Though laboratory information management systems (LIMSs) have become commonplace in high-throughput biomedical laboratories, standardized data storage and retrieval remain inconsistent in studies of organismal relationships and symbioses. Here we provide a case study on a biological sample management system designed for a small laboratory whose work with insects and culturable symbionts necessitates high sample tracking capacity but a low barrier to usage. In this paper, we discuss the development of this system from a design perspective, addressing other symbiologists who may not have an extensive database or application development background but still want a more efficient way to keep track of complicated data. We discuss problems related to complex networks of sample provenance, “human-readable” identifying information, standardization of terms and identification procedures, and designing a user interface for rapid data entry and retrieval. Our straightforward database structure and its corresponding application demonstrate that creating a flexible, customizable LIMS for studying symbiosis can be low-cost and does not require highly specialized technological expertise.
Mycorrhizal fungi are a critical ecological determinant for the survival and population sustainability of orchids, playing a decisive role in the success of conservation efforts for endangered species. However, the symbiotic relationship during the early life stages of the rare terrestrial orchid Mengzia foliosa remains unexplored. To address this knowledge gap, we investigated the mycorrhizal associations during the germination and seedling development of M. foliosa. Ten fungal strains, four isolated from the roots of Bletilla striata (MB-11, MB-13, MB-15 and MB-18) and six isolated from the protocorms of M. foliosa (MH1-A, MH1-B, MH1-E, MH3-2-A, MH4-2-A and MH4-B), were co-cultured with M. foliosa seeds in vitro for 16 weeks. Six fungal strains significantly promoted seed germination, while four strains (MH1-A, MB-15, MH4-B, and MB-13) markedly enhanced seedling development, with MH1-A showing the highest efficacy (76.50
Sponges create ecologically important habitat structures and achieve remarkable filtration efficiency through their porous morphology. Functionally, the interconnected pores, canal networks, flagellated choanocytes, and the excurrent openings (oscula) operate as an aquiferous system that generates unidirectional water flow critical for feeding, respiration, and waste removal. However, some sponge species possess pocket cavities that are distinct from the primary aquiferous system. The form and function of these structures remain poorly understood. Here we test whether the pocket cavities function as habitats for ophiuroids in poriferan-ophiuroid symbioses. Using CT scans, resin casts, morphometric analyses, fluorescent dye tracers and behavioral observations, we show that pocket cavities are morphologically distinct from oscula, non-contractile, and exhibit no apparent connectivity to the host’s primary excurrent pathways. Furthermore, the sponge body appears to create distinct microhabitats based on the localized flow regimes. The brittle star Ophiactis modesta, inhabiting the pocket cavities near the directional oscular jets, orients its tube feet in two rows, a configuration potentially advantageous in strong currents. Conversely, Megaophiothrix sp. living at the sponge base, exhibit a four-way radial tube feet posture typically associated with capturing food in diffuse, non-directional flow. These divergent behaviors likely allow both species to coexist on the host while providing reciprocal benefits as the brittle stars remove debris from the sponge surfaces. Our results highlight how non-aquiferous sponge features function to extend host roles beyond suspension feeding, by providing habitat to brittle stars and shaping ecological interactions within benthic communities.
