Beneficial Symbiosis Research Articles

Cyanobacteria–probiotics symbionts for modulation of intestinal inflammation and microbiome dysregulation in colitis

Inflammatory bowel disease (IBD) is often associated with excessive inflammatory response and highly dysregulated gut microbiota. Traditional treatments utilize drugs to manage inflammation, potentially with probiotic therapy as an adjuvant. However, current standard practices often suffer from detrimental side effects, low bioavailability, and unsatisfactory therapeutic outcomes. Microbial complexes characterized by mutually beneficial symbiosis hold great promise for IBD therapy. Here, we aggregated Synechocystis sp. PCC6803 (Sp) with Bacillus subtilis (BS) by biomimetic mineralization to form cyanobacteria-probiotics symbionts (ASp@BS), which reshaped a healthy immune system and gut microbiota in a murine model of acute colitis. The symbionts exhibited excellent tolerance to the harsh environment of the gastrointestinal tract. Importantly, probiotics within the symbionts created a local anaerobic environment to activate the [NiFe]-hydrogenase enzyme of cyanobacteria, facilitating the production of hydrogen gas (H2) to persistently scavenge elevated reactive oxygen species and alleviate inflammatory factors. The resulting reduced inflammation improves the viability of the probiotics to efficiently regulate the gut microbiota and reshape the intestinal barrier functions. Our research elucidates that ASp@BS leverages the synergistic interaction between Sp and BS to create a therapeutic platform that addresses multiple aspects of IBD, offering a promising and comprehensive solution for IBD treatment.

Exceptionally preserved burrows of ichnogenus Asterosoma from the lower Silurian of south China: systematic ichnology, palaeoecology and implications for ecosystem recovery following the late Ordovician mass extinction

Exceptionally preserved complex burrows are described from the lower Silurian of South China, and they are identified as Asterosoma ludwigae Schlirf, 2000 , which is characterized by straight or curved bulbs that bud from an axial, vertical or horizontal, cylindrical burrow following a dichotomous or fan-like pattern. Striae and concentric lamination of burrow fills indicate that the special mining behaviour of the tracemaker reflects appendages that imprinted the burrow wall during their activities, implying that polychaetes or holothuroids could be strong candidates for the tracemaker of A . ludwigae . Abundant organic-matter-rich peloids and muddy matrix in burrow fills may consist of tracemaker's secretions or excrement. Abundant extracellular polymeric substance and clay minerals in filling sediment indicate the possible presence of microbes, implying that Asterosoma is not a simple fodinichnion, but rather created a beneficial symbiosis between tracemakers and microbes in burrows. Phanerozoic spatiotemporal distributions indicate that Asterosoma was distributed in broad habitats from deep sea to delta, but showed a strong preference for the shallow sea. Compilation of new ichnofossils and previously reported ichnotaxa from South China reveals that ichnospecies richness, burrow size and complexity all increased significantly during the late Aeronian, indicating a full recovery after the late Ordovician mass extinction.

Variation in SSRs at different genomic regions and implications for the evolution and identification of Armillaria gallica.

Armillaria spp. are devastating forest pathogens. Due to its low pathogenicity and abundant genetic variation, Armillaria gallica exhibited a unique and beneficial symbiosis with Gastrodia elata, which was used as a traditional Chinese medicine. However, the variation and population structure of A. gallica populations have rarely been investigated. Hence, we analyzed the evolution and variation in simple sequence repeats (SSRs) in three Armillaria genomes: A. gallica, A. cepistipes, and A. ostoyae to assess the genetic diversity and population structure of 14 A. gallica strains. Genome analysis revealed that SSRs were more abundant in the intergenic region than the intron and exon region, as was the SSR density. Compared with other two genomes, SSR density was the lowest in exon region and largest in the intron region of A. gallica, with significant variation in genic region. There were 17 polymorphic markers in A. gallica genome was identified, with 26.7% in genic region, which is higher than that of 18.8% in the intergenic region. Moreover, a total of 50 alleles and 42 polymorphic loci were detected among these A. gallica strains. The averaged polymorphism information content (PIC) was 0.4487, ranged from 0.2577 to 0.6786. Both principal coordinate analysis (PCoA) and population structure analyses based on the genotype data of SSRs divided the strains into two clusters. The cluster I included all the strains from high-altitude G. elata producing areas and some low-altitude areas, while the strains in Cluster II originated from low-altitude G. elata producing areas. These results indicated that substantial genome-specific variation in SSRs within the genic region of A. gallica and provide new insights for further studies on the evolution and breeding of A. gallica.

