium colonies by microsensor measurements on > 170 colonies collected in the Gulf of Eilat over ∼ 2 months. O2 concentrations and pH values in the center of single colonies decreased in the dark due to respiration, reaching minimum values of 70 μmol L−1 and 7.7, whereas in the light, O2 and pH increased due to photosynthesis, reaching maximum values of 410 μmol L−1 and 8.6. Addition of dust and bacteria and increasing colony size influenced O2 and pH levels in the colonies, yet values remained within the range observed in single natural colonies. However, lower values down to 60 μmol L−1 O2 and pH 7.5 were recorded in the dark in dense surface accumulations of Trichodesmium. Using radiolabelled ferrihydrite, we examined the effect of these conditions on mineral iron dissolution and availability to Trichodesmium. Dark‐incubated colonies did not acquire iron from ferrihydrite faster than light‐incubated colonies, indicating that the dark‐induced decrease in pH and O2 within single colonies is too small to significantly increase mineral iron bioavailability. Yet, ligand‐promoted dissolution of ferrihydrite, a mechanism likely applied by Trichodesmum for acquiring mineral iron, did increase at the lower pH levels observed in surface accumulations. Thus, Trichodesmium surface blooms in their final stage may harbor chemical conditions that enhance the dissolution and bioavailability of mineral iron to the associated microbial community.
Selective collection of iron-rich dust particles by natural Trichodesmium colonies
Nivi Kessler, Rachel Armoza-Zvuloni, Siyuan Wang, Subhajit Basu, Peter K Weber, et al.
Isme Journal, 2020
Colonies of marine cyanobacteria Trichodesmium interact with associated bacteria to acquire iron from dust
Subhajit Basu, Martha Gledhill, Dirk de Beer, S. G. Prabhu Matondkar, Yeala Shaked
Communications Biology, 2019
Metallophores associated with: Trichodesmium erythraeum colonies from the Gulf of Aqaba
Martha Gledhill, Subhajit Basu, Yeala Shaked
Metallomics, 2019
Hydrogen dynamics in trichodesmiumcolonies and their potential role in mineral iron acquisition
Meri Eichner, Subhajit Basu, Martha Gledhill, Dirk de Beer, Yeala Shaked
Frontiers in Microbiology, 2019
Mineral iron utilization by natural and cultured Trichodesmium and associated bacteria
Subhajit Basu, Yeala Shaked
Limnology and Oceanography, 2018

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Scopus Publications