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Bibliography on: Symbiosis

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.


ESP: PubMed Auto Bibliography 10 Jun 2023 at 01:50 Created: 


Symbiosis refers to an interaction between two or more different organisms living in close physical association, typically to the advantage of both. Symbiotic relationships were once thought to be exceptional situations. Recent studies, however, have shown that every multicellular eukaryote exists in a tight symbiotic relationship with billions of microbes. The associated microbial ecosystems are referred to as microbiome and the combination of a multicellular organism and its microbiota has been described as a holobiont. It seems "we are all lichens now."

Created with PubMed® Query: ( symbiosis[tiab] OR symbiotic[tiab] ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2023-06-09

Grenier T, Consuegra J, Ferrarini MG, et al (2023)

Intestinal GCN2 controls Drosophila systemic growth in response to Lactiplantibacillus plantarum symbiotic cues encoded by r/tRNA operons.

eLife, 12: pii:76584 [Epub ahead of print].

Symbiotic bacteria interact with their host through symbiotic cues. Here, we took advantage of the mutualism between Drosophila and Lactiplantibacillus plantarum (Lp) to investigate a novel mechanism of host-symbiont interaction. Using chemically-defined diets, we found that association with Lp improves the growth of larvae fed amino acid-imbalanced diets, even though Lp cannot produce the limiting amino acid. We show that in this context Lp supports its host's growth through a molecular dialog that requires functional operons encoding ribosomal and transfer RNAs (r/tRNAs) in Lp and the GCN2 kinase in Drosophila's enterocytes. Our data indicate Lp's r/tRNAs are packaged in extracellular vesicles and activate GCN2 in a subset of larval enterocytes, a mechanism necessary to remodel the intestinal transcriptome and ultimately to support anabolic growth. Based on our findings, we propose a novel beneficial molecular dialog between host and microbes, which relies on a non-canonical role of GCN2 as a mediator of non-nutritional symbiotic cues encoded by r/tRNA operons.

RevDate: 2023-06-09

Kryukov AA, Gorbunova AO, Kudriashova TR, et al (2023)

SWEET transporters of Medicago lupulina in the arbuscular-mycorrhizal system in the presence of medium level of available phosphorus.

Vavilovskii zhurnal genetiki i selektsii, 27(3):189-196.

Arbuscular mycorrhiza (AM) fungi receive photosynthetic products and sugars from plants in exchange for contributing to the uptake of minerals, especially phosphorus, from the soil. The identification of genes controlling AM symbiotic efficiency may have practical application in the creation of highly productive plant-microbe systems. The aim of our work was to evaluate the expression levels of SWEET sugar transporter genes, the only family in which sugar transporters specific to AM symbiosis can be detected. We have selected a unique "host plant-AM fungus" model system with high response to mycorrhization under medium phosphorus level. This includes a plant line which is highly responsive to inoculation by AM fungi, an ecologically obligate mycotrophic line MlS-1 from black medick (Medicago lupulina) and the AM fungus Rhizophagus irregularis strain RCAM00320, which has a high efficiency in a number of plant species. Using the selected model system, differences in the expression levels of 11 genes encoding SWEET transporters in the roots of the host plant were evaluated during the development of or in the absence of symbiosis of M. lupulina with R. irregularis at various stages of the host plant development in the presence of medium level of phosphorus available for plant nutrition in the substrate. At most stages of host plant development, mycorrhizal plants had higher expression levels of MlSWEET1b, MlSWEET3c, MlSWEET12 and MlSWEET13 compared to AM-less controls. Also, increased expression relative to control during mycorrhization was observed for MlSWEET11 at 2nd and 3rd leaf development stages, for MlSWEET15c at stemming (stooling) stage, for MlSWEET1a at 2nd leaf development, stemming and lateral branching stages. The MlSWEET1b gene can be confidently considered a good marker with specific expression for effective development of AM symbiosis between M. lupulina and R. irregularis in the presence of medium level of phosphorus available to plants in the substrate.

RevDate: 2023-06-09

Chiu CI, Ou JH, Kuan KC, et al (2023)

Body size of fungus-growing termites infers on the volume and density of their fungal cultivar.

Royal Society open science, 10(6):230126.

The body size of an animal plays a crucial role in determining its trophic level and position within the food web, as well as its interactions with other species. In the symbiosis between Termitomyces and fungus-growing termites, termites rely on nutrition of fungal nodules produced by Termitomyces. To understand whether the size of termites and fungal nodules are related to their partner specificity, we quantified the size of termite farmer caste, and the size and density of nodules in termite nests of four genera of fungus-growing termites, and identified their cultivated Termitomyces fungus species based on internal transcribed spacer regions and partial large subunit ribosomal RNA gene sequences. The results showed that the size and density of fungal nodules were different among Termitomyces clades and revealed a constant trade-off between size and density among clades. The nodule size of each clade has low variation and fits normal distribution, indicating that size is a stabilized trait. Moreover, we found larger termite genera cultivated Termitomyces with larger but less numerous nodules. Based on these results, we concluded that there is a size specificity between Termitomyces and fungus-growing termites, which may lead to diversification of Termitomyces as adaptations to different termite genera.

RevDate: 2023-06-09

Yang F, Li Y, Gao M, et al (2023)

Comparative expression profiles of carboxylesterase orthologous CXE14 in two closely related tea geometrid species, Ectropis obliqua Prout and Ectropis grisescens Warren.

Frontiers in physiology, 14:1194997.

Insect carboxylesterases (CXEs) can be expressed in multiple tissues and play crucial roles in detoxifying xenobiotic insecticides and degrading olfactory cues. Therefore, they have been considered as an important target for development of eco-friendly insect pest management strategies. Despite extensive investigation in most insect species, limited information on CXEs in sibling moth species is currently available. The Ectropis obliqua Prout and Ectropis grisescens Warren are two closely related tea geometrid species, which share the same host of tea plant but differ in geographical distribution, sex pheromone composition, and symbiotic bacteria abundance, providing an excellent mode species for studies of functional diversity of orthologous CXEs. In this study, we focused on EoblCXE14 due to its previously reported non-chemosensory organs-biased expression. First, the EoblCXE14 orthologous gene EgriCXE14 was cloned and sequence characteristics analysis showed that they share a conserved motif and phylogenetic relationship. Quantitative real-time polymerase chain reaction (qRT-PCR) was then used to compare the expression profiles between two Ectropis spp. The results showed that EoblCXE14 was predominately expressed in E. obliqua larvae, whereas EgriCXE14 was abundant in E. grisescens at multiple developmental stages. Interestingly, both orthologous CXEs were highly expressed in larval midgut, but the expression level of EoblCXE14 in E. obliqua midgut was significantly higher than that of EgriCXE14 in E. grisescens midgut. In addition, the potential effect of symbiotic bacteria Wolbachia on the CXE14 was examined. This study is the first to provide comparative expression profiles of orthologous CXE genes in two sibling geometrid moth species and the results will help further elucidate CXEs functions and identify a potential target for tea geometrid pest control.

RevDate: 2023-06-09

Lee HE, Lee JH, Park SM, et al (2023)

Symbiotic relationship between filamentous algae (Halomicronema sp.) and extracellular polymeric substance-producing algae (Chlamydomonas sp.) through biomimetic simulation of natural algal mats.

Frontiers in microbiology, 14:1176069.

To lower the cost of biomass harvesting, the growth of natural biofilm is considered to be an optimal alternative to microalgae aggregation. This study investigated algal mats that naturally agglomerate into a lump and float on water surfaces. Halomicronema sp., a filamentous cyanobacterium with high cell aggregation and adhesion to substrates, and Chlamydomonas sp., which grows rapidly and produces high extracellular polymeric substances (EPS) in certain environments, are the main microalgae that make up selected mats through next-generation sequencing analysis. These two species play a major role in the formation of solid mats, and showed a symbiotic relationship as the medium and nutritional source, particularly owing to the large amount of EPS formed by the reaction between EPS and calcium ions through zeta potential and Fourier-transform infrared spectroscopy analysis. This led to the formation of an ecological biomimetic algal mat (BAM) that mimics the natural algal mat system, and this is a way to reduce costs in the biomass production process as there is no separate treatment process for harvesting.

RevDate: 2023-06-09

Yoo JS, Goh B, Heo K, et al (2023)

Functional and metagenomic level diversities of human gut symbiont-derived glycolipids.

bioRxiv : the preprint server for biology pii:2023.05.23.541633.

Bioactive metabolites produced by symbiotic microbiota causally impact host health and disease, nonetheless, incomplete functional annotation of genes as well as complexities and dynamic nature of microbiota make understanding species-level contribution in production and actions difficult. Alpha-galactosylceramides produced by Bacteroides fragilis (BfaGC) are one of the first modulators of colonic immune development, but biosynthetic pathways and the significance of the single species in the symbiont community still remained elusive. To address these questions at the microbiota level, we have investigated the lipidomic profiles of prominent gut symbionts and the metagenome-level landscape of responsible gene signatures in the human gut. We first elucidated the chemical diversity of sphingolipid biosynthesis pathways of major bacterial species. In addition to commonly shared ceramide backbone synthases showing two distinct intermediates, alpha-galactosyltransferase (agcT), the necessary and sufficient component for BfaGC production and host colonic type I natural killer T (NKT) cell regulation by B. fragilis, was characterized by forward-genetics based targeted metabolomic screenings. Phylogenetic analysis of agcT in human gut symbionts revealed that only a few ceramide producers have agcT and hence can produce aGCs, on the other hand, structurally conserved homologues of agcT are widely distributed among species lacking ceramides. Among them, alpha-glucosyl-diacylglycerol(aGlcDAG)-producing glycosyltransferases with conserved GT4-GT1 domains are one of the most prominent homologs in gut microbiota, represented by Enterococcus bgsB . Of interest, aGlcDAGs produced by bgsB can antagonize BfaGC-mediated activation of NKT cells, showing the opposite, lipid structure-specific actions to regulate host immune responses. Further metagenomic analysis of multiple human cohorts uncovered that the agcT gene signature is almost exclusively contributed by B. fragilis , regardless of age, geographical and health status, where the bgsB signature is contributed by >100 species, of which abundance of individual microbes is highly variable. Our results collectively showcase the diversities of gut microbiota producing biologically relevant metabolites in multiple layers-biosynthetic pathways, host immunomodulatory functions and microbiome-level landscapes in the host.

RevDate: 2023-06-09

Ramanan D, Chowdhary K, Candéias SM, et al (2023)

Homeostatic, repertoire and transcriptional relationships between colon T regulatory cell subsets.

bioRxiv : the preprint server for biology pii:2023.05.17.541199.

Foxp3 [+] regulatory T cells (Tregs) in the colon are key to promoting peaceful co-existence with symbiotic microbes. Differentiated in either thymic or peripheral locations, and modulated by microbes and other cellular influencers, colonic Treg subsets have been identified through key transcription factors (TF; Helios, Rorg, Gata3, cMaf), but their inter-relationships are unclear. Applying a multimodal array of immunologic, genomic, and microbiological assays, we find more overlap than expected between populations. The key TFs play different roles, some essential for subset identity, others driving functional gene signatures. Functional divergence was clearest under challenge. Single-cell genomics revealed a spectrum of phenotypes between the Helios+ and Rorγ+ poles, different Treg-inducing bacteria inducing the same Treg phenotypes to varying degrees, not distinct populations. TCR clonotypes in monocolonized mice revealed that Helios+ and Rorγ+ Tregs are related, and cannot be uniquely equated to tTreg and pTreg. We propose that rather than the origin of their differentiation, tissue-specific cues dictate the spectrum of colonic Treg phenotypes.

RevDate: 2023-06-09

Gerrick ER, DeSchepper LB, Mechler CM, et al (2023)

Commensal protists in reptiles display flexible host range and adaptation to ectothermic hosts.

bioRxiv : the preprint server for biology pii:2023.05.25.542353.

Parabasalid protists recently emerged as keystone members of the mammalian microbiota with important effects on their host's health. However, the prevalence and diversity of parabasalids in wild reptiles and the consequences of captivity and other environmental factors on these symbiotic protists are unknown. Reptiles are ectothermic, and their microbiomes are subject to temperature fluctuations, such as those driven by climate change. Thus, conservation efforts for threatened reptile species may benefit from understanding how shifts in temperature and captive breeding influence the microbiota, including parabasalids, to impact host fitness and disease susceptibility. Here, we surveyed intestinal parabasalids in a cohort of wild reptiles across three continents and compared these to captive animals. Reptiles harbor surprisingly few species of parabasalids compared to mammals, but these protists exhibited a flexible host-range, suggesting specific adaptations to reptilian social structures and microbiota transmission. Furthermore, reptile-associated parabasalids are adapted to wide temperature ranges, although colder temperatures significantly altered the protist transcriptomes, with increased expression of genes associated with detrimental interactions with the host. Our findings establish that parabasalids are widely distributed in the microbiota of wild and captive reptiles and highlight how these protists respond to temperature swings encountered in their ectothermic hosts.

RevDate: 2023-06-09

Sato H (2023)

The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes.

The New phytologist [Epub ahead of print].

Ectomycorrhizal (EcM) symbiosis, a ubiquitous plant-fungus interaction in forests, evolved in parallel in fungi. Why the evolution of EcM fungi did not necessarily increase ecological opportunities for explosive diversification remains unclear. This study aimed to reveal the driving mechanism of the evolutionary diversification in the fungal class Agaricomycetes, specifically by testing whether the evolution of EcM symbiosis in the Late Cretaceous increased ecological opportunities. The historical character transitions of trophic state and fruitbody form were estimated based on phylogenies inferred from fragments of 89 single-copy genes. Moreover, five analyses were used to estimate the net diversification rates (speciation rate minus extinction rate). The results indicate that the unidirectional evolution of EcM symbiosis occurred 27 times, ranging in date from the Early Triassic to the Early Paleogene. The increased diversification rates appeared to occur intensively at the stem of EcM fungal clades diverging in the Late Cretaceous, coinciding with the rapid diversification of EcM angiosperms. By contrast, the evolution of fruitbody form was not strongly linked with the increased diversification rates. These findings suggest that the evolution of EcM symbiosis in the Late Cretaceous, supposedly with coevolving EcM angiosperms, was the key drive of the explosive diversification in Agaricomycetes.

RevDate: 2023-06-09

Romo-Araiza A, Picazo-Aguilar RI, Griego E, et al (2023)

Symbiotic Supplementation (E. faecium and Agave Inulin) Improves Spatial Memory and Increases Plasticity in the Hippocampus of Obese Rats: A Proof-of-Concept Study.

Cell transplantation, 32:9636897231177357.

