Symbiotic Research Articles

Modelling marine heatwaves impact on shallow and upper mesophotic tropical coral reefs

Abstract Coral reefs ecosystems, often compared to rain forests for their high biodiversity, are threatened by ocean warming causing coral bleaching when the symbiotic relationship between dinoflagellates and corals breaks under high ocean temperatures. Thermal stress from marine heatwaves (MHWs) occur both at the surface and subsurface with subsurface MHWs lasting longer with potentially higher cumulative intensities. However, global coral bleaching models generally ignore the differences in thermal stress between surface and sea-bed levels. Here, we define MHWs at sea-bed level to model coral bleaching with daily resolution from 6 May 1993 to 31 October 2023, for 9944 tropical coral reefs between 0 and 60 m depths. We show that deeper reefs experience on average higher thermal stress and bleaching compared to surface reefs. Using surface temperature data to model bleaching for deeper corals underestimates bleaching intensities by an average of 6% ± 9% compared to the subsurface calibrated model. Our study is a starting point for more accurate coral bleaching modelling, providing additional evidence to reshape our perception of deeper coral reefs as potential refugees from climate change.

Subtyping colorectal cancer based on septic shock-associated genes: prognosis and immune characteristics

BackgroundSepsis and colorectal cancer (CRC) are leading causes of death. Given their mutual dependence for susceptibility, we used bioinformatics to explore potential connections between septic shock (SS) and CRC.MethodsWe identified 452 co-expressed genes between SS-related differential expression genes (SS-DEGs) and CRC patient-expressed genes (TCGA-CRC genes). CRC samples were categorized into two cluster subgroups through hierarchical clustering. We then compared the prognosis and immune landscapes of the two cluster subgroups through survival analysis, immune microenvironment analysis, and immune therapy response evaluation.ResultsClustering analysis of the 452 CRC patient-expressed SS-DEGs identified two subtypes: SS-like CRC (SL-CRC) and non-SS-like CRC (NSL-CRC). There were no significant differences in overall survival between the CRC subtypes. However, the subtypes displayed significant differences in immune score, stromal score, and ESTIMATE score. Based on immune therapy databases, there were also significant differences in responses to anti-CTLA-4 and anti-PD-1 immune checkpoint inhibitors between the subtypes.ConclusionOur study reveals significant differences in the immune microenvironment and immune therapy responses between SL-CRC and NSL-CRC subtypes. These findings provide a foundation for identifying new therapeutic targets and developing personalized treatment strategies for specific CRC subtypes.

Rumen-Targeted Mining of Enzymes for Bioenergy Production.

Second-generation biofuel production, which aims to convert lignocellulose to liquid transportation fuels, could be transformative in worldwide energy portfolios. A bottleneck impeding its large-scale deployment is conversion of the target polysaccharides in lignocellulose to their unit sugars for microbial fermentation to the desired fuels. Cellulose and hemicellulose, the two major polysaccharides in lignocellulose, are complex in nature, and their interactions with pectin and lignin further increase their recalcitrance to depolymerization. This review focuses on the intricate linkages present in the feedstocks of interest and examines the potential of the enzymes evolved by microbes, in the microbe/ruminant symbiotic relationship, to depolymerize the target polysaccharides. We further provide insights to how a rational and more efficient assembly of rumen microbial enzymes can be reconstituted for lignocellulose degradation. We conclude by expounding on how gains in this area can impact the sustainability of both animal agriculture and the energy sector.

Reimagining Kinship Systems and Networks:

Aboriginal people in Australia continue to endure the ongoing effects of 250 years of colonisation. However, the social and ontological basis of their Kinship Systems and networks highlights their resilience and resistance against western hierarchies and ideologies. Kinship Systems and networks represent the relationships between culture and nature and do not distinguish between the human and non-human world. The basis of the Kinship Systems and networks extends seamlessly beyond the human into the Ancestral and spiritual realms. As part of the creation process, Land was created first, followed by people and then languages belonging to the Land. Languages are living entities, connecting people with their Country, Ancestors and culture while transmitting intergenerational knowledges within and across thousands of generations. It is impossible to separate one from the other. These entities coexist through and beyond notions of space and time. This inseparable relationship between Land, language, and the rights of Aboriginal People forms the cornerstone of their activism. For example, Aboriginal activists in the Black Lives Matter movement in Australia fight for racial [human] rights and environmental justice consistent with their symbiotic relationship. Drawing on interviews carried out in early 2023 with Aboriginal activists engaged in the revival of languages and Land rights, this paper will examine how the relationships between sustainability, care for Country and language are articulated in and through Kinship systems and networks. It will explain the deep reciprocity, identified by activists, focusing on environmental care and sustainability of Country, language revival and social justice efforts.