The rootstock genotype shapes the diversity of pecan (Carya illinoinensis) rhizosphere microbial community.

Pecans (Carya illinoinensis), one of the most valuable native North American nut crops, are commonly propagated through grafting to preserve the desired characteristics from parent trees. Since successful cultivation of pecan trees relies on the interplay among scion varieties, rootstocks, and soil conditions, this study investigated the microbial change to communities in the soils and roots of southern (87MX5-1.7) and northern (Peruque) rootstocks in a rootstock test orchard. Both grafted with the 'Pawnee' scion cultivar. Bacterial 16S ribosomal RNA and fungal ITS were amplified from both roots and rhizosphere soils of the two 10-year-grafted trees, then sequenced and annotated into trophic and nutrient-related groups to characterize the rhizosphere microbiota. The Peruque roots had a higher relative abundance of saprotroph fungi, while 87MX5-1.7 exhibited higher levels of symbiotroph fungi and nitrogen fixation-related bacteria. Among them, the presence of symbiotroph fungi, particularly ectomycorrhizal fungi, notably differed between these two rootstocks, with a significantly higher presence observed in the root of 87MX5-1.7 compared to Peruque. This variation likely leads to divergent pathways of nutrient translocation: Peruque was in favor of multiple fungi (Russula and Inocybe) to gain nutrition, while 87MX5-1.7 preferred a specific domain of fungi (Tuber) and nitrogen fixation-related bacteria (Bradyrhizobia) to form beneficial symbiosis. Moreover, the presence of pathogens suggested a potential risk of Fusarium patch and snow molds in 87MX5-1.7, while canker and black foot disease pose threats in Peruque. The findings of this study suggest that rootstocks from different origins shape rhizosphere microbes differently, potentially affecting nutrient uptake and nut yield. Exploring rootstock-microbe combinations could provide insights into optimizing scion growth and ultimately increasing nut yield. By understanding how different rootstock-microbe interactions influence pecan tree development, growers can strategically select combinations that promote beneficial symbiotic relationships, enhancing nutrient uptake, disease resistance, and overall tree vigor.

Microbe Profile: Pseudonocardia: antibiotics for every niche.

Pseudonocardia species comprise a genus of filamentous, sporulating bacteria belonging to the phylum Actinomycetota, formerly Actinobacteria. They are found in marine and freshwater sediments and soils and associated with marine animals, insects, and plants. To date, they have mostly been studied because of their mutually beneficial symbiosis with fungus-growing ants in the tribe Attini. They have also attracted interest due to their biosynthetic capabilities, including the production of variably glycosylated polyenes and other novel antifungal compounds, and for their capacity to grow on a variety of hydrocarbons. The majority of clinically used antibiotics are derived from the specialised metabolites of filamentous actinomycete bacteria and most of these come from the genus Streptomyces. However, in the quest for novel chemistry there is increasing interest in studying other filamentous actinomycete genera, including Pseudonocardia. Here we outline the biological properties, genome size and structure and key features of the genus Pseudonocardia, namely their specialised metabolites and ecological roles.

Not-so-mutually beneficial coral symbiosis

The partnership between corals and their intracellular algal symbionts has long been a textbook example of a mutually beneficial association. Here I argue that this view has been made obsolete by a steady accumulation of evidence over the past three decades. The coral-algal relationship is perhaps better viewed as one of domestication - think of it like a cattle farm, in which the coral is the farmer and the algae are the cows. I synthesize old and new evidence in support of this updated view and highlight remaining knowledge gaps, the largest of which continues to be the natural history of algal symbionts.