Obesity has been linked to cognitive impairment through systemic low-grade inflammation. High fat and sugar diets (HFSDs) also induce systemic inflammation, either by induced Toll-like receptor 4 response, or by causing dysbiosis. This study aimed to evaluate the effect of symbiotics supplementation on spatial and working memory, butyrate concentration, neurogenesis, and electrophysiological recovery of HFSD-fed rats. In a first experiment, Sprague-Dawley male rats were given HFSD for 10 weeks, after which they were randomized into 2 groups (n = 10 per group): water (control), or Enterococcus faecium + inulin (symbiotic) administration, for 5 weeks. In the fifth week, spatial and working memory was analyzed through the Morris Water Maze (MWM) and Eight-Arm Radial Maze (RAM) tests, respectively, with 1 week apart between tests. At the end of the study, butyrate levels from feces and neurogenesis at hippocampus were determined. In a second experiment with similar characteristics, the hippocampus was extracted to perform electrophysiological studies. Symbiotic-supplemented rats showed a significantly better memory, butyrate concentrations, and neurogenesis. This group also presented an increased firing frequency in hippocampal neurons [and a larger N-methyl-d-aspartate (NMDA)/α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) current ratio] suggesting an increase in NMDA receptors, which in turn is associated with an enhancement in long-term potentiation and synaptic plasticity. Therefore, our results suggest that symbiotics could restore obesity-related memory impairment and promote synaptic plasticity.

RevDate: 2023-06-09

Nguyen L, Taerum SJ, Jasso-Selles DE, et al (2023)

True molecular phylogenetic position of the cockroach gut commensal Lophomonas blattarum (Lophomonadida, Parabasalia).

The Journal of eukaryotic microbiology [Epub ahead of print].

RevDate: 2023-06-08

Lamb CE, JEM Watts (2023)

Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa.

Environmental microbiome, 18(1):52.

BACKGROUND: Marine sponges are diverse and functionally important members of marine benthic systems, well known to harbour complex and abundant symbiotic microorganisms as part of their species-specific microbiome. Changes in the sponge microbiome have previously been observed in relation to natural environmental changes, including nutrient availability, temperature and light. With global climate change altering seasonal temperatures, this study aims to better understand the potential effects of natural seasonal fluctuations on the composition and functions of the sponge microbiome.

RESULTS: Metataxonomic sequencing of two marine sponge species native to the U.K. (Hymeniacidon perlevis and Suberites massa) was performed at two different seasonal temperatures from the same estuary. A host-specific microbiome was observed in each species between both seasons. Detected diversity within S. massa was dominated by one family, Terasakiellaceae, with remaining dominant families also being detected in the associated seawater. H. perlevis demonstrated sponge specific bacterial families including aforementioned Terasakiellaceae as well as Sphingomonadaceae and Leptospiraceae with further sponge enriched families present.

CONCLUSIONS: To our knowledge, these results describe for the first time the microbial diversity of the temperate marine sponge species H. perlevis and S. massa using next generation sequencing. This analysis detected the presence of core sponge taxa identified in each sponge species was not changed by seasonal temperature alterations, however, there were shifts observed in overall community composition due to fluctuations in less abundant taxa, demonstrating that microbiome stability across seasons is likely to be host species specific.

RevDate: 2023-06-08

Durant E, Hoysted GA, Howard N, et al (2023)

Herbivore-driven disruption of arbuscular mycorrhizal carbon-for-nutrient exchange is ameliorated by neighboring plants.

Current biology : CB pii:S0960-9822(23)00663-2 [Epub ahead of print].

Arbuscular mycorrhizal fungi colonize the roots of most plants, forming a near-ubiquitous symbiosis[1] that is typically characterized by the bi-directional exchange of fungal-acquired nutrients for plant-fixed carbon.[2] Mycorrhizal fungi can form below-ground networks[3][,][4][,][5][,][6] with potential to facilitate the movement of carbon, nutrients, and defense signals across plant communities.[7][,][8][,][9] The importance of neighbors in mediating carbon-for-nutrient exchange between mycorrhizal fungi and their plant hosts remains equivocal, particularly when other competing pressures for plant resources are present. We manipulated carbon source and sink strengths of neighboring pairs of host plants through exposure to aphids and tracked the movement of carbon and nutrients through mycorrhizal fungal networks with isotope tracers. When carbon sink strengths of both neighboring plants were increased by aphid herbivory, plant carbon supply to extraradical mycorrhizal fungal hyphae was reduced, but mycorrhizal phosphorus supply to both plants was maintained, albeit variably, across treatments. However, when the sink strength of only one plant in a pair was increased, carbon supply to mycorrhizal fungi was restored. Our results show that loss of carbon inputs into mycorrhizal fungal hyphae from one plant may be ameliorated through inputs of a neighbor, demonstrating the responsiveness and resilience of mycorrhizal plant communities to biological stressors. Furthermore, our results indicate that mycorrhizal nutrient exchange dynamics are better understood as community-wide interactions between multiple players rather than as strict exchanges between individual plants and their symbionts, suggesting that mycorrhizal C-for-nutrient exchange is likely based more on unequal terms of trade than the "fair trade" model for symbiosis.

RevDate: 2023-06-08

Li YL, Gao L, Yao YS, et al (2023)

Altered GC- and AT-biased genotypes of Ophiocordyceps sinensis in the stromal fertile portions and ascospores of natural Cordyceps sinensis.

PloS one, 18(6):e0286865 pii:PONE-D-22-28022.

OBJECTIVE: To examine multiple genotypes of Ophiocordyceps sinensis in a semi-quantitative manner in the stromal fertile portion (SFP) densely covered with numerous ascocarps and ascospores of natural Cordyceps sinensis and to outline the dynamic alterations of the coexisting O. sinensis genotypes in different developmental phases.

METHODS: Mature Cordyceps sinensis specimens were harvested and continuously cultivated in our laboratory (altitude 2,254 m). The SFPs (with ascocarps) and fully and semi-ejected ascospores were collected for histological and molecular examinations. Biochip-based single nucleotide polymorphism (SNP) MALDI-TOF mass spectrometry (MS) was used to genotype multiple O. sinensis mutants in the SFPs and ascospores.

RESULTS: Microscopic analysis revealed distinct morphologies of the SFPs (with ascocarps) before and after ascospore ejection and SFP of developmental failure, which, along with the fully and semi-ejected ascospores, were subjected to SNP MS genotyping analysis. Mass spectra showed the coexistence of GC- and AT-biased genotypes of O. sinensis that were genetically and phylogenetically distinct in the SFPs before and after ejection and of developmental failure and in fully and semi-ejected ascospores. The intensity ratios of MS peaks were dynamically altered in the SFPs and the fully and semi-ejected ascospores. Mass spectra also showed transversion mutation alleles of unknown upstream and downstream sequences with altered intensities in the SFPs and ascospores. Genotype #5 of AT-biased Cluster-A maintained a high intensity in all SFPs and ascospores. An MS peak with a high intensity containing AT-biased Genotypes #6 and #15 in pre-ejection SFPs was significantly attenuated after ascospore ejection. The abundance of Genotypes #5‒6 and #16 of AT-biased Cluster-A was differentially altered in the fully and semi-ejected ascospores that were collected from the same Cordyceps sinensis specimens.

CONCLUSION: Multiple O. sinensis genotypes coexisted in different combinations with altered abundances in the SFPs prior to and after ejection, the SFP of developmental failure, and the two types of ascospores of Cordyceps sinensis, demonstrating their genomic independence. Metagenomic fungal members present in different combinations and with dynamic alterations play symbiotic roles in different compartments of natural Cordyceps sinensis.

RevDate: 2023-06-08

Zhang N, Ye S, Wang X, et al (2023)

Hepatic Symbiotic Bacterium L. reuteri FLRE5K1 Inhibits the Development and Progression of Hepatocellular Carcinoma via Activating the IFN-γ/CXCL10/CXCR3 Pathway.

Probiotics and antimicrobial proteins [Epub ahead of print].

Symbiotic bacteria participate in the formation of the structure and function of the tissues and organs in which they live, and play an essential role in maintaining the balance between health and disease. Lactobacillus reuteri FLRE5K1 was isolated from the liver of healthy mice and proved to be a probiotic with anti-melanoma activity in previous studies. The relationship between hepatic symbiotic probiotics and hepatocellular carcinoma (HCC) has not been reported yet. In the present study, L. reuteri FLRE5K1 was initially confirmed to successfully enter the liver after being administered by gavage, and the efficacy of probiotic feeding on HCC and its potential mechanism of inhibiting tumor progression were investigated by an orthotopic liver cancer model established. The results showed that L. reuteri FLRE5K1 significantly reduced the tumor formation rate and inhibited tumor growth in mice. From the perspective of mechanism, activation of the IFN-γ/CXCL10/CXCR3 pathway, as well as its positive feedback on the secretion of IFN-γ, induced the polarization of Th0 cell to Th1 cells and inhibited the differentiation of Tregs, which played a key role in the inhibitory effect of L. reuteri FLRE5K1 on the development and progression of HCC.

RevDate: 2023-06-08

Tarabai H, Floriano AM, Zima J, et al (2023)

Microbiomes of Blood-Feeding Triatomines in the Context of Their Predatory Relatives and the Environment.

Microbiology spectrum [Epub ahead of print].

The importance of gut microbiomes has become generally recognized in vector biology. This study addresses microbiome signatures in North American Triatoma species of public health significance (vectors of Trypanosoma cruzi) linked to their blood-feeding strategy and the natural habitat. To place the Triatoma-associated microbiomes within a complex evolutionary and ecological context, we sampled sympatric Triatoma populations, related predatory reduviids, unrelated ticks, and environmental material from vertebrate nests where these arthropods reside. Along with five Triatoma species, we have characterized microbiomes of five reduviids (Stenolemoides arizonensis, Ploiaria hirticornis, Zelus longipes, and two Reduvius species), a single soft tick species, Ornithodoros turicata, and environmental microbiomes from selected sites in Arizona, Texas, Florida, and Georgia. The microbiomes of predatory reduviids lack a shared core microbiota. As in triatomines, microbiome dissimilarities among species correlate with dominance of a single bacterial taxon. These include Rickettsia, Lactobacillus, "Candidatus Midichloria," and Zymobacter, which are often accompanied by known symbiotic genera, i.e., Wolbachia, "Candidatus Lariskella," Asaia, Gilliamella, and Burkholderia. We have further identified a compositional convergence of the analyzed microbiomes in regard to the host phylogenetic distance in both blood-feeding and predatory reduviids. While the microbiomes of the two reduviid species from the Emesinae family reflect their close relationship, the microbiomes of all Triatoma species repeatedly form a distinct monophyletic cluster highlighting their phylosymbiosis. Furthermore, based on environmental microbiome profiles and blood meal analysis, we propose three epidemiologically relevant and mutually interrelated bacterial sources for Triatoma microbiomes, i.e., host abiotic environment, host skin microbiome, and pathogens circulating in host blood. IMPORTANCE This study places microbiomes of blood-feeding North American Triatoma vectors (Reduviidae) into a broader evolutionary and ecological context provided by related predatory assassin bugs (Reduviidae), another unrelated vector species (soft tick Ornithodoros turicata), and the environment these arthropods coinhabit. For both vectors, microbiome analyses suggest three interrelated sources of bacteria, i.e., the microbiome of vertebrate nests as their natural habitat, the vertebrate skin microbiome, and the pathobiome circulating in vertebrate blood. Despite an apparent influx of environment-associated bacteria into the arthropod microbiomes, Triatoma microbiomes retain their specificity, forming a distinct cluster that significantly differs from both predatory relatives and ecologically comparable ticks. Similarly, within the related predatory Reduviidae, we found the host phylogenetic distance to underlie microbiome similarities.

RevDate: 2023-06-08

Vargas S, Leiva L, Eitel M, et al (2023)

Body-plan reorganization in a sponge correlates with microbiome change.

Molecular biology and evolution pii:7191912 [Epub ahead of print].

Mounting evidence suggests that animals and their associated bacteria interact via intricate molecular mechanisms, and it is hypothesized that disturbances to the microbiome influence animal development. Here, we show that the loss of a key photosymbiont (i.e., bleaching) correlates with a stark body-plan reorganization in the common aquarium cyanosponge Lendenfeldia chondrodes. The morphological changes observed in shaded sponges include the development of a thread-like morphology that contrasts with the flattened, foliose morphology of control specimens. The microanatomy of shaded sponges markedly differed from that of control sponges, with shaded specimens lacking a well-developed cortex and choanosome. Also, the palisade of polyvacuolar gland-cells typical in control specimens was absent in shaded sponges. The morphological changes observed in shaded species are coupled with broad transcriptomic changes and include the modulation of signaling pathways involved in animal morphogenesis and immune response, such as the Wnt, TFG-β, and TLR-ILR pathways. This study provides a genetic, physiological, and morphological assessment of the effect of microbiome changes on sponge post-embryonic development and homeostasis. The correlated response of the sponge host to the collapse of the population of symbiotic cyanobacteria provides evidence for a coupling between the sponge transcriptomic state and the state of its microbiome. This coupling suggests that the ability of animals to interact with their microbiomes and respond to microbiome perturbations has deep evolutionary origins in this group.

RevDate: 2023-06-08

Zhao J, Liu Y, Xu S, et al (2023)

Mealybug salivary microbes inhibit induced plant defenses.

Pest management science [Epub ahead of print].

BACKGROUND: Phenacoccus solenopsis is a polyphagous invasive mealybug that caused serious damage to crops worldwide. Phloem-sucking hemipterans are known to carry symbiotic microbes in their saliva. However, the role of salivary bacteria of P. solenopsis in modulating plant defenses remains limited. Exploring the impact of salivary bacteria on plant defense responses will contribute to develop new targets for efficient control of invasive mealybugs.

RESULTS: Salivary bacteria of the invasive mealybug Phenacoccus solenopsis, can suppress herbivore-induced plant defenses and thus enhance mealybug fitness. Mealybugs treated with an antibiotic showed decreased weight gain, fecundity and survival. Untreated mealybugs suppressed jasmonic acid (JA)-regulated defenses but activated salicylic acid (SA)-regulated defenses in cotton plants. In contrast, antibiotic-treated mealybugs triggered JA responsive gene expression and JA accumulation and showed shortened phloem ingestion. Reinoculating antibiotic-treated mealybugs with Enterobacteriaceae or Stenotrophomonas cultivated from mealybug saliva promoted phloem ingestion, fecundity and restored the ability of mealybugs to suppress plant defenses. Fluorescence in situ hybridization (FISH) visualization revealed that Enterobacteriaceae and Stenotrophomonas colonize salivary gland and are secreted into the mesophyll cells and phloem vessels. Exogenous application of the bacterial isolates to plant leaves inhibited JA-responsive gene expression and activated SA-responsive gene expression.

CONCLUSION: Our findings imply that symbiotic bacteria in the saliva of the mealybug play an important role in manipulating herbivore-induced plant defenses, enabling this important pest to evade induced plant defenses and promoting its performance and destructive effects on crops. This article is protected by copyright. All rights reserved.