Wolbachia in Antarctic terrestrial invertebrates: Absent or undiscovered?

Interactions between a host organism and its associated microbiota, including symbiotic bacteria, play a crucial role in host adaptation to changing environmental conditions. Antarctica provides a unique environment for the establishment and maintenance of symbiotic relationships. One of the most extensively studied symbiotic bacteria in invertebrates is Wolbachia pipientis, which is associated with a wide variety of invertebrates. Wolbachia is known for manipulating host reproduction and having obligate or facultative mutualistic relationships with various hosts. However, there is a lack of clear understanding of the prevalence of Wolbachia in terrestrial invertebrates in Antarctica. We present the outcomes of a literature search for information on the occurrence of Wolbachia in each of the major taxonomic groups of terrestrial invertebrates (Acari, Collembola, Diptera, Rotifera, Nematoda, Tardigrada). We also performed profiling of prokaryotes based on three marker genes and Kraken2 in available whole genome sequence data obtained from Antarctic invertebrate samples. We found no reports or molecular evidence of Wolbachia in these invertebrate groups in Antarctica. We discuss possible reasons underlying this apparent absence and suggest opportunities for more targeted future research to confirm bacteria's presence or absence.

Exploring sociocultural factors and ubuntuism for women living with HIV in rural Zimbabwe

Background: The focus of this study was on women living with HIV in rural Zimbabwe, who face many challenges, both in the family and community. Patriarchy compounds these problems as these women navigate access to health and other services.Objectives: The study sought to explore ubuntuism and the sociocultural factors that facilitate or constrain women living with HIV from accessing community services and resources.Method: An interpretive phenomenological analysis research design was utilised for the study. Purposive and quota sampling were applied to recruit 40 participants from six villages. Data were collected using in-depth interviews and focus group discussions that were audio recorded and transcribed. The data were analysed using the interpretive phenomenological analysis framework.Results: The study found that women living with HIV face stigma and discrimination in the form of social exclusion and reduced access to community-based health activities and empowerment opportunities. These challenges were compounded by the negative impact of patriarchy that gives rise to land, resettlement and acculturation challenges.Conclusion: Ubuntu is a reflection of mutual dependence and can be used to promote more compassionate relationships with those who are HIV positive in the community.Contribution: The study provides unique insights into the challenges experienced by women living with HIV and how ubuntu could mitigate those challenges so that it adds to the humanistic philosophies in interpersonal relationships.

The scale effects of symbiotic relationships under complex driving factors: An empirical study in China

AbstractSymbiotic relationships between enterprises help mitigate resource and environmental impacts of industrial activities via exchanging waste or by‐products as material inputs among each other. However, the emergence of such symbiotic relationships under complex driving factors across different geographical scales remains hitherto not well understood. Here, we provide an analytic framework including a random forest model and Shannon index, to systematically describe and explain the scale effects of driving factors underlying the symbiotic relationships. Based on a questionnaire survey for 324 enterprises in Chun'an, a typical industrial city in eastern China, we applied this analytical framework. The results show that, first, the quantity of symbiotic relationships exhibits an inversely proportional function across various geographical scales. Second, there exist significant differences in the dominant factors at different scales. Finally, the diversity of importance of factors and the emergence of symbiotic relationships exhibit a consistent trend of fluctuation, providing evidence for the explanatory potential of our proposed analytical framework for the driving mechanisms of emergence. We find that when enterprises are simultaneously affected by multiple driving factors with potent forces (referred to as the diversity of importance), symbiotic behaviors are more likely to occur. Moreover, our results suggest that fostering symbiotic relationships necessitates considering the variations in driving factors across different scales comprehensively and formulating targeted promotional measures tailored to the specific driving factors of different enterprise types. Our proposed framework would help to maximize industrial symbiosis potentials in a specific region.

Can the Synergy of Digitalization and Greening Boost Manufacturing Industry Chain Resilience? Evidence from China’s Provincial Panel Data

The synergy of digitalization and greening (DGS) enhances the resilience of the industrial chain (ICR), a critical aspect for the sustainable growth of the national economy. This symbiotic relationship not only facilitates the enhancement of quality and efficiency within the manufacturing sector but also propels forward sustainable economic development. Therefore, how DGS can improve ICR deserves in-depth study. Drawing on the panel data encompassing manufacturing industries across 30 provincial-level administrative regions in China from 2013 to 2022, this study employs a regression model to delve into the mechanisms through which DGS within manufacturing industries impacts ICR. The main results are as follows: (1) DGS in manufacturing makes a positive contribution to ICR; (2) The impact of DGS on ICR varies across regions, with a diminishing effect from the eastern to the western region. (3) Technological innovation reinforces the influence of DGS on ICR. (4) Spatial measures show that the development of DGS in one location has a negative spatial spillover effect on ICR in neighboring areas. Based on the above conclusions, this paper puts forward a series of recommendations aimed at promoting industrial chain resilience.