Alder species have the ability to colonize and reclaim mining and industrial sites. At these sites, Parafrankia and Pseudofrankia strains have been isolated from alder root nodules, despite alders typically being nodulated by Frankia species. Following isolation, these strains are unable to reinfect alders under lab-controlled conditions. These findings suggest that there may be an environmental factor that plays a role in inducing flexibility in the interaction between host plant and symbiont in degraded soils. To investigate this phenomenon, nodule formation and community dynamics of black alders (Alnus glutinosa) under low (0.1 mM) or high (1.0 mM) copper stress were observed with a typical alder symbiont, Frankia sp. QA3, and an Elaeagnus-infective, copper-tolerant strain, Pseudofrankia inefficax EuI1c or co-culture. Low copper-stressed plants had significantly better plant health scores when they were co-inoculated with both strains versus single-inoculation with QA3. At concentrations of copper > 0.1 mM, the ability of Frankia sp. QA3 to nodulate its host plant was fully inhibited in both single- and co-inoculated conditions. Under low copper conditions, nodule occupancy was dominantly composed of Frankia sp. QA3 (> 99
Arbuscular mycorrhizal (AM) fungi display a wide range of life history strategies, yet these strategies remain insufficiently characterized in several Glomeromycota lineages, particularly within the understudied Entrophosporaceae. Elucidating this variation is important for understanding the influence of AM fungal diversity on symbiotic function and plant performance. This study quantified temporal patterns of sporulation, root colonization, extraradical hyphal production, and plant growth responses for 13 fungal isolates representing Entrophosporaceae, Acaulosporaceae, Gigasporaceae, and Glomeraceae. We predicted that (i) Entrophosporaceae would exhibit trait conservatism and (ii) traits of Entrophosporaceae is relatively more similar to Glomeraceae than to the other AM fungal families, considering their closer phylogenetic relationship. Sorghum bicolor was cultivated in compartmented pots equipped with 45-µm mesh bags and inoculated with individual fungal isolates; plants were harvested at 21, 28, 42, 56, and 84 days after germination. Significant differences among fungal isolates were observed in sporulation, root colonization, extraradical hyphal length, and effects on shoot biomass, with these responses varying over time. All Entrophosporaceae isolates significantly increased host shoot biomass relative to the non-mycorrhizal control but showed increased sporulation over time and contrasting colonization dynamics. We observed rapid early colonization followed by decline at 84 days or bell-shaped temporal patterns. In contrast, extraradical hyphal length in Entrophosporaceae remained relatively stable throughout the experiment. Host shoot biomass was positively correlated with both root colonization and extraradical hyphal length, but not with arbuscule abundance. Root colonization and extraradical hyphal length over time in Entrophosporaceae were comparable to those in Acaulosporaceae, Glomeraceae, and Gigasporaceae. Collectively, these findings demonstrate that Entrophosporaceae encompasses substantial functional diversity, including both ruderal, competitive, and stress-tolerant strategies. Evaluating temporal dynamics using trait-based approaches is important for resolving AM fungal life history variation and predicting contributions to plant growth.
Compost amendment is an eco-friendly means to enhance soil health and crop productivity. However, studies correlating the compost prokaryotic diversity and nutrient profiles with the soil and plant health remain limited. The present study compared the nutrient content and prokaryotic diversity associated with seven compost types derived from different feedstocks, and evaluated their effects on soil nutrients, and growth and yield parameters of tomato plant to identify the most suitable compost for tomato cultivation. Targeted 16S rRNA gene sequencing-based analysis revealed that rice compost was distinct from other compost samples, characterized by the lowest alpha diversity and a significantly divergent community composition. It showed a decreased abundance of important bacterial phyla, namely Actinobacteriota (1.33
Legume-rhizobial symbiosis plays a crucial role in agricultural sustainability. Mesorhizobium, a major root symbiont, is known to influence nodulation, nitrogen fixation, and yield in chickpea. However, there is a significant lack of research on its competitiveness and nodule occupancy in saline environments. In the present study, experiments were conducted to assess the growth kinetics of 12 Mesorhizobium strains and to evaluate their plant growth-promoting activities towards enhancing competitiveness for nodulation. All strains showed different growth rates, ranging from 0.10 to 0.26 per hour, and generation times ranging from 2.64 to 6.66 h. Strains C101 and C95 showed maximum bacteriocin production potential as compared to the other Mesorhizobium strains. Strain C101 showed considerable P, K, Zn solubilization potential and nitrate reductase activity. Furthermore, a field investigation was conducted by seed priming to evaluate the persistence and effectiveness of these treatments under environmental conditions. In strain C101-inoculated plants, significant enhancement in shoot length, fresh weight, leaf IAA, total pigments, and nitrate reductase activity by 52, 80, 54, 37, 72
Pteridophytes occupy a key evolutionary position in land plant evolution and provide a framework for understanding the early establishment and diversification of plant-fungus symbioses. Early anatomical observations identified arbuscule- and vesicle-like structures in ferns and lycophytes, providing some of the earliest evidence for arbuscular mycorrhizal associations in this lineage. Throughout much of the twentieth century, however, research mainly remained descriptive, focusing on colonization patterns and morphological features. With the advent of molecular phylogenetics and high-throughput sequencing, this perspective has significantly expanded. Later studies revealed that pteridophytes associate not only with Glomeromycotina but also with Mucoromycotina, fine root endophytes, and dark septate endophytes, indicating a more diverse and complex symbiotic network than previously thought. Nevertheless, a comprehensive functional understanding of these interactions remains limited. Molecular insights into pteridophyte–mycorrhizal symbiosis remain underdeveloped compared with those in angiosperm model systems. Important aspects such as symbiotic signaling pathways, gene expression dynamics, nutrient exchange mechanisms, and regulatory networks are poorly understood. Furthermore, the extent of fungal specificity across different life stages of pteridophytes, such as gametophyte and sporophyte, and across various evolutionary lineages, remains unclear. Integrative approaches combining phylogenomics, transcriptomics, metabolomics, and microbiome profiling are scarce. Addressing these gaps will enhance our understanding of the origins and evolution of symbiotic mechanisms in early vascular plants and support the use of these associations in biodiversity conservation and ecosystem restoration.