RevDate: 2023-06-07

Li H, Zhang L, Wu B, et al (2023)

Physiological and proteomic analyses reveal the important role of arbuscular mycorrhizal fungi on enhancing photosynthesis in wheat under cadmium stress.

Ecotoxicology and environmental safety, 261:115105 pii:S0147-6513(23)00609-7 [Epub ahead of print].

Arbuscular mycorrhizal fungi (AMF) are important in the phytoremediation of cadmium (Cd). Improving photosynthesis under Cd stress helps to increase crop yields. However, the molecular regulatory mechanisms of AMF on photosynthetic processes in wheat (Triticum aestivum) under Cd stress remain unclear. This study utilized physiological and proteomic analyses to reveal the key processes and related genes of AMF that regulate photosynthesis under Cd stress. The results showed that AMF promoted the accumulation of Cd in the roots of wheat but significantly reduced the content of Cd in the shoots and grains. The photosynthetic rates, stomatal conductance, transpiration rates, chlorophyll content, and accumulation of carbohydrates under Cd stress were increased by AMF symbiosis. Proteomic analysis showed that AMF significantly induced the expression of two enzymes involved in the chlorophyll biosynthetic pathway (coproporphyrinogen oxidase and Mg-protoporphyrin IX chelatase), improved the expression of two proteins related to CO2 assimilation (ribulose-1,5-bisphosphate carboxylase and malic enzyme), and increased the expression of S-adenosylmethionine synthase, which positively regulates abiotic stress. Therefore, AMF may regulate photosynthesis under Cd stress by promoting chlorophyll biosynthesis, carbon assimilation, and S-adenosylmethionine metabolism.

RevDate: 2023-06-07

Mohammed S, Sha'aban YA, Umoh IJ, et al (2023)

A hybrid smell agent symbiosis organism search algorithm for optimal control of microgrid operations.

PloS one, 18(6):e0286695 pii:PONE-D-23-06901.

This paper presents a hybrid Smell Agent Symbiosis Organism Search Algorithm (SASOS) for optimal control of autonomous microgrids. In microgrid operation, a single optimization algorithm often lacks the required balance between accuracy and speed to control power system parameters such as frequency and voltage effectively. The hybrid algorithm reduces the imbalance between exploitation and exploration and increases the effectiveness of control optimization in microgrids. To achieve this, various energy resource models were coordinated into a single model for optimal energy generation and distribution to loads. The optimization problem was formulated based on the network power flow and the discrete-time sampling of the constrained control parameters. The development of SASOS comprises components of Symbiotic Organism Search (SOS) and Smell Agent Optimization (SAO) codified in an optimization loop. Twenty-four standard test function benchmarks were used to evaluate the performance of the algorithm developed. The experimental analysis revealed that SASOS obtained 58.82% of the Desired Convergence Goal (DCG) in 17 of the benchmark functions. SASOS was implemented in the Microgrid Central Controller (MCC) and benchmarked alongside standard SOS and SAO optimization control strategies. The MATLAB/Simulink simulation results of the microgrid load disturbance rejection showed the viability of SASOS with an improved reduction in Total Harmonic Distortion (THD) of 19.76%, compared to the SOS, SAO, and MCC methods that have a THD reduction of 15.60%, 12.74%, and 6.04%, respectively, over the THD benchmark. Based on the results obtained, it can be concluded that SASOS demonstrates superior performance compared to other methods. This finding suggests that SASOS is a promising solution for enhancing the control system of autonomous microgrids. It was also shown to apply to other sectors of engineering optimization.

RevDate: 2023-06-07

Wei H, Wang J, Wang Q, et al (2023)

Role of melatonin in enhancing arbuscular mycorrhizal symbiosis and mitigating cold stress in perennial ryegrass (Lolium perenne L.).

Frontiers in microbiology, 14:1123632.

Melatonin is a biomolecule that affects plant development and is involved in protecting plants from environmental stress. However, the mechanisms of melatonin's impact on arbuscular mycorrhizal (AM) symbiosis and cold tolerance in plants are still unclear. In this research, AM fungi inoculation and exogenous melatonin (MT) were applied to perennial ryegrass (Lolium perenne L.) seedlings alone or in combination to investigate their effect on cold tolerance. The study was conducted in two parts. The initial trial examined two variables, AM inoculation, and cold stress, to investigate the involvement of the AM fungus Rhizophagus irregularis in endogenous melatonin accumulation and the transcriptional levels of its synthesis genes in the root system of perennial ryegrass under cold stress. The subsequent trial was designed as a three-factor analysis, encompassing AM inoculation, cold stress, and melatonin application, to explore the effects of exogenous melatonin application on plant growth, AM symbiosis, antioxidant activity, and protective molecules in perennial ryegrass subjected to cold stress. The results of the study showed that compared to non-mycorrhizal (NM) plants, cold stress promoted an increase in the accumulation of melatonin in the AM-colonized counterparts. Acetylserotonin methyltransferase (ASMT) catalyzed the final enzymatic reaction in melatonin production. Melatonin accumulation was associated with the level of expression of the genes, LpASMT1 and LpASMT3. Treatment with melatonin can improve the colonization of AM fungi in plants. Simultaneous utilization of AM inoculation and melatonin treatment enhanced the growth, antioxidant activity, and phenylalanine ammonia-lyase (PAL) activity, while simultaneously reducing polyphenol oxidase (PPO) activity and altering osmotic regulation in the roots. These effects are expected to aid in the mitigation of cold stress in Lolium perenne. Overall, melatonin treatment would help Lolium perenne to improve growth by promoting AM symbiosis, improving the accumulation of protective molecules, and triggering in antioxidant activity under cold stress.

RevDate: 2023-06-07

De Lorenzi-Tognon M, Genton L, J Schrenzel (2023)

[Summary of the 8[th] Symposium "Feeding the microbiota": prebiotics and probiotics].

Revue medicale suisse, 19(830):1149-1153.

The microbiota represents all the microorganisms including viruses, bacteria, fungi, and parasites, that have a symbiotic relationship with their host and that are present in a particular system (or niche) of the human body such as the skin, the respiratory tract, the urogenital tract or the digestive tract. This paper is a narrative review of all talks given at the 8th edition of the « Feeding the Microbiota » symposium organized at the Geneva University Hospitals. The symposium gathered 346 participants, both onsite and online, from 23 countries all-around the world. The main thematic of this edition focused on the composition of the gut microbiota as affected by prebiotics and postbiotics and their effects on various diseases.

RevDate: 2023-06-07

Chen JD, Jiang W, Song MQ, et al (2023)

[Identification and expression of uridine diphosphate glycosyltransferase(UGT) gene family from Dendrobium officinale].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 48(7):1840-1850.

Uridine diphosphate glycosyltransferase(UGT) is a highly conserved protein in plants, which usually functions in secondary metabolic pathways. This study used the Hidden Markov Model(HMM) to screen out members of UGT gene family in the whole genome of Dendrobium officinale, and 44 UGT genes were identified. Bioinformatics was used to analyze the structure, phylogeny, and promoter region components of D. officinale genes. The results showed that UGT gene family could be divided into four subfamilies, and UGT gene structure was relatively conserved in each subfamily, with nine conserved domains. The upstream promoter region of UGT gene contained a variety of cis-acting elements related to plant hormones and environmental factors, indicating that UGT gene expression may be induced by plant hormones and external environmental factors. UGT gene expression in different tissues of D. officinale was compared, and UGT gene expression was found in all parts of D. officinale. It was speculated that UGT gene played an important role in many tissues of D. officinale. Through transcriptome analysis of D. officinale mycorrhizal symbiosis environment, low temperature stress, and phosphorus deficiency stress, this study found that only one gene was up-regulated in all three conditions. The results of this study can help understand the functions of UGT gene family in Orchidaceae plants and provide a basis for further study on the molecular regulation mechanism of polysaccharide metabolism pathway in D. officinale.

RevDate: 2023-06-07

Strano F, Micaroni V, Thomas T, et al (2023)

Marine heatwave conditions drive carryover effects in a temperate sponge microbiome and developmental performance.

Proceedings. Biological sciences, 290(2000):20222539.

Marine heatwaves are increasingly subjecting organisms to unprecedented stressful conditions, but the biological consequences of these events are still poorly understood. Here we experimentally tested the presence of carryover effects of heatwave conditions on the larval microbiome, settlers growth rate and metamorphosis duration of the temperate sponge Crella incrustans. The microbial community of adult sponges changed significantly after ten days at 21°C. There was a relative decrease in symbiotic bacteria, and an increase in stress-associated bacteria. Sponge larvae derived from control sponges were mainly characterised by a few bacterial taxa also abundant in adults, confirming the occurrence of vertical transmission. The microbial community of sponge larvae derived from heatwave-exposed sponges showed significant increase in the endosymbiotic bacteria Rubritalea marina. Settlers derived from heatwave-exposed sponges had a greater growth rate under prolonged heatwave conditions (20 days at 21°C) compared to settlers derived from control sponges exposed to the same conditions. Moreover, settler metamorphosis was significantly delayed at 21°C. These results show, for the first time, the occurrence of heatwave-induced carryover effects across life-stages in sponges and highlight the potential role of selective vertical transmission of microbes in sponge resilience to extreme thermal events.

RevDate: 2023-06-07

Mauger S, Ricono C, Mony C, et al (2021)

Differentiation of endospheric microbiota in ancient and modern wheat cultivar roots.

Plant-environment interactions (Hoboken, N.J.), 2(5):235-248.

Modern plant breeding and agrosystems artificialization could have altered plants' ability to filter and recruit beneficial microorganisms in its microbiota. Thus, compared to modern cultivars, we hypothesized that root-endosphere microbiota in modern wheat cultivars are less resistant to colonization by fungi and bacteria and thus more susceptible to also recruit more pathogens. We used an in-field experimental design including six wheat varieties (three ancient vs. three modern) grown in monoculture and in mixture (three replicates each). Endospheric microbiota of wheat roots were analyzed on four individuals sampled randomly in each plot. Composition-based clustering of sequences was then characterized from amplicon mass-sequencing. We show that the bacterial and fungal microbiota composition in wheat roots differed between ancient and modern wheat cultivar categories. However, the responses observed varied with the group considered. Modern cultivars harbored higher richness of bacterial and fungal pathogens than ancient cultivars. Both cultivar types displayed specific indicator species. A synergistic effect was identified in mixtures of modern cultivars with a higher root endospheric mycobiota richness than expected from a null model. The present study shows the effect of plant breeding on the microbiota associated plant roots. The results call for making a diagnosis of the cultivar's endospheric-microbiota composition. These new results also suggest the importance of a holobiont-vision while considering plant selection in crops and call for better integration of symbiosis in the development of next-generation agricultural practices.

RevDate: 2023-06-07

Singer SD, Chatterton S, Soolanayakanahally RY, et al (2020)

Potential effects of a high CO2 future on leguminous species.

Plant-environment interactions (Hoboken, N.J.), 1(2):67-94.

Legumes provide an important source of food and feed due to their high protein levels and many health benefits, and also impart environmental and agronomic advantages as a consequence of their ability to fix nitrogen through their symbiotic relationship with rhizobia. As a result of our growing population, the demand for products derived from legumes will likely expand considerably in coming years. Since there is little scope for increasing production area, improving the productivity of such crops in the face of climate change will be essential. While a growing number of studies have assessed the effects of climate change on legume yield, there is a paucity of information regarding the direct impact of elevated CO2 concentration (e[CO2]) itself, which is a main driver of climate change and has a substantial physiological effect on plants. In this review, we discuss current knowledge regarding the influence of e[CO2] on the photosynthetic process, as well as biomass production, seed yield, quality, and stress tolerance in legumes, and examine how these responses differ from those observed in non-nodulating plants. Although these relationships are proving to be extremely complex, mounting evidence suggests that under limiting conditions, overall declines in many of these parameters could ensue. While further research will be required to unravel precise mechanisms underlying e[CO2] responses of legumes, it is clear that integrating such knowledge into legume breeding programs will be indispensable for achieving yield gains by harnessing the potential positive effects, and minimizing the detrimental impacts, of CO2 in the future.

RevDate: 2023-06-06

Iyobosa E, Wang R, J Zhao (2023)

Antibiotic removal by microalgae-bacteria consortium: Metabolic pathways and microbial responses.

The Science of the total environment pii:S0048-9697(23)03110-8 [Epub ahead of print].

The proliferation of antibiotic-resistance genes is a result of the rise in the discharge of residual antibiotics into waterbodies from a variety of sources. Antibiotic removal by microalgae-bacteria consortium has been shown to be effective, therefore, there is a need to understand the involved microbial processes. This review summarizes the microbiological removal mechanisms of antibiotics by the microalgae-bacteria consortium, such as biosorption, bioaccumulation, and biodegradation. Factors that influence antibiotic removal are discussed. Co-metabolism of nutrients and antibiotics in the microalgae-bacteria consortium and the metabolic pathways revealed by omics technologies are also highlighted. Furthermore, the responses of microalgae and bacteria to antibiotic stress are elaborated, including reactive oxidizing species (ROS) generation and its effects on photosynthesis machinery, antibiotic stress tolerance, microbial community shift, and the emergence of antibiotic resistance genes (ARGs). Finally, we offer a perspective on the optimization and applications of microalgae-bacteria symbiotic systems for antibiotic removal.

RevDate: 2023-06-06

Hawkins HJ, Cargill RIM, Van Nuland ME, et al (2023)

Mycorrhizal mycelium as a global carbon pool.

Current biology : CB, 33(11):R560-R573.

For more than 400 million years, mycorrhizal fungi and plants have formed partnerships that are crucial to the emergence and functioning of global ecosystems. The importance of these symbiotic fungi for plant nutrition is well established. However, the role of mycorrhizal fungi in transporting carbon into soil systems on a global scale remains under-explored. This is surprising given that ∼75% of terrestrial carbon is stored belowground and mycorrhizal fungi are stationed at a key entry point of carbon into soil food webs. Here, we analyze nearly 200 datasets to provide the first global quantitative estimates of carbon allocation from plants to the mycelium of mycorrhizal fungi. We estimate that global plant communities allocate 3.93 Gt CO2e per year to arbuscular mycorrhizal fungi, 9.07 Gt CO2e per year to ectomycorrhizal fungi, and 0.12 Gt CO2e per year to ericoid mycorrhizal fungi. Based on this estimate, 13.12 Gt of CO2e fixed by terrestrial plants is, at least temporarily, allocated to the underground mycelium of mycorrhizal fungi per year, equating to ∼36% of current annual CO2 emissions from fossil fuels. We explore the mechanisms by which mycorrhizal fungi affect soil carbon pools and identify approaches to increase our understanding of global carbon fluxes via plant-fungal pathways. Our estimates, although based on the best available evidence, are imperfect and should be interpreted with caution. Nonetheless, our estimations are conservative, and we argue that this work confirms the significant contribution made by mycorrhizal associations to global carbon dynamics. Our findings should motivate their inclusion both within global climate and carbon cycling models, and within conservation policy and practice.