Cotton-mycorrhizal symbiosis: a comprehensive review of benefits for sustainable agriculture

Abstract Fertilizers and plant protection chemicals have played crucial role in modern agriculture. However, their excessive and imbalanced use over decades has resulted in the degradation and deterioration of soil health. The sustainability of agricultural systems largely depends on improving soil health. In this context, the arbuscular mycorrhizal fungi (AMF) association is a well-known interaction among plant microbial symbiotic associations that plays a multifunctional role in maintaining plant-soil health. More than 90% of terrestrial crop plants, including cultivated cotton, have a mutualistic symbiotic association with AMF. Symbiosis provides several benefits, such as the acquisition of mineral nutrients (primarily phosphorus), protection against biotic and abiotic stresses, and improved yield and fiber quality, contributing to the growth and development of the host plant. Under controlled conditions, the percent root length colonization of cotton was 50 to 70%, indicating the potential of AMF as a biological agent and plant growth promoter for sustainable cotton production. This review provides an updated and comprehensive overview of cotton-mycorrhizal symbiosis and its benefits.

Design of Integrated Energy–Water Systems Using Automated Targeting Modeling Considering the Energy–Water–Carbon Nexus

The swift expansion of the global population and economy has spurred growing requirements for energy and water in recent decades. Inefficient energy and water consumption, however, has led to an increase in CO2 emissions. Hence, the socio-economic development of a country must consider the interconnections between energy, water and carbon, as there are mutual dependencies among these three elements. This work considers the nexus between energy, water and carbon in the design of integrated energy–water systems using a new automated targeting modeling (ATM) framework. ATM incorporates the advantages of the insight-based Pinch method and a mathematical programming approach to provide visual understanding for a thorough analysis of the problem while guaranteeing accurate solutions. Minimum targets of power and water based on the integrated network operation were established by the ATM, with corresponding carbon emissions. A specific goal of annual carbon emissions reduction was set as the constraint and the ATM optimized the capacities of the components in the system accordingly to achieve minimum overall cost. The application of ATM on an industrial plant case study shows that a target of 45% reduction in the carbon discharge amount was achieved by shifting to greener fuel in the energy system at a minimum overall cost increase of 0.45% only. The framework can assist users in meeting power and water loads in their plant while planning for the appropriate decarbonization efforts at the minimum possible cost.

Evolutionary Perspectives on Human-Artificial Intelligence Convergence.

In this analytical review, we explore the potential impact of the rapid proliferation of artificial intelligence (AI) tools on the biosphere and noosphere, suggesting that the trend may lead to a transformative event that could be termed "Human-AI integration." We argue that this integration could give rise to novel lifeforms, associations, and hierarchies, resulting in competitive advantages and increased complexity of structural organizations within both the biosphere and noosphere. Our central premise emphasizes the importance of human-AI integration as a global adaptive response crucial for our civilization's survival amidst a rapidly changing environment. The convergence may initially manifest itself through symbiotic, endosymbiotic, or other mutualistic relationships, such as domestication, contingent on the rate at which AI systems achieve autonomy and develop survival instincts akin to those of biological organisms. We investigate potential drivers of these scenarios, addressing the ethical and existential challenges arising from the AI-driven transformation of the biosphere and noosphere, and considering potential trade-offs. Additionally, we discuss the application of complexity and the balance between competition and cooperation to better comprehend and navigate these transformative scenarios.

AI in Data Analysis

AI in Data Analysis Abstract: Welcome to the inaugural issue of AI Insights, a groundbreaking journal at the forefront of exploring the symbiotic relationship between artificial intelligence (AI) and data analysis. In this inaugural edition, we embark on a journey to unravel the transformative potential of AI-driven approaches in extracting actionable insights from complex datasets. Through a combination of theoretical discussions, practical applications, and visionary outlooks, this journal aims to chart a new course in the field of data analysis.