Chitinase-assisted winner: nematodes antagonize symbiotic microbes

Nematodes do not merely siphon off plant resources but also sabotage the plant’s mutualistic relationships with beneficial microbes. Yang and colleagues elegantly elucidated this generalizable molecular antagonism, revealing how Heterodera glycines, the notorious soybean cyst nematode (SCN), suppresses beneficial microbial symbiosis through a specific chitinase, HgCht2.

Wheat dwarfing reshapes plant and fungal development in arbuscular mycorrhizal symbiosis.

The introduction of Reduced height (Rht) dwarfing genes into elite wheat varieties has contributed to enhanced yield gain in high input agrosystems by preventing lodging. Yet, how modern selection for dwarfing has affected symbiosis remains poorly documented. In this study, we evaluated the response of both the plant and the arbuscular mycorrhizal fungus to plant genetic variation at a major Quantitative Trait Locus called QTL 4B2, known to harbor a Rht dwarfing gene, when forming the symbiosis. We used twelve inbred genotypes derived from a diversity base broadened durum wheat Evolutionary Pre-breeding Population and genotyped with a high-throughput Single Nucleotide Polymorphism (SNP) genotyping array. In a microcosm setup segregating roots and the extra-radical mycelium, each wheat genotype was grown with or without the presence of Rhizophagus irregularis. To characterize arbuscular mycorrhizal symbiosis, we assessed hyphal density, root colonization, spore production, and plant biomass. Additionally, we split the variation of these variables due either to genotypes or to the Rht dwarfing genes alone. The fungus exhibited greater development in the roots of Dwarf plants compared to non-Dwarf plants, showing increases of 27%, 37% and 51% in root colonization, arbuscules, and vesicles, respectively. In addition, the biomass of the extra-radical fungal structures increased by around 31% in Dwarf plants. The biomass of plant roots decreased by about 43% in mycorrhizal Dwarf plants. Interestingly, extraradical hyphal production was found to be partly genetically determined with no significant effect of Rht, as for plant biomasses. In contrast, variations in root colonization, arbuscules and extraradical spore production were explained by Rht dwarfing genes. Finally, when mycorrhizal, Dwarf plants had significantly lower total P content, pointing towards a less beneficial symbiosis for the plant and increased profit for the fungus. These results highlight the effect of Rht dwarfing genes on both root and fungal development. This calls for further research into the molecular mechanisms governing these effects, as well as changes in plant physiology, and their implications for fostering arbuscular mycorrhizal symbiosis in sustainable agrosystems.

A symbiont fungal effector relocalizes a plastidic oxidoreductase to nuclei to induce resistance to pathogens and salt stress

The root endophytic fungus Serendipita indica establishes beneficial symbioses with a broad spectrum of plants and enhances host resilience against biotic and abiotic stresses. However, little is known about the mechanisms underlying S.indica-mediated plant protection. Here, we report S.indica effector (SIE) 141 and its host target CDSP32, a conserved thioredoxin-like protein, and underlying mechanisms for enhancing pathogen resistance and abiotic salt tolerance in Arabidopsis thaliana. SIE141 binding interfered with canonical targeting of CDSP32 to chloroplasts, leading to its re-location into the plant nucleus. This nuclear translocation is essential for both their interaction and resistance function. Furthermore, SIE141 enhanced oxidoreductase activity of CDSP32, leading to CDSP32-mediated monomerization and activation of NON-EXPRESSOR OF PATHOGENESIS-RELATED 1 (NPR1), a key regulator of systemic resistance. Our findings provide functional insights on how S.indica transfers well-known beneficial effects to host plants and indicate CDSP32 as a genetic resource to improve plant resilience to abiotic and biotic stresses.

Impact of modeled microgravity stress on innate immunity in a beneficial animal-microbe symbiosis

The innate immune response is the first line of defense for all animals to not only detect invading microbes and toxins but also sense and interface with the environment. One such environment that can significantly affect innate immunity is spaceflight. In this study, we explored the impact of microgravity stress on key elements of the NFκB innate immune pathway. The symbiosis between the bobtail squid Euprymna scolopes and its beneficial symbiont Vibrio fischeri was used as a model system under a simulated microgravity environment. The expression of genes associated with the NFκB pathway was monitored over time as the symbiosis progressed. Results revealed that although the onset of the symbiosis was the major driver in the differential expression of NFκB signaling, the stress of simulated low-shear microgravity also caused a dysregulation of expression. Several genes were expressed at earlier time points suggesting that elements of the E. scolopes NFκB pathway are stress-inducible, whereas expression of other pathway components was delayed. The results provide new insights into the role of NFκB signaling in the squid-vibrio symbiosis, and how the stress of microgravity negatively impacts the host immune response. Together, these results provide a foundation to develop mitigation strategies to maintain host-microbe homeostasis during spaceflight.