RevDate: 2023-06-06

Xu P, E Wang (2023)

Diversity and regulation of symbiotic nitrogen fixation in plants.

Current biology : CB, 33(11):R543-R559.

Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.

RevDate: 2023-06-06

Scharnagl K, Tagirdzhanova G, NJ Talbot (2023)

The coming golden age for lichen biology.

Current biology : CB, 33(11):R512-R518.

Lichens are a diverse group of organisms. They are both commonly observed but also mysterious. It has long been known that lichens are composite symbiotic associations of at least one fungus and an algal or cyanobacterial partner, but recent evidence suggests that they may be much more complex. We now know that there can be many constituent microorganisms in a lichen, organized into reproducible patterns that suggest a sophisticated communication and interplay between symbionts. We feel the time is right for a more concerted effort to understand lichen biology. Rapid advances in comparative genomics and metatranscriptomic approaches, coupled with recent breakthroughs in gene functional studies, suggest that lichens may now be more tractable to detailed analysis. Here we set out some of the big questions in lichen biology, and we speculate about the types of gene functions that may be critical to their development, as well as the molecular events that may lead to initial lichen formation. We define both the challenges and opportunities in lichen biology and offer a call to arms to study this remarkable group of organisms.

RevDate: 2023-06-06

Xavier CAD, AE Whitfield (2023)

Plant virology.

Current biology : CB, 33(11):R478-R484.

The first infectious agent to bear the name 'virus' was described in 1898: a plant pathogen called tobacco mosaic virus that infects a wide range of plants and results in a yellow mosaic of the leaves. Since then, the study of plant viruses has facilitated new discoveries in both virology and plant biology. Traditionally, research has focused on viruses that cause severe disease in plants used for human and animal food or recreation. However, closer inspection of the plant-associated virome is now revealing interactions that range from pathogenic to symbiotic. Although they are often studied in isolation, plant viruses are usually found as part of a broader community that includes other plant-associated microbes and pests. For example, biological vectors of plant viruses (arthropods, nematodes, fungi, and protists) can facilitate the transmission of viruses between plants in an intricate interaction. To enhance transmission, viruses can induce the plant to 'lure' the vector by modulating plant chemistry and defenses. Once delivered to a new host, viruses are dependent on specific proteins that modify the structural components of the cell to enable transport of viral proteins and genomic material. Links between antiviral plant defenses and key steps in virus movement and transmission are being revealed. Upon infection, a suite of antiviral responses is triggered, including the expression of resistance genes - a favored strategy to control plant viruses. In this primer, we discuss these features and more, highlighting the exciting world of plant-virus interactions.

RevDate: 2023-06-06

Zayed N, Ghesquière J, Kamarudin NHN, et al (2023)

Oral Biofilm Cryotherapy as a Novel Ecological Modulation Approach.

Journal of dental research [Epub ahead of print].

Oral cryotherapy is used in dentistry as a safe, simple, and low-cost treatment for a variety of oral lesions. It is well known for its ability to aid in the healing process. However, its effect on oral biofilms is unknown. As a result, the purpose of this study was to assess the effects of cryotherapy on in vitro oral biofilms. In vitro multispecies oral biofilms were grown on the surface of hydroxyapatite discs in symbiotic or dysbiotic states. CryoPen X+ was used to treat the biofilms, whereas untreated biofilms served as control. One set of biofilms was collected for study immediately after cryotherapy, whereas another group was reincubated for 24 h to permit biofilm recovery. Changes in biofilm structure were analyzed with a confocal laser scanning microscope (CLSM) and a scanning electron microscope (SEM), while biofilm ecology and community compositional changes were analyzed with viability DNA extraction and quantitative polymerase chain reaction (v-qPCR) analysis. One cryo-cycle immediately reduced biofilm load by 0.2 to 0.4 log10 Geq/mL, which increased with additional treatment cycles. Although the bacterial load of the treated biofilms recovered to the same level as the control biofilms within 24 h, the CLSM detected structural alterations. Compositional alterations were also detected by SEM, corroborating the v-qPCR findings that showed ≈≤10% incidence of pathogenic species compared to nontreated biofilms that encompassed ≈45% and 13% pathogenic species in dysbiotic and symbiotic biofilms, respectively. Spray cryotherapy showed promising results in a novel conceptual approach to the control of oral biofilms. Acting selectively by targeting oral pathobionts and retaining commensals, spray cryotherapy could modify the ecology of in vitro oral biofilms to become more symbiotic and prevent the evolution of dysbiosis without the use of antiseptics/antimicrobials.

RevDate: 2023-06-05

Warnasuriya SD, Udayanga D, Manamgoda DS, et al (2023)

Fungi as environmental bioindicators.

The Science of the total environment pii:S0048-9697(23)03204-7 [Epub ahead of print].

Environmental bioindicators are species or communities of animals, plants, bacteria, fungi, algae, lichens, and planktons whose existence, quantity, and nature can be used to make inferences on the quality of the environment. Bioindicators can be used to detect environmental contaminants by on-site visual inspections or through laboratory analysis. Fungi are one of the most important groups of environmental bioindicators due to their ubiquitous distribution, diverse ecological roles, remarkable biological diversity, and high sensitivity to environmental changes. This review provide a comprehensive reappraisal of using various groups of fungi, fungal communities, symbiotic associations with fungal component, biomarkers of fungi as "mycoindicators" to assess the quality of air, water and soil. Fungi are exploited by researchers as double-edged tools for both biomonitoring and mycoremediation simultaneously. The applications of bioindicators have advanced through the integration of genetic engineering, high-throughput DNA sequencing, and gene editing techniques. Therefore mycoindicators are significant as an emerging tool for more accurate and affordable early detection of environmental contaminants toward the mitigation efforts of pollution in both natural and man-made environment.

RevDate: 2023-06-05

Timmusk S, Pall T, Raz S, et al (2023)

The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology.

Frontiers in microbiology, 14:1141862.

Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.

RevDate: 2023-06-05

Zhu Y, Wang Y, Zhang S, et al (2023)

Association of polymicrobial interactions with dental caries development and prevention.

Frontiers in microbiology, 14:1162380.

Dental caries is a common oral disease. In many cases, disruption of the ecological balance of the oral cavity can result in the occurrence of dental caries. There are many cariogenic microbiota and factors, and their identification allows us to take corresponding prevention and control measures. With the development of microbiology, the caries-causing bacteria have evolved from the traditional single Streptococcus mutans to the discovery of oral symbiotic bacteria. Thus it is necessary to systematically organized the association of polymicrobial interactions with dental caries development. In terms of ecology, caries occurs due to an ecological imbalance of the microbiota, caused by the growth and reproduction of cariogenic microbiota due to external factors or the disruption of homeostasis by one's own factors. To reduce the occurrence of dental caries effectively, and considering the latest scientific viewpoints, caries may be viewed from the perspective of ecology, and preventive measures can be taken; hence, this article systematically summarizes the prevention and treatment of dental caries from the aspects of ecological perspectives, in particular the ecological biofilm formation, bacterial quorum sensing, the main cariogenic microbiota, and preventive measures.

RevDate: 2023-06-05

Sandhu AK, Brown MR, Subramanian S, et al (2023)

Bradyrhizobium diazoefficiens USDA 110 displays plasticity in the attachment phenotype when grown in different soybean root exudate compounds.

Frontiers in microbiology, 14:1190396.

INTRODUCTION: Bradyrhizobium diazoefficiens, a symbiotic nitrogen fixer for soybean, forms nodules after developing a symbiotic association with the root. For this association, bacteria need to move toward and attach to the root. These steps are mediated by the surface and phenotypic cell properties of bacteria and secreted root exudate compounds. Immense work has been carried out on nodule formation and nitrogen fixation, but little is known about the phenotype of these microorganisms under the influence of different root exudate chemical compounds (RECCs) or how this phenotype impacts the root attachment ability.

METHODS: To address this knowledge gap, we studied the impact of 12 different RECCs, one commonly used carbon source, and soil-extracted solubilized organic matter (SESOM) on attachment and attachment-related properties of B. diazoefficiens USDA110. We measured motility-related properties (swimming, swarming, chemotaxis, and flagellar expression), attachment-related properties (surface hydrophobicity, biofilm formation, and attachment to cellulose and soybean roots), and surface polysaccharide properties (colony morphology, exopolysaccharide quantification, lectin binding profile, and lipopolysaccharide profiling).

RESULTS AND DISCUSSION: We found that USDA 110 displays a high degree of surface phenotypic plasticity when grown on the various individual RECCs. Some of the RECCs played specific roles in modulating the motility and root attachment processes. Serine increased cell surface hydrophobicity and root and cellulose attachment, with no EPS formed. Gluconate and lactate increased EPS production and biofilm formation, while decreasing hydrophobicity and root attachment, and raffinose and gentisate promoted motility and chemotaxis. The results also indicated that the biofilm formation trait on hydrophilic surfaces (polystyrene) cannot be related to the attachment ability of Bradyrhizobium to the soybean root. Among the tested phenotypic properties, bacterial cell surface hydrophobicity was the one with a significant impact on root attachment ability. We conclude that USDA 110 displays surface plasticity properties and attachment phenotype determined by individual RECCs from the soybean. Conclusions made based on its behavior in standard carbon sources, such as arabinose or mannitol, do not hold for its behavior in soil.

RevDate: 2023-06-05

Hassanzadeh P, Nouri Gharajalar S, S Mohammadzadeh (2022)

Antimicrobial Effects of Different Synbiotic Compounds against Pathogenic Bacteria Isolated from Beef, Mutton, and Chicken.

Archives of Razi Institute, 77(6):2105-2113 pii:ARI-77-6.

Today, there has been a growing interest in synbiotic usage in the food industry to solve the problems related to food contaminations. The present study aimed to evaluate the antibacterial effects of nine symbiotic compounds on bacteria isolated from different meat types. Pathogenic bacteria were isolated from 60 different meat samples. Then, the antibacterial effects of nine synbiotic components were assessed against isolated bacteria using well diffusion and radial streak methods. In addition, minimum inhibitory and minimum bactericidal concentrations of each synbiotic formulation were determined. The highest antibacterial activity against Listeria monocytogenes and Staphylococcus aureus was for synbiotic compounds consisting of Streptococcus salivarius, raffinose, inulin, and trehalose, respectively. Furthermore, the highest antibacterial efficacies against Escherichia coli and Salmonella were for synbiotic formulations consisting of Bacillus cereus and inulin, raffinose, and trehalose, respectively. In conclusion, synbiotic formulations containing S. salivarius and B. cereus may be an alternative approach to preventing food-borne pathogens.

RevDate: 2023-06-05

Agrawal S, NA Broderick (2023)

Inside help from the microbiome.

eLife, 12: pii:88873.

Elucidating the role of one of the proteins produced by Lactiplantibacillus plantarum reveals a new molecule that allows this gut bacterium to support the development of fruit fly larvae.

RevDate: 2023-06-05

Williams DA, MH Flood (2023)

Haematoloechus sp. attachment shifts endothelium in vivo from pro- to anti-inflammatory profile in Rana pipiens: evidence from systemic and capillary physiology.

American journal of physiology. Regulatory, integrative and comparative physiology [Epub ahead of print].

This prospective, descriptive study focused on lung flukes (Haematoloechus sp., H) and their impact on systemic and individual capillary variables measured in pithed Rana pipiens, a long-standing model for studies of capillary physiology. Three groups were identified based on H attachment: no Haematoloechus (No H), Haematoloechus not attached (H Not Att), and Haematoloechus attached (H Att). Among 38 descriptive, cardiovascular, and immunological variables, 18 changed significantly with H. Symptoms of H included weight loss, elevated immune cells, heart rate variability, faster coagulation, lower hematocrit, and fluid accumulation. Important capillary function discoveries included median baselines for hydraulic conductivity (Lp) of 7.0 (No H), 12.4 (H Not Att), and 4.2 (H Att) x 10[-7] cm[.]s[-1.]cm H2O[-1](P<0.0001) plus seasonal adaptation of sigma delta pi (s(pc - pi), P=0.03). Pro- and anti-inflammatory phases were revealed for Lp and plasma nitrite/nitrate concentration ([NOx]) in H Not Att and H Att and capillary wall tensile strength increased in H Att. H attachment was advantageous for the host due to lower edema and for the parasite via a sustained food source illustrating an excellent example of natural symbiosis. However, H attachment also resulted in host weight loss: in time, a conundrum for the highly dependent parasite. The study increases overall knowledge of Rana pipiens by revealing intriguing effects of H and previously unknown, naturally occurring seasonal changes in many variables. The data improve Rana pipiens as a general scientific and capillary physiology model. Diseases of inflammation and stroke are among the clinical applications.

RevDate: 2023-06-05

Wang XJ, Shao ZY, Zhu MR, et al (2023)

[Intestinal and pharyngeal microbiota in early neonates: an analysis based on high-throughput sequencing].

Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics, 25(5):508-515.

OBJECTIVES: To investigate the distribution characteristics and correlation of intestinal and pharyngeal microbiota in early neonates.

METHODS: Full-term healthy neonates who were born in Shanghai Pudong New Area Maternal and Child Health Hospital from September 2021 to January 2022 and were given mixed feeding were enrolled. The 16S rRNA sequencing technique was used to analyze the stool and pharyngeal swab samples collected on the day of birth and days 5-7 after birth, and the composition and function of intestinal and pharyngeal microbiota were analyzed and compared.

RESULTS: The diversity analysis showed that the diversity of pharyngeal microbiota was higher than that of intestinal microbiota in early neonates, but the difference was not statistically significant (P>0.05). On the day of birth, the relative abundance of Proteobacteria in the intestine was significantly higher than that in the pharynx (P<0.05). On days 5-7 after birth, the relative abundance of Actinobacteria and Proteobacteria in the intestine was significantly higher than that in the pharynx (P<0.05), and the relative abundance of Firmicutes in the intestine was significantly lower than that in the pharynx (P<0.05). At the genus level, there was no significant difference in the composition of dominant bacteria between the intestine and the pharynx on the day of birth (P>0.05), while on days 5-7 after birth, there were significant differences in the symbiotic bacteria of Streptococcus, Staphylococcus, Rothia, Bifidobacterium, and Escherichia-Shigella between the intestine and the pharynx (P<0.05). The analysis based on the database of Clusters of Orthologous Groups of proteins showed that pharyngeal microbiota was more concentrated on chromatin structure and dynamics and cytoskeleton, while intestinal microbiota was more abundant in RNA processing and modification, energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, coenzyme transport and metabolism, and others (P<0.05). The Kyoto Encyclopedia of Genes and Genomes analysis showed that compared with pharyngeal microbiota, intestinal microbiota was more predictive of cell motility, cellular processes and signal transduction, endocrine system, excretory system, immune system, metabolic diseases, nervous system, and transcription parameters (P<0.05).