Endophytic Bacterial Community, Core Taxa, and Functional Variations Within the Fruiting Bodies of Laccaria

Macrofungi do not exist in isolation but establish symbiotic relationships with microorganisms, particularly bacteria, within their fruiting bodies. Herein, we examined the fruiting bodies’ bacteriome of seven species of the genus Laccaria collected from four locations in Yunnan, China. By analyzing bacterial diversity, community structure, and function through 16S rRNA sequencing, we observed the following: (1) In total, 4,840,291 high-quality bacterial sequences obtained from the fruiting bodies were grouped into 16,577 amplicon sequence variants (ASVs), and all samples comprised 23 shared bacterial ASVs. (2) The Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex was found to be the most abundant and presumably coexisting bacterium. (3) A network analysis revealed that endophytic bacteria formed functional groups, which were dominated by the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Novosphingobium, and Variovorax. (4) The diversity, community structure, and dominance of ecological functions (chemoheterotrophy and nitrogen cycling) among endophytic bacteria were significantly shaped by geographic location, habitat, and fungal genotype, rather than fruiting body type. (5) A large number of the endophytic bacteria within Laccaria are bacteria that promote plant growth; however, some pathogenic bacteria that pose a threat to human health might also be present. This research advances our understanding of the microbial ecology of Laccaria and the factors shaping its endophytic bacterial communities.

EXPERIENCE IN ORGANIZING STUDENT RESEARCH CLUB FOR UNDERGRADUATE STUDENTS IN HIGHER EDUCATIONAL INSTITUTION

The relevance of this article is underscored by recent legislative changes in Ukraine, including the “Higher Education Law” and the “Law on Scientific and Technical Activity”, which have increased focus on integrating research into the educational framework of higher education institutions. These laws emphasize the need for a symbiotic relationship between higher education and scientific research, particularly in the training of medical students. They mandate new standards for the structure and objectives of scientific research activities within these institutions, encouraging the development of clear research agendas, updated educational resources to foster relevant competencies, and environments that support effective research endeavors. Cultivating a research-oriented professional requires concerted effort starting from the very beginning of a student’s academic journey. Broadening the engagement of medical students in Student Research Club activities is essential. Through participation in Student Research Club, students gain proficiency in navigating scholarly sources, acquire fundamental research skills, learn to apply theoretical knowledge in clinical contexts, and develop the ability to bridge theory with practice. Encouraging medical students to participate in professional competitions, conferences, and symposia at various levels is of great importance as well. Such activities hone public speaking skills, teach students how to engage and retain an audience, and prepare future healthcare professionals to be confident and persuasive communicators. Professional mentorship is vital for Student Research Club members. Faculty involvement, the guidance of Student Research Club advisors, scientific mentors, and leadership from the Student Research Club team are all critical to cultivating the research skills of emerging medical scientists. This article outlines the strategies implemented by the Department of Human Anatomy, Clinical Anatomy, and Operative Surgery at Dnipro State Medical University to engage early undergraduate students in scientific research.

A unique symbiosome in an anaerobic single-celled eukaryote

Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes – the vast majority of such hosts in nature – remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.

Immunoinformatics investigation on pathogenic Escherichia coli proteome to develop an epitope-based peptide vaccine candidate.

Escherichia coli (E. coli), a gram-negative bacterium, quickly colonizes in the human gastrointestinal tract after birth and typically sustains a long-term, symbiotic relationship with the host. However, certain virulent strains of E. coli can cause diseases such as urinary tract infections, meningitis, and enteric disorders. The rising antibiotic resistance among these strains has heightened the urgency for an effective vaccine. This study employs immunoinformatics and a reverse vaccinology technique to identify prospective antigens and create an efficient vaccine construct. In this study, we reported the "Attaching and Effacing Protein" a novel outer-membrane protein conserved in all pathogenic E. coli strains, based on proteome screening. We developed an in silico multi-epitope vaccine that includes helper T lymphocyte (HTL), cytotoxic T lymphocyte (CTL), B cell lymphocyte (BCL), and pan HLA DR-binding reactive epitope (PADRE) sequences, along with appropriate linkers and adjuvants. Machine Learning algorithms were used to evaluate antigenicity, solubility, stability, and non-allergenicity of the vaccine construct. Additionally, molecular docking analysis revealed that vaccine construct has a strong predicted binding affinity for human toll-like receptors on the cell surface. In this context, laboratory validations are necessary to demonstrate the effectiveness of the possible vaccine design that showed encouraging findings through computational validation.