Symbiotic Evolution Mechanism of the Digital Innovation Ecosystem for the Smart Car Industry

As an essential product in the automotive industry, the smart car industry has attracted widespread attention from scholars. However, there are few studies on the evolution of innovation ecosystems under different modes for the smart car industry. Thus, we construct evolution equations based on the symbiosis theory and Lotka–Volterra. Specifically, MATLAB simulations are utilized to comprehensively analyze the specific conditions for different symbiotic modes. The results indicate that (1) the smart car digital innovation ecosystem includes four symbiotic units. They are vehicle manufacturers, internet enterprises, supporting enterprises, and application groups. The symbiotic relationship among units depends on the symbiosis coefficient. (2) According to the symbiosis coefficient, the system is mainly divided into five symbiotic models: independent symbiosis, competitive symbiosis, parasitic symbiosis, partial symbiosis, and mutually beneficial symbiosis. Moreover, the mutually beneficial symbiosis is the optimal evolution model, and it is also a model that can enable the sustainable development of the smart car industry, which has been verified through case studies.

Toward explainable artificial intelligence: A survey and overview on their intrinsic properties

Artificial intelligence and its derivative technologies are not only playing a role in the fields of medicine, economy, policing, transportation, and natural science computing today but also in future industries such as electric vehicles and meta-universe. However, because of the black-box nature of most common artificial neural networks (DNNs), there needs to be more understanding of what is happening behind these astounding performances. The abstract reasoning process in the networks raises concerns about the security of AI systems. Because of this, more and more researchers are turning their attention to the explainability of black-box neural networks to find some attributions that explain the reasoning performed by the networks by studying the black-box nature of the networks. Deep neural networks and their explainability act as a mutually beneficial symbiosis, facilitating each other’s development. This survey reviews the deep network explainable methods applicable for the field of computing vision proposed within the last decade and categorizes these methods in terms of their starting point to explain deep neural networks. Focusing on their intrinsics, we review the methods that are applicable for object classification, object detection, and looked forward that of object tracking. In each cluster, we show that the methods share some similarities but have their own highlight. Furthermore, we shed light on the future development of the field of explainable AI.

Insects and their antibiotic-producing bacteria

Many, if not all, plants and animals form mutually beneficial symbioses (mutualisms) with microbes and a subset of these mutualisms are defensive, in which the host provides food and housing in return for defence against disease. These symbioses typically involve antibiotic-producing bacteria, the best known of which are filamentous actinomycetes in the genera Streptomyces and Pseudonocardia and unicellular species in the genus Pseudomonas. Such mutualisms are likely to be widespread in nature, but they are best characterised in insects, which provide experimentally tractable models for studying symbiosis and microbiome formation because they typically host less complex microbial communities. Here, we examine the mutualisms formed between insects and antibiotic-producing bacteria using well-characterised examples, including digger wasps and their endosymbiotic Streptomyces species, attine ants and their mutualist Pseudonocardia species and Paederus beetles with their pederin-producing Pseudomonas species. We also discuss how searching such symbiotic niches can give insights into the evolution and functions of microbial specialised metabolites and provide new platforms for antibiotic discovery.