Coral-associated microbiomes play crucial roles in the resilience and adaptation of reef-building corals to environmental changes. While most research has focused on scleractinian corals, the microbiomes of octocorals remain largely unexplored, particularly in the Red Sea. Here, we characterise the bacterial and Symbiodiniaceae communities associated with two endemic species of the reef-building octocoral Tubipora in the central Saudi Arabian Red Sea. Using high-throughput sequencing of the bacterial 16S rRNA gene and the Symbiodiniaceae ITS2 region across 82 colonies and three reef sites ranging from 0 to 30 m depth, we found that microbial assemblages were broadly similar between the two Tubipora species. Depth distribution exerted a significant influence on the composition of bacterial communities, while Symbiodiniaceae assemblages showed both species- and depth-specific patterns. Moreover, Tubipora hosted distinct bacterial assemblages compared to co-occurring scleractinian species in the same area. Our findings provide the first insights into the Tubipora-associated microbiome in shallow-water coral reefs of the Red Sea, establishing a baseline for understanding octocoral holobionts in the basin, and their potential adaptive strategies in response to climate change.
The photobionts of lichenized basidiomycetes remain poorly understood compared with those of many lichenized ascomycetes. In this study, we investigated the photobionts of three Japanese species of Multiclavula—M. mucida, M. petricola, and M. vernalis—using culture isolation, light microscopy, transmission electron microscopy, molecular phylogenetic analyses, ITS2 secondary structure comparisons, and co-culture experiments. Photobiont cells within the thalli possessed pyrenoids, excluding Coccomyxa as the primary photobiont of the examined specimens. Cultured photobionts were morphologically and ultrastructurally consistent with Elliptochloris, and phylogenetic analyses of 18S rDNA, ITS, and rbcL datasets placed all isolates within or near the E. subsphaerica–E. marina complex. The photobionts of M. mucida were assigned to E. subsphaerica subsp. subsphaerica, and co-culture experiments with the corresponding fungal isolate successfully resynthesized globular lichenized thalli. In contrast, isolates from M. petricola and M. vernalis formed a distinct lineage, supported by ITS and rbcL phylogenies, ITS2 sequence divergence, and hemi-CBCs. This lineage is described here as E. subsphaerica subsp. subalpina subsp. nov.
Mite domatia — small structures on plant leaves that house mutualistic mites — are widespread across plants yet remain relatively understudied. Here we investigate the chemistry and micromorphology of mite domatia across sympatric species of broadleaf deciduous woody species that have convergently evolved tuft-form mite domatia. Specifically, we test whether domatia display similar micromorphological and chemical properties using metabolomics and scanning electron microscopy across multiple independent sympatric lineages. To identify domatia-specific phenotypes, we also compare tissue within domatia to that of nearby leaf tissue on each of the four domatium-bearing species, and test whether species with domatia exhibit reduced chemical defense relative to species that lack domatia using four additional species that lack prominent domatia as a control. We found that domatium-bearing species had significantly lower total phenolic concentrations and lower total defense compound abundance compared to control species, consistent with an evolutionary trade-off between chemical and mutualistic defense. However, within leaves, domatium tissue chemical defense did not differ from surrounding laminar tissue. In contrast, trichome morphology showed clear convergent modification: domatium trichomes were 24–31
Since phosphorus (P) availability is critical to plant productivity and crop performance, there is a growing focus on eco-friendly strategies to enhance its uptake. One of the most sustainable agricultural approach is the use of phosphorus-solubilising microorganisms. The present study aims to compare the inoculation of the forage legume Medicago sativa with rhizospheric microorganisms: a consortium of native arbuscular mycorrhizal fungi (AMF), native Phosphorus Solubilising Bacteria (PSB) (Pseudomonas luteola), and their co-inoculation under steppe saline soil conditions, using a factorial design combining microbial inoculation treatments and P fertilisation. Results showed that co-inoculation increased shoot biomass by 17 and 14
Endophytic and mycorrhizal fungi are vital for the life cycle of orchid species, as they lack nutrient reserves and rely entirely on these symbionts for early growth and seedling establishment in their natural environment. Identifying the symbiotic fungi of orchids enhances understanding of this relationship, especially mycorrhizal fungi characterized by the formation of pelotons, structures formed by the coiling of hyphae within the cortical cells of roots. This study aimed to analyze the diversity and dynamics of culturable endophytic and putatively mycorrhizal fungi associated with the endemic and endangered orchid species Rhynchostele cervantesii. Seventeen fungal strains were isolated from the roots and protocorms of R. cervantesii collected from a single natural population located at the Tenderio Property within the Voluntary Conservation Area of the Indigenous Community of