Biospeckle techniques for evaluating the radial growth rate of a fungal colony

Microorganisms play essential roles in the environment, forming symbiotic relationships with plants and animals, though many can be pathogenic and cause significant harm. Investigating microorganism development through monitoring their radial growth offers valuable insights into growth kinetics, biomass, and metabolite synthesis, emphasizing the need for advanced methodologies in radial growth calculation. We utilize laser-based biospeckle techniques to visualize microorganism activity on semi-solid culture media and propose a comprehensive framework to determine the radial growth curve and its rate. This framework efficiently extracts these growth parameters from biospeckle microorganism patterns, as demonstrated through experimental validation. Additionally, we propose a new procedure, to the best of our knowledge, for calculating optimal parameters within the proposed framework, which impacts radial growth calculation. This procedure was tested through a series of experiments, demonstrating its effectiveness in identifying optimal parameters using the biospeckle patterns of microorganism colonies under various conditions. The results highlight the improvement in radial growth calculation when these parameters are applied within the proposed framework.

Influence of reef habitat on coral microbial associations.

Corals have complex symbiotic associations that can be influenced by the environment. We compare symbiotic dinoflagellate (family: Symbiodiniaceae) associations and the microbiome of five scleractinian coral species from three different reef habitats in Palau, Micronesia. Although pH and temperature corresponded with specific host-Symbiodiniaceae associations common to the nearshore and offshore habitats, bacterial community dissimilarity analyses indicated minimal influence of these factors on microbial community membership for the corals Coelastrea aspera, Psammocora digitata, and Pachyseris rugosa. However, coral colonies sampled close to human development exhibited greater differences in microbial community diversity compared to the nearshore habitat for the coral species Coelastrea aspera, Montipora foliosa, and Pocillopora acuta, and the offshore habitat for Coelastrea aspera, while also showing less consistency in Symbiodiniaceae associations. These findings indicate the influence that habitat location has on the bacterial and Symbiodiniaceae communities comprising the coral holobiont and provide important considerations for the conservation of coral reef communities, especially for island nations with increasing human populations and development.

Community assembly and potential function analysis of the endophyte in Eucommia ulmoides

Endophytes play a pivotal role in protecting host plants from both biotic and abiotic stresses, promoting the production of active components (AC) and plant growth. However, the succession of the endophyte community in Eucommia ulmoides (E. ulmoides), particularly the community assembly and function, has not been extensively investigated. In this study, we employed high-throughput sequencing and bioinformatics tools to analyze endophyte diversity across different tree ages, parts, and periods. We examined the population differences, correlations, community assembly mechanisms, and functional roles of these endophytes. Functional predictions via PICRUSt2 revealed that most endophytic fungal functions were linked to biosynthesis, with significant differences in biosynthetic functional abundance across parts and periods. In contrast, the metabolic activity of endophytic bacteria remained stable across different periods and parts. Correlation analysis further confirmed a strong positive relationship between ACs and certain endophytic fungi. Among them, the fungal phyla Ascomycota and Basidiomycota were identified as key contributors to the metabolism of chlorogenic acid (CA), while Aucubin was significantly positively correlated with several endophytic bacteria. These findings provide valuable insights into the functional roles and community assembly mechanism of E. ulmoides endophytes, as well as their symbiotic relationships.

Phenotyping of a new yeast mapping population reveals differences in the activation of the TORC1 signalling pathway between wild and domesticated yeast strains

Domestication can be understood as a symbiotic relationship that benefits both domesticator and domesticated species, involving multiple genetic changes that configure the phenotype of the domesticated species. One of the most important domesticated species is the yeast Saccharomyces cerevisiae, with both domesticated strains used for different fermentations processes for thousands of years and wild strains existing only in environments without human intervention; however, little is known about the phenotypic effects associated with its domestication. In the present work, we studied the effect of domestication on yeast TORC1 activation, a pleiotropic signalling pathway conserved across the eukaryotic domain. To achieve this goal, we improved a previously generated methodology to assess TORC1 activation, which turned out to be as effective as the original one but also presents several practical advantages for its application (such as facilitating confirmation of transformants and putting the Luc reporter gene under the control of the same PRPL26A promoter for each transformed strain). We then generated a mapping population, the so-called TOMAN-G population, derived from the “1002 Yeast Genomes Project” population, the most comprehensive catalogue of the genetic variation in yeasts. Finally, strains belonging to the TOMAN-G population were phenotyped for TORC1 activation, and then we compared the results obtained between yeast strains with different ecological origins, finding differences in TORC1 activation between wild and domesticated strains, particularly wine strains. These results are indicative of the effect of domestication on TORC1 activation, specifically that the different evolutionary trajectories of wild and domesticated strains have in fact caused differences in the activation of this pathway; furthermore, the phenotypic data obtained in this work could be used to continue underlying the genetic bases of TORC1 activation, a process that is still not fully understood, using techniques such as GWAS to search for specific genetic variants underlying the observed phenotypic variability and phylogenetic tree inferences to gain insight into the evolutionary relationships between these genetic variants.