Host macrocyclic acylcarnitines mediate symbiotic interactions between frogs and their skin microbiome

The host-microbiome associations occurring on the skin of vertebrates significantly influence hosts' health. However, the factors mediating their interactions remain largely unknown. Herein, we used integrated technical and ecological frameworks to investigate the skin metabolites sustaining a beneficial symbiosis between tree frogs and bacteria. We characterize macrocyclic acylcarnitines as the major metabolites secreted by the frogs' skin and trace their origin to an enzymatic unbalance of carnitine palmitoyltransferases. We found that these compounds colocalize with bacteria on the skin surface and are mostly represented by members of the Pseudomonas community. We showed that Pseudomonas sp. MPFS isolated from frogs' skin can exploit acylcarnitines as its sole carbon and nitrogen source, and this metabolic capability is widespread in Pseudomonas. We summarize frogs' multiple mechanisms to filter environmental bacteria and highlight that acylcarnitines likely evolved for another function but were co-opted to provide nutritional benefits to the symbionts.

Effectiveness of Cultivation of Tiger Shrimp, Milk and Seaweed Using the Policultural Method: A Review

Polyculture is a cultivation method used to cultivate many fishery commodities in one area. The selection of fishery commodities for polyculture cultivation must be regulated so that there is no competition in obtaining feed. The purpose of this study was to determine the effectiveness of polyculture system cultivation (tiger shrimp, milkfish and seaweed). The method used is a literature review. The results obtained are the average quality of the waters for polyculture cultivation of 3 commodities, namely milkfish shrimp and seaweed, as follows; temperature 32.97, salinity 8.75, brightness 24.67, Ph 7.29, DO 3.57, TOM 72.27, NH3 0.24, H2S 0.05, NO2 0.3802, PO4 0.8694, alkalinity 7.33 total suspended solids 43.253. Polyculture of 3 commodities namely milkfish, shrimp and seaweed provides more effectiveness and benefits, especially in terms of production, land efficiency and water quality, this is because the three commodities above provide a mutually beneficial symbiosis

Control of arbuscule development by a transcriptional negative feedback loop in Medicago

Most terrestrial plants establish a symbiosis with arbuscular mycorrhizal fungi (AMF), which provide them with lipids and sugars in exchange for phosphorus and nitrogen. Nutrient exchange must be dynamically controlled to maintain a mutually beneficial relationship between the two symbiotic partners. The WRI5a and its homologues play a conserved role in lipid supply to AMF. Here, we demonstrate that the AP2/ERF transcription factor MtERM1 binds directly to AW-box and AW-box-like cis-elements in the promoters of MtSTR2 and MtSTR, which are required for host lipid efflux and arbuscule development. The EAR domain-containing transcription factor MtERF12 is also directly activated by MtERM1/MtWRI5a to negatively regulate arbuscule development, and the TOPLESS co-repressor is further recruited by MtERF12 through EAR motif to oppose MtERM1/MtWRI5a function, thereby suppressing arbuscule development. We therefore reveal an ERM1/WRI5a–ERF12–TOPLESS negative feedback loop that enables plants to flexibly control nutrient exchange and ensure a mutually beneficial symbiosis.

First Report of Tripartite Symbiosis Potential among Soybean, Bradyrhizobium japonicum, and Dark Septate Endophytes

Successful soybean and rhizobium interaction is characterized by the formation of root nodules. This symbiosis significantly affects the growth and yield of soybeans and has long been recognized as a key factor in sustainable agricultural systems. Naturally, soybeans could form a tripartite symbiotic relationship with rhizobium and arbuscular mycorrhizal fungi (AMF). However, there is no information regarding the symbiotic potential of soybean, nodulating bacteria, and dark septate endophytic (DSE) fungi. This study aims to delve into new tripartite symbiosis potential, shedding light on its efficacy in improving soybean growth while reducing environmental impacts. We examined the effect of incorporating two DSEs: Cladophialophora chaetospira SK51 (Cc) and Veronaeopsis simplex Y34 (Vs), into the classic soybean-rhizobium symbiosis. Under sterile conditions, the co-inoculation of DSEs with Bradyrhizobium japonicum IncB6 (Bj) significantly increased the nodule number and dry weight, leading to the acceleration of soybean vegetative growth. Soybean nodule numbers under co-inoculation treatments-CcBj and VsBj-were significantly increased by 77.6 and 43.6%, respectively, compared to the Bj treatment. Furthermore, under the CcBj and VsBj treatments, the soybean nodule dry mass was significantly increased by 455 and 363%, respectively, compared to Bj. This finding represents the first report of new beneficial tripartite symbiosis potential for soybean nodulation and vegetative growth.