Santiago Tingambato, Michoacán, Mexico. Blastn search and complementary phylogenetic analysis of the ribosomal DNA internal transcribed spacer (ITS1-5.8 S-ITS2) of these fungal isolates allowed the identification of ten different OTUs, all belonging to the phylum Ascomycota, within the genera Apiospora, Aspergillus, Diaporthe, Didymella, Leptosphaeria, Nemania, Penicillium, and Xylaria. The community of culturable endophytic fungi associated with R. cervantesii roots shows seasonal and developmental variation. The specific roles of these taxonomic groups in establishing and providing resistance to abiotic stress in R. cervantesii remain to be clarified. Notably, Diaporthe sp. stands out as a strain capable of supporting in vitro plant cultivation due to its ability to produce indole-3-acetic acid (IAA), while Apiospora appears to play a significant role throughout the life cycle of this endangered species.
Antimicrobial resistance (AMR) in the Anopheles midgut microflora is recognised as major factor playing a significant role in malaria transmission. Anopheles midgut symbionts form dense and taxonomically diverse community that shapes vector fitness by modulating the characteristics of AMR and anti-Plasmodium immunity. The current health emergency caused by antimicrobial resistance has profound impact on the effectiveness of various malaria eradication approaches. To better understand these mechanisms, prediction of the failure of vector control strategies and the design of interventions based on the microbial community in malaria transmission. Recent work demonstrates that naturally occurring Serratia and engineered paratransgenic strains can reduce oocysts of Plasmodium. Metagenomics and culture-based assays on Anopheles gambiae and Anopheles stephensi have identified multiple β-lactamase, efflux pump and tetracycline resistance determinants in gut bacteria. In laboratory and field populations, Proteobacteria typically represent 60–90
Environmental disturbances can cause microbial dysbiosis in corals, leading to coral bleaching and other diseases. The primary focus is on developing a synthetic microbial consortium using the Design-Build-Test-Learn framework. Strategies such as synthetic microbes with natural microbes, symbiont shuffling, coral microbiome transplantation, and assisted evolution (selective breeding, cross-breeding, epigenetic reprogramming, laboratory manipulation, and symbiont manipulation) are being explored. This review discusses the heat tolerance, nutrient cycling, and pathogen defense modules, as well as the programmable microbes under development. The programmable microbes can sense the environmental stressors and trigger the environmentally responsive genetic circuits. Central to this approach is the engineering and delivery of the synthetic microbial consortia. Different methods, such as microbial encapsulation, bio-immobilization, and symbiont recognition mechanisms, are being tested under dynamic environmental conditions. In contrast, factors such as water pressure, temperature, microbial competition, and long-term viability are taken into account. The crucial challenges involve ensuring microbial stability in dynamic marine environments and navigating the ethical implications of these genetic interventions. By bridging the lab-scale innovations with ecosystem-scale deployment, a transformative pathway for reef restoration in the Anthropocene can be strengthened.
Mycorrhizal symbiosis is a key biological strategy for improving nutrient acquisition, stress tolerance, and soil health in crop production systems. Mycorrhizal fungi colonize plant roots and form specialized interfaces through which phosphorus, nitrogen, micronutrients, and water are transferred from the soil to the host plant in exchange for photosynthetically derived carbon. These interactions can enhance plant growth, yield, and quality while reducing reliance on synthetic fertilizers and other agrochemicals. Although most previous work has focused on arbuscular mycorrhizal fungi (AMF) in field crops, many economically important species host a wider range of mycorrhizal types and experience intense abiotic and biotic stresses. This review synthesizes current knowledge on the structural and functional diversity of major mycorrhizal associations, arbuscular, ectomycorrhizal, arbutoid, ericoid, and orchid mycorrhizae, in relation to crop performance. We first describe how these symbioses enhance nutrient uptake and utilization, including extension of the soil exploration zone by fungal hyphae, mobilization of poorly available nutrient pools, and regulation of nutrient transporter expression. We then examine the roles of mycorrhiza in mitigating drought, salinity, heavy metal toxicity, temperature extremes, and pathogen pressure, with emphasis on physiological and emerging molecular mechanisms such as hormonal signaling and activation of antioxidant and defence pathways. Selected case studies highlight improvements in yield, product quality, and functional metabolites across fruits, vegetables, ornamentals, and medicinal plants. By integrating evidence across different mycorrhizal types and crop species, this review underscores mycorrhiza as a multifunctional biotechnological tool rather than only a biological fertilizer. It also identifies key research gaps and practical considerations for deploying diverse mycorrhizal inoculants to support climate-resilient and sustainable production systems.