CONCLUSIONS: The composition and diversity of intestinal and pharyngeal microbiota of neonates are not significantly different at birth. The microbiota of these two ecological niches begin to differentiate and gradually exhibit distinct functions over time.

RevDate: 2023-06-03

Chaisiri K, Linsuwanon P, BL Makepeace (2023)

The chigger microbiome: big questions in a tiny world.

Trends in parasitology pii:S1471-4922(23)00120-4 [Epub ahead of print].

'Chiggers' (trombiculid mite larvae) are best known as vectors of rickettsial pathogens, Orientia spp., which cause a zoonosis, scrub typhus. However, several other pathogens (e.g., Hantaan orthohantavirus, Dabie bandavirus, Anaplasma spp., Bartonella spp., Borrelia spp., and Rickettsia spp.) and bacterial symbionts (e.g., Cardinium, Rickettsiella, and Wolbachia) are being reported from chiggers with increasing frequency. Here, we explore the surprisingly diverse chigger microbiota and potential interactions within this microcosm. Key conclusions include a possible role for chiggers as vectors of viral diseases; the dominance in some chigger populations of unidentified symbionts in several bacterial families; and increasing evidence for vertical transmission of potential pathogens and symbiotic bacteria in chiggers, suggesting intimate interactions and not simply incidental acquisition of bacteria from the environment or host.

RevDate: 2023-06-03

Fardi F, Bahari Khasraghi L, Shahbakhti N, et al (2023)

An interplay between non-coding RNAs and gut microbiota in human health.

Diabetes research and clinical practice pii:S0168-8227(23)00502-8 [Epub ahead of print].

Humans have a complicated symbiotic relationship with their gut microbiome, which is postulated to impact host health and disease broadly. Epigenetic alterations allow host cells to regulate gene expression without altering the DNA sequence. The gut microbiome, offering environmental hints, can influence responses to stimuli by host cells with modifications on their epigenome and gene expression. Recent increasing data suggest that regulatory non-coding RNAs (miRNAs, circular RNAs, and long lncRNA) may affect host-microbe interactions. These RNAs have been suggested as potential host response biomarkers in microbiome-associated disorders, including diabetes and cancer. This article reviews the current understanding of the interplay between gut microbiota and non-coding RNA, including lncRNA, miRNA, and circular RNA. This can lead to a profound understanding of human disease and influence therapy. Furthermore, microbiome engineering as a mainstream strategy for improving human health has been discussed and confirms the hypothesis about a direct cross-talk between microbiome composition and non-coding RNA.

RevDate: 2023-06-03

Nakamura S, Kurata R, Tonozuka T, et al (2023)

Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.

The Journal of biological chemistry pii:S0021-9258(23)01913-0 [Epub ahead of print].

Dextran is an α-(1→6)-glucan that is synthesized by some lactic acid bacteria, and branched dextran with α-(1→2)-, α-(1→3)-, and α-(1→4)-linkages are often produced. Although many dextranases are known to act on the α-(1→6)-linkage of dextran, few studies have functionally analyzed the proteins involved in degrading branched dextran. The mechanism by which bacteria utilize branched dextran is unknown. Earlier, we identified dextranase (FjDex31A) and kojibiose hydrolase (FjGH65A) in the dextran utilization locus (FjDexUL) of a soil Bacteroidota Flavobacterium johnsoniae and hypothesized that FjDexUL is involved in the degradation of α-(1→2)-branched dextran. In this study, we demonstrate that FjDexUL proteins recognize and degrade α-(1→2)- and α-(1→3)-branched dextrans produced by Leuconostoc citreum S-32 (S-32 α-glucan). The FjDexUL gene was significantly upregulated when S-32 α-glucan was the carbon source compared with α-glucooligosaccharides and α-glucans, such as linear dextran and branched α-glucan from L. citreum S-64. FjDexUL GHs synergistically degraded S-32 α-glucan. The crystal structure of FjGH66 shows that some sugar-binding subsites can accommodate α-(1→2)- and α-(1→3)-branches. The structure of FjGH65A in complex with isomaltose supports that FjGH65A acts on α-(1→2)-glucosyl isomaltooligosaccharides. Furthermore, two cell surface sugar-binding proteins (FjDusD and FjDusE) were characterized, and FjDusD showed affinity for isomaltooligosaccharides and FjDusE for dextran, including linear and branched dextrans. Collectively, FjDexUL proteins are suggested to be involved in the degradation of α-(1→2)- and α-(1→3)-branched dextrans. Our results will be helpful in understanding the bacterial nutrient requirements and symbiotic relationships between bacteria at the molecular level.

RevDate: 2023-06-03

Pacheco R, C Quinto (2023)

Corrigendum to "Phospholipase Ds in plants: Their role in pathogenic and symbiotic interactions" [Plant Physiol. Biochem. 173 (2022) 76-86].

RevDate: 2023-06-03

Zhao Z, Wang L, Kelley K, et al (2023)

GFP labeling of a Bradyrhizobium strain and an attempt to track the crack entry process during symbiosis with peanuts.

World journal of microbiology & biotechnology, 39(8):219.

Compared to the well-studied model legumes, where symbiosis is established via root hair entry, the peanut is infected by Bradyrhizobium through the crack entry, which is less common and not fully understood. Crack entry is, however, considered a primitive symbiotic infection pathway, which could be potentially utilized for engineering non-legume species with nitrogen fixation ability. We utilized a fluorescence-labeled Bradyrhizobium strain to help in understanding the crack entry process at the cellular level. A modified plasmid pRJPaph-bjGFP, harboring the codon-optimized GFP gene and tetracycline resistance gene, was created and conjugated into Bradyrhizobium strain Lb8, an isolate from peanut nodules, through tri-parental mating. Microscopic observation and peanut inoculation assays confirmed the successful GFP tagging of Lb8, which is capable of generating root nodules. A marking system for peanut root potential infection sites and an optimized sample preparation protocol for cryostat sectioning was developed. The feasibility of using the GFP-tagged Lb8 for observing crack entry was examined. GFP signal was detected at the nodule primordial stage and the following nodule developmental stages with robust GFP signals observed in infected cells in the mature nodules. Spherical bacteroids in the root tissue were visualized at the nodules' inner cortex under higher magnification, reflecting the trace along the rhizobial infection path. The GFP labeled Lb8 can serve as an essential tool for plant-microbe studies between the cultivated peanut and Bradyrhizobium, which could facilitate further study of the crack entry process during the legume-rhizobia symbiosis.

RevDate: 2023-06-02

de Souza MR, Caruso C, Ruiz-Jones L, et al (2023)

Importance of depth and temperature variability as drivers of coral symbiont composition despite a mass bleaching event.

Scientific reports, 13(1):8957.

Coral reefs are iconic examples of climate change impacts because climate-induced heat stress causes the breakdown of the coral-algal symbiosis leading to a spectacular loss of color, termed 'coral bleaching'. To examine the fine-scale dynamics of this process, we re-sampled 600 individually marked Montipora capitata colonies from across Kāne'ohe Bay, Hawai'i and compared the algal symbiont composition before and after the 2019 bleaching event. The relative proportion of the heat-tolerant symbiont Durusdinium in corals increased in most parts of the bay following the bleaching event. Despite this widespread increase in abundance of Durusdinium, the overall algal symbiont community composition was largely unchanged, and hydrodynamically defined regions of the bay retained their distinct pre-bleaching compositions. We explain ~ 21% of the total variation, of which depth and temperature variability were the most significant environmental drivers of Symbiodiniaceae community composition by site regardless of bleaching intensity or change in relative proportion of Durusdinium. We hypothesize that the plasticity of symbiont composition in corals may be constrained to adaptively match the long-term environmental conditions surrounding the holobiont, despite an individual coral's stress and bleaching response.

RevDate: 2023-06-02

Shi G, Hou R, Li T, et al (2023)

Effects of biochar and freeze‒thaw cycles on the bacterial community and multifunctionality in a cold black soil area.

Journal of environmental management, 342:118302 pii:S0301-4797(23)01090-3 [Epub ahead of print].

Global climate change has altered soil freeze‒thaw cycle events, and little is known about soil microbe response to and multifunctionality regarding freeze‒thaw cycles. Therefore, in this study, biochar was used as a material to place under seasonal freeze-thaw cycling conditions. The purpose of this study was to explore the ability of biochar to regulate the function of freeze-thaw soil cycles to ensure spring sowing and food production. The results showed that biochar significantly increased the richness and diversity of soil bacteria before and after freezing-thawing. In the freezing period, the B50 treatment had the greatest improvement effect (2.6% and 5.5%, respectively), while in the thawing period, the B75 treatment had the best improvement effect. Biochar changed the composition and distribution characteristics of the bacterial structure and enhanced the multifunctionality of freeze-thaw soil and the stability of the bacterial symbiotic network. Compared with the CK treatment, the topological characteristics of the bacterial ecological network of the B50 treatment increased the most. They were 0.89 (, 9.79 (Modularity), 9 (Nodes), and 255 (Links). The freeze-thaw cycle decreased the richness and diversity of the bacterial community and changed the composition and distribution of the bacterial community, and the total bacterial population decreased by 658 (CK), 394 (B25), 644 (B50) and 86 (B75) during the thawing period compared with the freezing period. The soil multifunctionality in the freezing period was higher than that during the thawing period, indicating that the freeze-thaw cycle reduced soil ecological function. From the perspective of abiotic analysis, the decrease in soil multifunctionality was due to the decrease in soil nutrients, enzyme activities, soil basic respiration and other singular functions. From the perspective of bacteria, the decrease in soil multifunctionality was mainly due to the change in the Actinobacteriota group. This work expands the understanding of biochar ecology in cold black soil. These results are conducive to the sustainable development of soil ecological function in cold regions and ultimately ensure crop growth and food productivity.

RevDate: 2023-06-02

Yazıcı E, Alakaş HM, T Eren (2023)

Prioritizing of sectors for establishing a sustainable industrial symbiosis network with Pythagorean fuzzy AHP- Pythagorean fuzzy TOPSIS method: a case of industrial park in Ankara.

Environmental science and pollution research international [Epub ahead of print].

Difficulty in accessing resources and increasing environmental concerns encourage industrial manufacturing enterprises to establish a symbiosis network. The identification of symbiotic relationships contributes to the more sustainable development of industrial activities. However, businesses operating in industrial parks are diversified by sector. In order to establish a sustainable symbiosis network in industrial parks, the symbiotic relations of each sector in industrial parks should be evaluated separately. Thus, the installation process of the symbiosis network will be easier and more sustainable. In this context, this study aims to prioritize the sector in which a symbiosis network will be established by presenting an innovative approach for the evaluation of symbiosis potentials. For this purpose, criteria for the implementation process affecting the establishment of the symbiosis network were determined. Multi-criteria decision-making methods were used to solve the problem. Considering the uncertainties in the process, fuzzy multi-criteria decision-making methods were used. As a result, a decision-making model has been proposed to determine the priority sector in order to establish a symbiosis network in industrial parks. According to the results obtained with the multi-criteria decision-making methods, the number of enterprises that will evaluate the waste, that is, the number of customers with waste, has been determined as the criterion with the highest level of importance. While evaluating the alternatives, the casting sector was chosen as a priority. This sector is followed by the petro and chemical sector as the second alternative.

RevDate: 2023-06-02

Rodrigues J, Lefoulon E, Gavotte L, et al (2023)

Wolbachia springs eternal: symbiosis in Collembola is associated with host ecology.

Royal Society open science, 10(5):230288 pii:rsos230288.

Wolbachia are endosymbiotic alpha-proteobacteria infecting a wide range of arthropods and nematode hosts with diverse interactions, from reproductive parasites to obligate mutualists. Their taxonomy is defined by lineages called supergroups (labelled by letters of the alphabet), while their evolutionary history is complex, with multiple horizontal transfers and secondary losses. One of the least recently derived, supergroup E, infects springtails (Collembola), widely distributed hexapods, with sexual and/or parthenogenetic populations depending on species. To better characterize the diversity of Wolbachia infecting springtails, the presence of Wolbachia was screened in 58 species. Eleven (20%) species were found to be positive, with three Wolbachia genotypes identified for the first time in supergroup A. The novel genotypes infect springtails ecologically and biologically different from those infected by supergroup E. To root the Wolbachia phylogeny, rather than distant other Rickettsiales, supergroup L infecting plant-parasitic nematodes was used here. We hypothesize that the ancestor of Wolbachia was consumed by soil-dwelling nematodes, and was transferred horizontally via plants into aphids, which then infected edaphic arthropods (e.g. springtails and oribatid mites) before expanding into most clades of terrestrial arthropods and filarial nematodes.

RevDate: 2023-06-02

Smith MJ, JE Geach (2023)

Astronomia ex machina: a history, primer and outlook on neural networks in astronomy.

Royal Society open science, 10(5):221454 pii:rsos221454.

In this review, we explore the historical development and future prospects of artificial intelligence (AI) and deep learning in astronomy. We trace the evolution of connectionism in astronomy through its three waves, from the early use of multilayer perceptrons, to the rise of convolutional and recurrent neural networks, and finally to the current era of unsupervised and generative deep learning methods. With the exponential growth of astronomical data, deep learning techniques offer an unprecedented opportunity to uncover valuable insights and tackle previously intractable problems. As we enter the anticipated fourth wave of astronomical connectionism, we argue for the adoption of GPT-like foundation models fine-tuned for astronomical applications. Such models could harness the wealth of high-quality, multimodal astronomical data to serve state-of-the-art downstream tasks. To keep pace with advancements driven by Big Tech, we propose a collaborative, open-source approach within the astronomy community to develop and maintain these foundation models, fostering a symbiotic relationship between AI and astronomy that capitalizes on the unique strengths of both fields.

RevDate: 2023-06-02

Gu Y, Han W, Wang Y, et al (2023)

Xylocopa caerulea and Xylocopa auripennis harbor a homologous gut microbiome related to that of eusocial bees.

Frontiers in microbiology, 14:1124964.

BACKGROUND: Eusocial bees, such as bumblebees and honey bees, harbor host-specific gut microbiota through their social behaviors. Conversely, the gut microbiota of solitary bees is erratic owing to their lack of eusocial activities. Carpenter bees (genus Xylocopa) are long-lived bees that do not exhibit advanced eusociality like honey bees. However, they often compete for nests to reproduce. Xylocopa caerulea and Xylocopa auripennis are important pollinators of wild plants on Hainan Island. Whether they have host-specific bacteria in their guts similar to eusocial bees remains unknown.