Transcriptomic response of Sinorhizobium meliloti to the predatory attack of Myxococcus xanthus.

Bacterial predation impacts microbial community structures, which can have both positive and negative effects on plant and animal health and on environmental sustainability. Myxococcus xanthus is an epibiotic soil predator with a broad range of prey, including Sinorhizobium meliloti, which establishes nitrogen-fixing symbiosis with legumes. During the M. xanthus-S. meliloti interaction, the predator must adapt its transcriptome to kill and lyse the target (predatosome), and the prey must orchestrate a transcriptional response (defensome) to protect itself against the biotic stress caused by the predatory attack. Here, we describe the transcriptional changes taking place in S. meliloti in response to myxobacterial predation. The results indicate that the predator induces massive changes in the prey transcriptome with up-regulation of protein synthesis and secretion, energy generation, and fatty acid (FA) synthesis, while down-regulating genes required for FA degradation and carbohydrate transport and metabolism. The reconstruction of up-regulated pathways suggests that S. meliloti modifies the cell envelop by increasing the production of different surface polysaccharides (SPSs) and membrane lipids. Besides the barrier role of SPSs, additional mechanisms involving the activity of efflux pumps and the peptide uptake transporter BacA, together with the production of H2O2 and formaldehyde have been unveiled. Also, the induction of the iron-uptake machinery in both predator and prey reflects a strong competition for this metal. With this research we complete the characterization of the complex transcriptional changes that occur during the M. xanthus-S. meliloti interaction, which can impact the establishment of beneficial symbiosis with legumes.

Analysis of the coupling correlation between environmental protection efforts and economic development level based on artificial intelligence technology

Abstract In order to study the influence of environmental protection and economic development level under artificial intelligence technology, and to help achieve the goal of carbon peak in China, this paper studies the coupling degree of socio-economic and ecological environment system, establishes the evaluation index system of coupling between socio-economic system and ecological environment system, calculates the weight of each evaluation index and comprehensive evaluation index by using entropy value assignment method, construct the coupling degree of two systems model, and empirically analyze the coupling degree and coupling coordination socio-economic and eco-environmental systems. In addition, the comprehensive evaluation index of socio-economic and ecological environmental protection systems based on artificial intelligence technology was analyzed. The results show that AI technology benefits environmental protection, the urban economy and environmental protection as a whole are currently in a mutually beneficial symbiosis, and the two systems of ecological environment and high-quality economic development promote each other and develop together. The evaluation indexes of economic scale and economic capacity and social development as a whole are steadily increasing, from 0.00, 0.00, and 0.07 in 2010 to 0.28, 0.15, and 0.53 in 2019, respectively, where the evaluation indexes of economic scale and economic capacity are steadily increasing from 2010 to 2019 due to the rapid development of the tertiary industry, and the evaluation indexes of social development. The evaluation index of the economic scale, economic capacity, and social development drove the rapid development of the economy in 2012-2013, and the rapid development of the economy also led to the rapid development of society. After 2015, the coupling between the two systems has become more and more perfect.

${N}$-Player Trust Game With Second-Order Reputation Evaluation in the Networked Population

Trust has played a significant role in the maintenance of social links, which has attracted a great deal of concern from a diverse range of fields including economics, finance, and social science. In this article, we investigate the effect of second-order reputation evaluation on trust game dilemma and explore how individuals establish an indirect reciprocal relationship by adjusting their reputation. First, a novel <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">${N}$</tex-math></inline-formula> -player trust game is proposed by combining the payoff-driven and reputation-driven update processes. Second, four classical “second-order” norms are introduced to evaluate individual reputation, which will be judged by both their own strategies and the reputation status of their counterparts. Finally, through extensive simulations on different network topologies, we find that untrustworthy trustees would change their strategies with the help of a reputation signal. Meanwhile, the structured population presents a nonmonotonic cooperation trend with the increase of reputation strength in the mixed imitation process. Besides, there is an optimal interval that can promote the continuous emergence of trust between investors and trustworthy trustees. The current results are of high importance to understand the emergence of mutually beneficial symbiosis of biological groups inside an unknown environment.