Spiroplasma, a bacterium that infects some insects, is known to induce male-specific mortality in its hosts. It has been identified in the spongy moth (Lymantria dispar japonica), but it remains unclear whether it causes male mortality in this host. Therefore, in this study, we collected 271 spongy moth egg masses from 27 locations in Japan to identify Spiroplasma-infected egg masses. Using 16S rRNA-targeted PCR, 27 of the 271 egg masses were Spiroplasma-positive. Most of these egg masses originated from L. umbrosa, whereas only three originated from L. dispar japonica. Phylogenetic analysis revealed that the detected Spiroplasma belonged to the Spiroplasma ixodetis clade and was identical to previously reported strains derived from L. dispar japonica. Bacterial density varied significantly among egg masses, and we observed a tendency toward higher vertical transmission efficiency when the maternal bacterial density was high. As development progressed, bacterial density increased, reaching approximately 50–150 cells/host cell in the Malpighian tubules at the pre-pupal stage. Nevertheless, no female-biased sex ratio was observed; thus, no notable male-killing effect was confirmed. To our knowledge, this is the first study to report Spiroplasma infection in L. umbrosa. Our findings strongly suggest that the identified Spiroplasma species is a non-male-killing type.
Bark beetles are fundamental drivers of forest ecosystem dynamics. However, some species within this group have recently also emerged as significant pests in environments managed by humans, including nurseries, orchards, and urban areas. Specifically, certain Scolytus species pose potential economic and ecological threats to stone fruit cultivation across the Mediterranean basin. Although the role of the mycobiome in mediating bark beetle–host interactions has been well documented for many forest models, the symbiotic associations between beetles and fungi in cultivated Mediterranean agroecosystems remain poorly understood. This study provides the first comprehensive characterization of the fungal community associated with the almond bark beetle Scolytus amygdali in southern Mediterranean almond orchards. Integrating culture-dependent isolations with culture-independent approaches, i.e., high-throughput sequencing, allowed us to assess the beetle mycobiome across beetle adults, gallery systems, and associated necrotic wood lesions. Molecular characterization revealed Geosmithia, Paecilomyces, and Quambalaria to be the dominant taxa within the S. amygdali mycobiome. Their frequent occurrence suggests that they may be recurrent associates in the gallery environment, although their functional roles remain unclear. Furthermore, metabarcoding analyses provided additional novel insights into the beetle mycobiome, identifying Candida and Yamadazyma yeasts as potential core constituents of the gut microbiome. Future research should prioritize elucidating the role of these putative fungal symbionts for the beetles, particularly the pathogenic potential on almonds, and the functional efficiency of S. amygdali as a vector. Overall, our findings elucidate the complex taxonomic diversity of these associations. Moreover, obtained results provide a foundational ecological framework to better understand to what extent these associations can threaten host plants and to develop future sustainable management strategies in managed ecosystems.
Ophiocordyceps sinensis is a rare medicinal fungal complex formed by the parasitism of the Hirsutella sinensis on the larvae of the Hepialidae family. Driven by climate warming and over-harvesting, wild resources have declined sharply, making artificial cultivation an inevitable trend. Strain infectivity is the key factor determining the formation efficiency and success rate of artificial cultivation, encompassing the entire process of spore attachment and germination, cuticle penetration, hemocoel colonization, immune evasion, chronic infection, and stroma formation. Focusing on infectivity, this article systematically integrates regulatory factors such as fungal genetic background, host specificity, environmental adaptation, and inoculation techniques to establish the link between “infectivity―host compatibility―ecological adaptation―cultivation success rate.” Future efforts should focus on developing genetic manipulation systems suitable for O. sinensis, combining temporal multi-omics and host microbiome analysis to gain in-depth insights into the unique chronic parasitic symbiotic mechanism between the fungus and its host, thereby promoting efficient artificial cultivation and sustainable resource utilization.