METHODS: We targeted the bacterial 16S rRNA V3-V4 region to investigate the diversity of bacterial symbionts in the fore-midgut and hindgut of two carpenter bees, X. caerulea and X. auripennis.

RESULTS: A maximum of 4,429 unique amplicon sequence variants (ASVs) were detected from all samples, belonging to 10 different phyla. X. caerulea and X. auripennis shared similar bacterial community profiles, with Lactobacillaceae, Bifidobacteriaceae, and Orbaceae being dominant in their entire guts. X. caerulea and X. auripennis harbor a highly conserved core set of bacteria, including the genera Candidatus Schmidhempelia and Bombiscardovia. These two bacterial taxa from carpenter bees are closely related to those isolated from bumblebees. The LEfSe analysis showed that Lactobacillaceae, Bifidobacteriaceae, and the genus Bombilactobacillus were significantly enriched in the hindguts of both carpenter bees. Functional prediction suggested that the most enriched pathways were involved in carbohydrate and lipid metabolism.

CONCLUSIONS: Our results revealed the structure of the gut microbiota in two carpenter bees and confirmed the presence of some core bacterial taxa that were previously only found in the guts of social bees.

RevDate: 2023-06-02

N M Furtado A, Leonardi M, Comandini O, et al (2023)

Restinga ectomycorrhizae: a work in progress.

F1000Research, 12:317.

Background: The Brazilian Atlantic Forest is one of the most biodiverse terrestrial ecoregions of the world. Among its constituents, restinga vegetation makes a particular case, acting as a buffer zone between the oceans and the forest. Covering some 80% of Brazilian coastline (over 7,300 km in length), restinga is a harsh environment where plants and fungi interact in complex ways that just now are beginning to be unveiled. Ectomycorrhizal symbiosis, in particular, plays a so far ungauged and likely underestimated role. We recently described the morpho-anatomical and molecular features of the ectomycorrhizae formed by several basidiomycetous mycobionts on the host plant Guapira opposita, but the mycorrhizal biology of restinga is still largely unexplored. Here, we report new data on the ectomycorrhizal fungal symbionts of G. opposita, based on the collection of sporomata and ectomycorrhizal root tips in restinga stands occurring in southern Brazil. Methods: To obtain a broader view of restinga mycorrhizal and ecological potential, we compiled a comprehensive and up-to-date checklist of fungal species reported or supposed to establish ectomycorrhizae on restinga-inhabiting host plants, mainly on the basis of field observations. Results: Our list comprises some 726 records, 74 of which correspond to putative ectomycorrhizal taxa specifically associated with restinga. These include several members of Boletaceae, Amanita, Tomentella/ Thelephora, Russula/ Lactifluus, and Clavulina, as well as hypogeous fungi, like the recently described Longistriata flava. Conclusions: Our survey reveals a significant diversity of the restinga ectomycorrhizal mycobiota, indicating the importance of this symbiosis for the ecological functioning of a unique yet poorly known and threatened ecosystem.

RevDate: 2023-06-02

Windsor FM (2023)

Expanding network ecology in freshwater ecosystems.

The Journal of animal ecology [Epub ahead of print].

Research in freshwater ecosystems has always had a strong focus on ecological interactions. The vast majority of studies, however, have investigated trophic interactions and food webs, overlooking a wider suite of non-trophic interactions (e.g. facilitation, competition, symbiosis and parasitism) and the ecological networks they form. Without a complete understanding of all potential interactions, ranging from mutualistic through to antagonistic, we may be missing important ecological processes with consequences for ecosystem assembly, structure and function. Ecological networks can be constructed at different scales, from genes to ecosystems, but also local to global, and as such there is significant opportunity to put them to work in freshwater research. To expand beyond food webs, we need to leverage technological and methodological advances and look to recent research in marine and terrestrial systems-which are far more advanced in terms of detecting, measuring and contextualising ecological interactions. Future studies should look to emerging technologies to aid in merging the wide range of ecological interactions in freshwater ecosystems into networks to advance our understanding and ultimately increase the efficacy of conservation, management, restoration and other applications.

RevDate: 2023-06-01

Wicaksono WA, Semler B, Pöltl M, et al (2023)

The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts.

Environmental microbiome, 18(1):46.

BACKGROUND: The microbiota of liverworts provides an interesting model for plant symbioses; however, their microbiome assembly is not yet understood. Here, we assessed specific factors that shape microbial communities associated with Riccia temporary agricultural crusts in harvested fields by investigating bacterial, fungal and archaeal communities in thalli and adhering soil from different field sites in Styria and Burgenland, Austria combining qPCR analyses, amplicon sequencing and advanced microscopy.

RESULTS: Riccia spec. div. was colonized by a very high abundance of bacteria (10[10] 16S rRNA gene copies per g of thallus) as well as archaea and fungi (10[8] ITS copies per g of thallus). Each Riccia thallus contain approx. 1000 prokaryotic and fungal ASVs. The field type was the main driver for the enrichment of fungal taxa, likely due to an imprint on soil microbiomes by the cultivated crop plants. This was shown by a higher fungal richness and different fungal community compositions comparing liverwort samples collected from pumpkin fields, with those from corn fields. In contrast, bacterial communities linked to liverworts are highly specialized and the soil attached to them is not a significant source of these bacteria. Specifically, enriched Cyanobacteria, Bacteroidetes and Methylobacteria suggest a symbiotic interaction. Intriguingly, compared to the surrounding soil, the thallus samples were shown to enrich several well-known bacterial and fungal phytopathogens indicating an undescribed role of liverworts as potential reservoirs of crop pathogens.

CONCLUSIONS: Our results provide evidence that a stable bacterial community but varying fungal communities are colonizing liverwort thalli. Post-harvest, temporary agricultural biocrusts are important reservoirs for microbial biodiversity but they have to be considered as potential reservoirs for pathogens as well.

RevDate: 2023-06-01

Sen A, Tanguy G, Galand PE, et al (2023)

Bacterial symbiont diversity in Arctic seep Oligobrachia siboglinids.

Animal microbiome, 5(1):30.

BACKGROUND: High latitude seeps are dominated by Oligobrachia siboglinid worms. Since these worms are often the sole chemosymbiotrophic taxon present (they host chemosynthetic bacteria within the trophosome organ in their trunk region), a key question in the study of high latitude seep ecology has been whether they harbor methanotrophic symbionts. This debate has manifested due to the mismatch between stable carbon isotope signatures of the worms (lower than -50‰ and usually indicative of methanotrophic symbioses) and the lack of molecular or microscopic evidence for methanotrophic symbionts. Two hypotheses have circulated to explain this paradox: (1) the uptake of sediment carbon compounds with depleted δC[13] values from the seep environment, and (2) a small, but significant and difficult to detect population of methanotrophic symbionts. We conducted 16S rRNA amplicon sequencing of the V3-V4 regions on two species of northern seep Oligobrachia (Oligobrachia webbi and Oligobrachia sp. CPL-clade), from four different high latitude sites, to investigate the latter hypothesis. We also visually checked the worms' symbiotic bacteria within the symbiont-hosting organ, the trophosome, through transmission electron microscopy.

RESULTS: The vast majority of the obtained reads corresponded to sulfide-oxidizers and only a very small proportion of the reads pertained to methane-oxidizers, which suggests a lack of methanotrophic symbionts. A number of sulfur oxidizing bacterial strains were recovered from the different worms, however, host individuals tended to possess a single strain, or sometimes two closely-related strains. However, strains did not correspond specifically with either of the two Oligobrachia species we investigated. Water depth could play a role in determining local sediment bacterial communities that were opportunistically taken up by the worms. Bacteria were abundant in non-trophosome (and thereby symbiont-free) tissue and are likely epibiotic or tube bacterial communities.

CONCLUSIONS: The absence of methanotrophic bacterial sequences in the trophosome of Arctic and north Atlantic seep Oligobrachia likely indicates a lack of methanotrophic symbionts in these worms, which suggests that nutrition is sulfur-based. This is turn implies that sediment carbon uptake is responsible for the low δ[13]C values of these animals. Furthermore, endosymbiotic partners could be locally determined, and possibly only represent a fraction of all bacterial sequences obtained from tissues of these (and other) species of frenulates.

RevDate: 2023-06-01

Noel B, Denoeud F, Rouan A, et al (2023)

Pervasive tandem duplications and convergent evolution shape coral genomes.

Genome biology, 24(1):123.

BACKGROUND: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species.

RESULTS: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience.

CONCLUSIONS: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

RevDate: 2023-06-01

Veglia AJ, Bistolas KSI, Voolstra CR, et al (2023)

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes.

Communications biology, 6(1):566.

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

RevDate: 2023-06-01

Belser C, Poulain J, Labadie K, et al (2023)

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.

Scientific data, 10(1):326.

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

RevDate: 2023-06-01

Yee DP, Samo TJ, Abbriano RM, et al (2023)

The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis.

Current biology : CB pii:S0960-9822(23)00615-2 [Epub ahead of print].

Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.[1] These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.[2] However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H[+]-ATPase (VHA),[3] proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.[4][,][5] We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates[6][,][7][,][8] provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.

RevDate: 2023-06-01

Hong H, Wang L, Y Qi (2023)

Characteristics of the oropharyngeal microbiota among infants with pneumonia and their effects on immune response and subsequent respiratory morbidity.

European journal of pediatrics [Epub ahead of print].

UNLABELLED: Changes in airway microbiota among infants with pneumonia and their impact on subsequent respiratory health are largely unknown. The present study aimed to analyze the oropharyngeal microbiota of infants with pneumonia and to explore the impact of disturbances of the microbiota on disease severity and long-term respiratory morbidities. The oropharyngeal microbiome was characterized using 16S ribosomal RNA-based sequencing, while serum immune mediators were assessed using cytometric bead array, and invariant natural killer T (iNKT) cells were detected using flow cytometry in infants with pneumonia < 6 months of age. Patients were followed up to 3 years of age, and clinical and respiratory morbidity data were collected. A total of 106 infants with pneumonia were enrolled in this study. Diversity of the respiratory microbiota was inversely correlated with the severity of pneumonia and length of hospitalization. Patients who experienced wheezing during pneumonia exhibited lower percentages of total iNKT cells, CD8-positive (+), and CD4-CD8- subsets, and higher CD4 + subsets than those without. The relative abundances of Prevotella and Veillonella species were lower in patients with severe pneumonia. The abundance of Veillonella was higher in patients who experienced wheezing during pneumonia and in those with subsequent recurrent wheezing than in those without wheezing. The relative abundance and total counts of Bifidobacterium, Lactobacillus, and Neisseria were higher in patients who did not experience subsequent recurrent wheezing.

CONCLUSIONS: Diversity of the respiratory microbiota was inversely associated with pneumonia severity, and the percentage of iNKT cells was associated with wheezing during pneumonia. Several species may be associated with subsequent respiratory morbidities and warrant further investigation.

WHAT IS KNOWN: • Early life airway microbiota symbiosis affects the severity of respiratory infection and the risk for the development of asthma. • Changes in airway microbiota among infants with pneumonia and their impact on subsequent respiratory health are largely unknown.

WHAT IS NEW: • The diversity of the airway microbiome was inversely associated with the severity of pneumonia and length of hospitalization. • The abundance of Veillonella was higher in patients who experienced wheezing during pneumonia and in those with subsequent recurrent wheezing.

RevDate: 2023-06-01

Lu Y, Lin Y, Li M, et al (2023)

Roles of Streptococcus mutans-Candida albicans interaction in early childhood caries: a literature review.

Frontiers in cellular and infection microbiology, 13:1151532.

As one of the most common oral diseases in kids, early childhood caries affects the health of children throughout the world. Clinical investigations show the copresence of Candida albicans and Streptococcus mutans in ECC lesions, and mechanistic studies reveal co-existence of C. albicans and S. mutans affects both of their cariogenicity. Clearly a comprehensive understanding of the interkingdom interaction between these two microorganisms has important implications for ECC treatment and prevention. To this end, this review summarizes advances in our understanding of the virulence of both C. albicans and S. mutans. More importantly, the synergistic and antagonistic interactions between these two microbes are discussed.

RevDate: 2023-06-01

Ballesteros-Gutiérrez M, Albareda M, Barbas C, et al (2023)

A host-specific diaminobutyrate aminotransferase contributes to symbiotic performance, homoserine metabolism, and competitiveness in the Rhizobium leguminosarum/Pisum sativum system.

Frontiers in microbiology, 14:1182563.

Rhizobium leguminosarum bv. viciae (Rlv) UPM791 effectively nodulates pea and lentil, but bacteroids contain a number of proteins differentially expressed depending on the host. One of these host-dependent proteins (C189) is similar to a diaminobutyrate-2-oxoglutarate aminotransferase (DABA-AT). DABA-AT activity was demonstrated with cell extracts and with purified protein, so C189 was renamed as Dat. The dat gene was strongly induced in the central, active area of pea nodules, but not in lentil. Mutants defective in dat were impaired in symbiotic performance with pea plants, exhibiting reduced shoot dry weight, smaller nodules, and a lower competitiveness for nodulation. In contrast, there were no significant differences between mutant and wild-type in symbiosis with lentil plants. A comparative metabolomic approach using cell-free extracts from bacteroids induced in pea and lentil showed significant differences among the strains in pea bacteroids whereas no significant differences were found in lentil. Targeted metabolomic analysis revealed that the dat mutation abolished the presence of 2,4-diaminobutyrate (DABA) in pea nodules, indicating that DABA-AT reaction is oriented toward the production of DABA from L-aspartate semialdehyde. This analysis also showed the presence of L-homoserine, a likely source of aspartate semialdehyde, in pea bacteroids but not in those induced in lentil. The dat mutant showed impaired growth when cells were grown with L-homoserine as nitrogen source. Inclusion of DABA or L-homoserine as N source suppressed pantothenate auxotropy in Rlv UPM791, suggesting DABA as source of the pantothenate precursor β-alanine. These data indicate that Rlv UPM791 Dat enzyme is part of an adaptation mechanism of this bacterium to a homoserine-rich environment such as pea nodule and rhizosphere.

RevDate: 2023-05-31

Garritano AN, Majzoub ME, Ribeiro B, et al (2023)

Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae.

The ISME journal [Epub ahead of print].

Sponges thrive in the deep, dark and nutrient-depleted ocean and may rely on microbial symbionts for carbon acquisition and energy generation. However, these symbiotic relationships remain largely unexplored. In this study, we analyze the microbiome of deep-sea sponges and show that ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae make up at least 75% of the microbial communities of the sponges Aphrocallistes sp., Farrea sp. and Paratimea sp.. Given the known autotrophic metabolism of AOAs, this implies that these sponge holobionts can have the capacity for primary production in the deep-sea. We also show that specific AOA lineages are highly specific towards their hosts, hinting towards an unprecedent vertical transmission of these symbionts in deep-sea sponges. Our results show that the ecology and evolution of symbiotic relationships in deep-sea sponge is distinct from that of their shallow-water counterparts.

RevDate: 2023-05-31

Teulet A, Quan C, Evangelisti E, et al (2023)

A pathogen effector FOLD diversified in symbiotic fungi.

The New phytologist [Epub ahead of print].

Pathogenic fungi use secreted effector proteins to suppress immunity and support their infection, but effectors have also been reported from fungi that engage in nutritional symbioses with plants. Sequence-based effector comparisons between pathogens and symbiotic arbuscular mycorrhizal (AM) fungi are hampered by the huge diversity of effector sequences even within closely related microbes. To find sequence-divergent but structurally similar effectors shared between symbiotic and pathogenic fungi, we compared secreted protein structure models of the AM fungus Rhizophagus irregularis to known pathogen effectors. We identified proteins with structural similarity to known Fusarium oxysporum f. sp. lycopersici dual domain (FOLD) effectors, which occur in low numbers in several fungal pathogens. Contrastingly, FOLD genes from AM fungi (MycFOLDs) are found in enlarged and diversified gene families with higher levels of positive selection in their C-terminal domains. Our structure model comparison suggests that MycFOLDs are similar to carbohydrate-binding motifs. Different MycFOLD genes are expressed during colonisation of different hosts and MycFOLD-17 transcripts accumulate in plant intracellular arbuscules. The exclusive presence of MycFOLDs across unrelated plant-colonising fungi, their inducible expression, lineage-specific sequence diversification and transcripts in arbuscules suggest that FOLD proteins act as effectors during plant colonisation of symbiotic and pathogenic fungi.

RevDate: 2023-05-31

Costa-Conceicao K, Villamar Ayala CA, Dávila T, et al (2023)

Performance of hybrid biofilter based on rice husks/sawdust treating grey wastewater.

Water science and technology : a journal of the International Association on Water Pollution Research, 87(10):2416-2431.

An innovative nature-based technology for wastewater treatment is the hybrid biofiltration, which combines complex symbiotic relationships between plants, earthworms and microorganisms with adequate support components. This latter could be optimized using organic supports. The aim of this research was to evaluate the performance of hybrid biofilters based on rice husks/sawdust treating grey wastewater from mining camps. Four biofilters using an active layer (rice husks/sawdust: 50/50%, v/v) at 60(B60) and 45(B45) cm height and operating for 64 days at a hydraulic loading rate between 1 and 5 m[3]/m[2]d were monitored. Eisenia foetida Savigny and Cyperus papyrus L. were used as a biotic component. COD, N-NH4[+], NO3[-], NO2[-], PO4[3-] and fecal coliforms were weekly monitored. Results showed that the most efficient HB was using 60 cm as an active layer and operating at 3 m[3]/m[2]d, which reported average removal efficiencies for COD, NH4[+], NO3[-], PO4[3-] and fecal coliforms up to 85, 89, 47, 49 and 99.9%, respectively. Organic support improved the rate growth for Cyperus papirus L. and E. foetida Savigny up to 50%. Hybrid biofiltration using organic residues is low-cost, providing all-encompassing operational and performance features, improving the wastewater reclamation opportunities.

RevDate: 2023-05-31

Mihirogi Y, Kaneda M, Yamagishi D, et al (2023)

Establishment of a New Model Sea Anemone for Comparative Studies on Cnidarian-Algal Symbiosis.

Zoological science, 40(3):235-245.

Frequent coral bleaching has drawn attention to the mechanisms of coral dinoflagellate endosymbiosis. Owing to the difficulty of rearing corals in the laboratory, model symbiosis systems are desired. The sea anemone Exaiptasia diaphana, hosting clade B1 of the genus Breviolum, has long been studied as a model system; however, a single species is insufficient for comparative studies and thus provides only limited resources for symbiosis research, especially regarding the specificity of host-symbiont associations. We established a clonal strain of the sea anemone Anthopleura atodai, whose symbiont was identified as a novel subclade of Symbiodinium (clade A) using a novel feeding method. We also developed a method to efficiently bleach various sea anemone species using a quinoclamine-based herbicide. Bleached A. atodai polyps were vital and able to reproduce asexually, exhibiting no signs of harmful effects of the drug treatment. Pilot studies have suggested that host-symbiont specificity is influenced by multiple steps differently in A. atodai and E. diaphana. RNAseq analyses of A. atodai showed that multiple NPC2 genes were expressed in the symbiotic state, which have been suggested to function in the transport of sterols from symbionts to host cells. These results reveal the usefulness of A. atodai in comparative studies of cnidarian-algal symbiosis.

RevDate: 2023-05-31

Kobayashi G, Itoh H, N Nakajima (2023)

Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes.

Zoological science, 40(3):224-234.

Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.

RevDate: 2023-05-31

Kaur S, Espinosa-Sáiz D, Velázquez E, et al (2023)

Complete Genome Sequences of the Species Type Strains Sinorhizobium garamanticum LMG 24692 and Sinorhizobium numidicum LMG 27395 and CIP 109850.

Microbiology resource announcements [Epub ahead of print].

The genus Sinorhizobium comprises rhizobia that fix nitrogen in symbiosis with legumes. To support taxonomic studies of this genus and of rhizobia more broadly, we report complete genome sequences and annotations for the species type strains Sinorhizobium garamanticum LMG 24692 and Sinorhizobium numidicum LMG 27395 and CIP 109850.

RevDate: 2023-05-31

Wangthaisong P, Piromyou P, Songwattana P, et al (2023)

The Type IV Secretion System (T4SS) Mediates Symbiosis between Bradyrhizobium sp. SUTN9-2 and Legumes.

Applied and environmental microbiology [Epub ahead of print].

There has been little study of the type IV secretion system (T4SS) of bradyrhizobia and its role in legume symbiosis. Therefore, broad host range Bradyrhizobium sp. SUTN9-2 was selected for study. The chromosome of Bradyrhizobium sp. SUTN9-2 contains two copies of the T4SS gene, homologous with the tra/trb operons. A phylogenetic tree of the T4SS gene traG was constructed, which exemplified its horizontal transfer among Bradyrhizobium and Mesorhizobium genera. They also showed similar gene arrangements for the tra/trb operons. However, the virD2 gene was not observed in Mesorhizobium, except M. oppotunistum WSM2075. Interestingly, the orientation of copG, traG, and virD2 cluster was unique to the Bradyrhizobium genus. The phylogenetic tree of copG, traG, and virD2 demonstrated that copies 1 and 2 of these genes were grouped in different clades. In addition, the derived mutant and complementation strains of T4SS were investigated in representative legumes Genistoids, Dalbergioids, and Millettiods. When T4SS copy 1 (T4SS1) was deleted, the nodule number and nitrogenase activity decreased. This supports a positive effect of T4SS1 on symbiosis. In addition, delayed nodulation was observed 7 dpi, which was restored by the complementation of T4SS1. Therefore, T4SS plays an important role in the symbiotic interaction between Bradyrhizobium sp. SUTN9-2 and its leguminous hosts. IMPORTANCE SUTN9-2 is a broad host range strain capable of symbiosis with several legumes. Two copies of T4SS clusters belonging to the tra/trb operon are observed on chromosomes with different gene arrangements. We use phylogenetic tree and gene annotation analysis to predict the evolution of the tra/trb operon of rhizobia. Our finding suggests that the gene encoding the T4SS gene among Bradyrhizobium and Mesorhizobium may have coevolution. In addition, Bradyrhizobium has a uniquely arranged copG, traG, and virD2 gene cluster. The results of T4SS1 gene deletion and complementation revealed its positive effect on nodulation. Therefore, T4SS seems to be another determinant for symbiosis. This is the first report on the role of T4SS in Bradyrhizobium symbiosis.

RevDate: 2023-05-31

Rich M (2023)

Phylogenomics reveal that plants colonized land together with their fungal symbiotic partners.

Comptes rendus biologies, 346:1-11.

Most extant land plants establish a mutually beneficial relationship with soil fungi called mycorrhizal symbiosis. From their partners, plants get access to mineral nutrient and water resources transported via a fungal network that acts like an extension of their root systems. Using genetic and molecular tools, we showed that distant plant species use similar molecular mechanisms during the symbiosis. This similarity suggests that those mechanisms were inherited from their last common ancestor, a lineage that emerged from an aquatic environment 450 million years ago. Thus, this plant fungal interaction could have helped the first land plants without structures adapted to soil exploration to survive and colonize this new environment.

RevDate: 2023-05-31

López-García P, D Moreira (2023)

The symbiotic origin of the eukaryotic cell.

Comptes rendus biologies, 346:55-73.

Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.

RevDate: 2023-05-30

Kim JY, Yi MH, Kim M, et al (2023)

Production of Dermatophagoides farinae Having Low Bacterial Content Using Ampicillin.

Journal of immunology research, 2023:9024595.

BACKGROUND: Symbiotic bacteria in house dust mites pose a risk of immunological side effects in the clinical use of immunotherapeutic agents. In this study, we investigated the duration for which the bacterial concentration in Dermatophagoides farinae could be kept low with antibiotic treatment, and whether the allergenic properties of the mite changed under ampicillin treatment.

METHODS: D. farinae was cultivated in the presence of ampicillin powder in an autoclaved medium for 6 weeks. After subsequent subcultures without ampicillin, the mites were harvested, and the extract was prepared. The amounts of bacteria, lipopolysaccharides (LPS), and two major allergens (Der f 1 and Der f 2) were measured. Human bronchial epithelial cells and mice were treated with the D. farinae extract to assess the allergic airway inflammation.

RESULTS: The number of bacteria and level of LPS were reduced by 150-fold and 33-fold, respectively, at least 18 weeks after ampicillin treatment. The concentration of Der f 1 and Der f 2 remained unchanged by ampicillin treatment. The secretion of interleukin (IL)-6 and IL-8 from the human airway epithelial cells decreased when treated with the extract of ampicillin-treated D. farinae compared with that of ampicillin-untreated D. farinae. A mouse asthma model was developed using ampicillin-treated D. farinae. We observed that the level of lung function, airway inflammation, and serum-specific immunoglobulin were not different for the mouse asthma model developed using ampicillin-treated D. farinae than the model developed using ampicillin-untreated D. farinae.

CONCLUSIONS: We showed that bacterial content in D. farinae was reduced by ampicillin treatment, which was sufficient to induce allergic sensitization and an immune response. This method will be used to develop more controlled allergy immunotherapeutic agents.

RevDate: 2023-05-30

Cossart P, Kolter R, Lemaitre B, et al (2023)

The New Microbiology: an international lecture course on the island of Spetses.

microLife, 4:uqac026.

In September 2022, an international summer course entitled 'The new microbiology' took place in Greece, on the island of Spetses. The organizers aimed to highlight the spectacular advances and the renaissance occurring in Microbiology, driven by developments in genomics, proteomics, imaging techniques, and bioinformatics. Combinations of these advances allow for single cell analyses, rapid and relatively inexpensive metagenomic and transcriptomic data analyses and comparisons, visualization of previously unsuspected mechanisms, and large-scale studies. A 'New Microbiology' is emerging which allows studies that address the critical roles of microbes in health and disease, in humans, animals, and the environment. The concept of one health is now transforming microbiology. The goal of the course was to discuss all these topics with members of the new generation of microbiologists all of whom were highly motivated and fully receptive.

RevDate: 2023-05-30

Wu-Chuang A, Hartmann D, Maitre A, et al (2023)

Variation of bacterial community assembly over developmental stages and midgut of Dermanyssus gallinae.

Microbial ecology [Epub ahead of print].

Bacterial microbiota play an important role in the fitness of arthropods, but the bacterial microflora in the parasitic mite Dermanyssus gallinae is only partially explored; there are gaps in our understanding of the microbiota localization and in our knowledge of microbial community assembly. In this work, we have visualized, quantified the abundance, and determined the diversity of bacterial occupancy, not only across developmental stages of D. gallinae, but also in the midgut of micro-dissected female D. gallinae mites. We explored community assembly and the presence of keystone taxa, as well as predicted metabolic functions in the microbiome of the mite. The diversity of the microbiota and the complexity of co-occurrence networks decreased with the progression of the life cycle. However, several bacterial taxa were present in all samples examined, indicating a core symbiotic consortium of bacteria. The relatively higher bacterial abundance in adult females, specifically in their midguts, implicates a function linked to the biology of D. gallinae mites. If such an association proves to be important, the bacterial microflora qualifies itself as an acaricidal or vaccine target against this troublesome pest.

RevDate: 2023-05-30

Fields B, Moeskjaer S, Deakin WJ, et al (2023)

Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions.

Molecular ecology [Epub ahead of print].

While shaping of plant microbiome composition through 'host filtering' is well documented in legume-rhizobium symbioses, it is less clear to what extent different varieties and genotypes of the same plant species differentially influence symbiont community diversity and composition. Here, we compared how clover host varieties and genotypes affect the structure of Rhizobium populations in root nodules under conventional field and controlled greenhouse conditions. We first grew four Trifolium repens (white clover) F2 crosses and one variety in a conventional field trial and compared differences in root nodule Rhizobium leguminosarum symbiovar trifolii (Rlt) genotype diversity using high-throughput amplicon sequencing of chromosomal housekeeping (rpoB and recA) genes and auxiliary plasmid-borne symbiosis genes (nodA and nodD). We found that Rlt nodule diversities significantly differed between clover crosses, potentially due to host filtering. However, variance in Rlt diversity largely overlapped between crosses and was also explained by the spatial distribution of plants in the field, indicative of the role of local environmental conditions for nodule diversity. To test the effect of host filtering, we conducted a controlled greenhouse trial with a diverse Rlt inoculum and several host genotypes. We found that different clover varieties and genotypes of the same variety selected for significantly different Rlt nodule communities and that the strength of host filtering (deviation from the initial Rhizobium inoculant composition) was positively correlated with the efficiency of symbiosis (rate of plant greenness colouration). Together, our results suggest that selection by host genotype and local growth conditions jointly influence white clover Rlt nodule diversity and community composition.

RevDate: 2023-05-29

Liu Y, Shu X, Chen L, et al (2023)

Plant commensal type VII secretion system causes iron leakage from roots to promote colonization.

Nature microbiology [Epub ahead of print].

Competition for iron is an important factor for microbial niche establishment in the rhizosphere. Pathogenic and beneficial symbiotic bacteria use various secretion systems to interact with their hosts and acquire limited resources from the environment. Bacillus spp. are important plant commensals that encode a type VII secretion system (T7SS). However, the function of this secretion system in rhizobacteria-plant interactions is unclear. Here we use the beneficial rhizobacterium Bacillus velezensis SQR9 to show that the T7SS and the major secreted protein YukE are critical for root colonization. In planta experiments and liposome-based experiments demonstrate that secreted YukE inserts into the plant plasma membrane and causes root iron leakage in the early stage of inoculation. The increased availability of iron promotes root colonization by SQR9. Overall, our work reveals a previously undescribed role of the T7SS in a beneficial rhizobacterium to promote colonization and thus plant-microbe interactions.

RevDate: 2023-05-29

Peters EE, Cahn JKB, Lotti A, et al (2023)

Distribution and diversity of 'Tectomicrobia', a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites.

ISME communications, 3(1):50.

Genomic and functional analyses of bacterial sponge symbionts belonging to the uncultivated candidate genus 'Entotheonella' has revealed them as the prolific producers of bioactive compounds previously identified from their invertebrate hosts. These studies also suggested 'Entotheonella' as the first members of a new candidate phylum, 'Tectomicrobia'. Here we analyzed the phylogenetic structure and environmental distribution of this as-yet sparsely populated phylum-like lineage. The data show that 'Entotheonella' and other 'Tectomicrobia' are not restricted to marine habitats but widely distributed among terrestrial locations. The inferred phylogenetic trees suggest several intra-phylum lineages with diverse lifestyles. Of these, the previously described 'Entotheonella' lineage can be more accurately divided into at least three different candidate genera with the terrestrial 'Candidatus Prasianella', the largely terrestrial 'Candidatus Allonella', the 'Candidatus Thalassonella' comprising sponge-associated members, and the more widely distributed 'Candidatus Entotheonella'. Genomic characterization of 'Thalassonella' members from a range of sponge hosts did not suggest a role as providers of natural products, despite high genomic similarity to 'Entotheonella' regarding primary metabolism and implied lifestyle. In contrast, the analysis revealed a correlation between the revised 'Entotheonella' 16S rRNA gene phylogeny and a specific association with sponges and their natural products. This feature might serve as a discovery method to accelerate the identification of new chemically rich 'Entotheonella' variants, and led to the identification of the first 'Entotheonella' symbiont in a non-tetractinellid sponge, Psammocinia sp., indicating a wide host distribution of 'Entotheonella'-based chemical symbiosis.

RevDate: 2023-05-29

Shi J, Wang W, Wang F, et al (2023)

Efficient inactivation of harmful algae K. mikimotoi by a novel algicidal bacterium via a rare direct contact pathway: Performances and mechanisms.

The Science of the total environment pii:S0048-9697(23)03022-X [Epub ahead of print].

Harmful algal blooms (HABs) caused by Karenia mikimotoi have posed great threats to marine ecosystems, and algal inactivation by symbiotic bacteria has been recognized as environmental benign methods for controlling HABs. However, the identified algicidal bacteria for K. mikimotoi is limited and exclusively based on indirect algicidal pathways, which may cause secondary pollution due to releasing toxic algicidal agents. In this study, a novel strain of algicidal bacteria Tenacibaculum sp. GD3 was isolated from the phycosphere of K. mikimotoi. The bacterial strain GD3 could achieve 92.6 % of inactivation efficiency against K. mikimotoi within 8 h of co-culturing period, which outperformed those in existing literatures reported so far. The algicidal mechanisms were revealed to be a rare direct cell-to-cell contact pathway, and the GD3 could grow by utilizing metabolites from K. mikimotoi, exhibiting excellent bacterial adaptability in the phycosphere. Cell morphology changes were monitored by live cell imaging system combined with SEM and TEM observations, which showed that the GD3 was first attached to the algal cell membrane, followed by lipid peroxidation and lysis of membrane protein. Oxidative stress responses were induced as reveled by up-regulation of intracellular ROSs and antioxidant enzyme activity. Photosynthetic parameters including rETRmax, Fv/Fm, YII and NPQ were reduced, and expression of functional genes involved in decomposition of chlorophyll and cell wall was significantly suppressed. Moreover, the intracellular release profile and acute toxicity assessment indicated that the GD3 could also detoxify the K. mikimotoi cultures and the released biomolecules would not cause adverse effect to marine environment. This study not only provides a novel algicidal bacterium against K. mikimotoi via a rare direct mode, but also helps to better understand the algicidal mechanisms at physiological and genetic level, thus moving forward the areas of HABs control by microbiological strategies.

RevDate: 2023-05-28

Gong X, Ge Z, Ma Z, et al (2023)

Effect of different size microplastic particles on the construction of algal-bacterial biofilms and microbial communities.

Journal of environmental management, 343:118246 pii:S0301-4797(23)01034-4 [Epub ahead of print].

Algal-bacterial symbiotic system is a biological purification system that combines sewage treatment with resource utilization and has the dual effects of carbon sequestration and pollution reduction. In this study, an immobilized algal-bacterial biofilm system was constructed for the treatment of natural sewage. Effects of exposure to microplastics (MPs) with different particle diameters (0.065 μm, 0.5 μm and 5 μm) were determined in terms of algal biomass recovery efficiency, the composition of extracellular polymeric substances (EPS) and morphologic characteristics. The impacts of MPs on the bacterial diversity and community structure of biofilms were also examined. The metagenomic analysis of key microorganisms and related metabolism pathways involved in system was further investigated. Results showed that following exposure to 5 μm MP, a maximum algal recovery efficiency of 80% was achieved, with a minimum PSII primary light energy conversion efficiency (Fv/Fm ratio) of 0.513. Furthermore, 5 μm MP caused the highest level of damage to the algal-bacterial biofilm, enhancing the secretion of protein-rich EPS. The biofilm morphology became rough and loose following exposure to 0.5 μm and 5 μm MP. Community diversity and richness were significantly high in biofilms exposed to 5 μm MP. Proteobacteria (15.3-24.1%), Firmicutes (5.0-7.8%) and Actinobacteria (4.2-4.9%) were dominant in all groups, with exposure to 5 μm MP resulting in the highest relative abundance for these species. The addition of MPs promoted the related metabolic functions while inhibited the degradation of harmful substances by algal-bacterial biofilms. The findings have environmental significance for the practical application of algal-bacterial biofilms for sewage treatment, providing novel insights into the potential effects of MPs on immobilized algal-bacterial biofilm systems.

RevDate: 2023-05-27

Abdi N, Van Biljon A, Steyn C, et al (2023)

Zn Fertilizer and Mycorrhizal Inoculation Effect on Bread Wheat Cultivar Grown under Water Deficit.

Life (Basel, Switzerland), 13(5): pii:life13051078.

During drought stress, many enzymes are inactivated in plants due to Zn deficiency. Zn application and arbuscular mycorrhiza fungi (AMF)-wheat symbiosis reportedly improve the tolerance of plants to drought stress. This study was done to investigate the effect of Zn and AMF on plant growth, yield attributes, relative water content (RWC), harvest index (HI), photosynthetic activity, solute accumulation, glycine betaine (GB) accumulation, antioxidant activities [(catalase (CAT) and superoxide dismutase (SOD)], and ionic attributes in a bread wheat cultivar (SST806) under drought-stress in plants grown under greenhouse conditions. Zn application and AMF inoculation, separately and combined, enhanced all plant growth parameters and yield. Root dry weight (RDW) was increased by 25, 30, and 46% for these three treatments, respectively, under drought conditions compared to the control treatment. Overall, Zn application, AMF inoculation, and their combination increased protein content, RWC, and harvest index (HI) under drought stress. However, AMF inoculation improved proline content more than Zn application under the same conditions. Regarding GB accumulation, AMF, Zn, and the combination of Zn and AMF increased GB under drought compared to well-watered conditions by 31.71, 10.36, and 70.70%, respectively. For the antioxidant defense, AMF inoculation and Zn application improved SOD and CAT activity by 58 and 56%, respectively. This study showed that Zn and/or AMF increased antioxidant levels and ionic attributes under abiotic stress.

RevDate: 2023-05-27

Zuccaro V, Ponziani FR, R Bruno (2023)

Editorial of Special Issues "Gut Microbiota-Host Interactions: From Symbiosis to Dysbiosis 2.0".

International journal of molecular sciences, 24(10): pii:ijms24108977.

The gastrointestinal (GI) tract is where external agents meet the internal environment [...].

RevDate: 2023-05-27

Jia Y, Y Li (2023)

Genome-Wide Identification and Comparative Analysis of RALF Gene Family in Legume and Non-Legume Species.

International journal of molecular sciences, 24(10): pii:ijms24108842.

Rapid alkalinization factor (RALF) are small secreted peptide hormones that can induce rapid alkalinization in a medium. They act as signaling molecules in plants, playing a critical role in plant development and growth, especially in plant immunity. Although the function of RALF peptides has been comprehensively analyzed, the evolutionary mechanism of RALFs in symbiosis has not been studied. In this study, 41, 24, 17 and 12 RALFs were identified in Arabidopsis, soybean, Lotus and Medicago, respectively. A comparative analysis including the molecular characteristics and conserved motifs suggested that the RALF pre-peptides in soybean represented a higher value of isoelectric point and more conservative motifs/residues composition than other species. All 94 RALFs were divided into two clades according to the phylogenetic analysis. Chromosome distribution and synteny analysis suggested that the expansion of the RALF gene family in Arabidopsis mainly depended on tandem duplication, while segment duplication played a dominant role in legume species. The expression levels of most RALFs in soybean were significantly affected by the treatment of rhizobia. Seven GmRALFs are potentially involved in the release of rhizobia in the cortex cells. Overall, our research provides novel insights into the understanding of the role of the RALF gene family in nodule symbiosis.

RevDate: 2023-05-27

Mohammad Aslam S, Vass I, M Szabó (2023)

Characterization of the Flash-Induced Fluorescence Wave Phenomenon in the Coral Endosymbiont Algae, Symbiodiniaceae.

International journal of molecular sciences, 24(10): pii:ijms24108712.

The dinoflagellate algae, Symbiodiniaceae, are significant symbiotic partners of corals due to their photosynthetic capacity. The photosynthetic processes of the microalgae consist of linear electron transport, which provides the energetic balance of ATP and NADPH production for CO2 fixation, and alternative electron transport pathways, including cyclic electron flow, which ensures the elevated ATP requirements under stress conditions. Flash-induced chlorophyll fluorescence relaxation is a non-invasive tool to assess the various electron transport pathways. A special case of fluorescence relaxation, the so-called wave phenomenon, was found to be associated with the activity of NAD(P)H dehydrogenase (NDH) in microalgae. We showed previously that the wave phenomenon existed in Symbiodiniaceae under acute heat stress and microaerobic conditions, however, the electron transport processes related to the wave phenomenon remained unknown. In this work, using various inhibitors, we show that (i) the linear electron transport has a crucial role in the formation of the wave, (ii) the inhibition of the donor side of Photosystem II did not induce the wave, whereas inhibition of the Calvin-Benson cycle accelerated it, (iii) the wave phenomenon was related to the operation of type II NDH (NDH-2). We therefore propose that the wave phenomenon is an important marker of the regulation of electron transport in Symbiodiniaceae.

RevDate: 2023-05-27

Gorshkov AP, Kusakin PG, Borisov YG, et al (2023)

Effect of Triazole Fungicides Titul Duo and Vintage on the Development of Pea (Pisum sativum L.) Symbiotic Nodules.

International journal of molecular sciences, 24(10): pii:ijms24108646.

Triazole fungicides are widely used in agricultural production for plant protection, including pea (Pisum sativum L.). The use of fungicides can negatively affect the legume-Rhizobium symbiosis. In this study, the effects of triazole fungicides Vintage and Titul Duo on nodule formation and, in particular, on nodule morphology, were studied. Both fungicides at the highest concentration decreased the nodule number and dry weight of the roots 20 days after inoculation. Transmission electron microscopy revealed the following ultrastructural changes in nodules: modifications in the cell walls (their clearing and thinning), thickening of the infection thread walls with the formation of outgrowths, accumulation of poly-β-hydroxybutyrates in bacteroids, expansion of the peribacteroid space, and fusion of symbiosomes. Fungicides Vintage and Titul Duo negatively affect the composition of cell walls, leading to a decrease in the activity of synthesis of cellulose microfibrils and an increase in the number of matrix polysaccharides of cell walls. The results obtained coincide well with the data of transcriptomic analysis, which revealed an increase in the expression levels of genes that control cell wall modification and defense reactions. The data obtained indicate the need for further research on the effects of pesticides on the legume-Rhizobium symbiosis in order to optimize their use.

RevDate: 2023-05-27

Koshida K, Ito M, Yakabe K, et al (2023)

Dysfunction of Foxp3[+] Regulatory T Cells Induces Dysbiosis of Gut Microbiota via Aberrant Binding of Immunoglobulins to Microbes in the Intestinal Lumen.

International journal of molecular sciences, 24(10): pii:ijms24108549.

Foxp3[+] regulatory T (Treg) cells prevent excessive immune responses against dietary antigens and commensal bacteria in the intestine. Moreover, Treg cells contribute to the establishment of a symbiotic relationship between the host and gut microbes, partly through immunoglobulin A. However, the mechanism by which Treg cell dysfunction disturbs the balanced intestinal microbiota remains unclear. In this study, we used Foxp3 conditional knockout mice to conditionally ablate the Foxp3 gene in adult mice and examine the relationship between Treg cells and intestinal bacterial communities. Deletion of Foxp3 reduced the relative abundance of Clostridia, suggesting that Treg cells have a role in maintaining Treg-inducing microbes. Additionally, the knockout increased the levels of fecal immunoglobulins and immunoglobulin-coated bacteria. This increase was due to immunoglobulin leakage into the gut lumen as a result of loss of mucosal integrity, which is dependent on the gut microbiota. Our findings suggest that Treg cell dysfunction leads to gut dysbiosis via aberrant antibody binding to the intestinal microbes.

RevDate: 2023-05-27

Bopape FL, Chiulele RM, Shonhai A, et al (2023)

The Genome of a Pigeonpea Compatible Rhizobial Strain '10ap3' Appears to Lack Common Nodulation Genes.

Genes, 14(5): pii:genes14051084.

The symbiotic fixation of atmospheric nitrogen (N) in root nodules of tropical legumes such as pigeonpea (Cajanus cajan) is a complex process, which is regulated by multiple genetic factors at the host plant genotype microsymbiont interface. The process involves multiple genes with various modes of action and is accomplished only when both organisms are compatible. Therefore, it is necessary to develop tools for the genetic manipulation of the host or bacterium towards improving N fixation. In this study, we sequenced the genome of a robust rhizobial strain, Rhizobium tropici '10ap3' that was compatible with pigeonpea, and we determined its genome size. The genome consisted of a large circular chromosome (6,297,373 bp) and contained 6013 genes of which 99.13% were coding sequences. However only 5833 of the genes were associated with proteins that could be assigned to specific functions. The genes for nitrogen, phosphorus and iron metabolism, stress response and the adenosine monophosphate nucleoside for purine conversion were present in the genome. However, the genome contained no common nod genes, suggesting that an alternative pathway involving a purine derivative was involved in the symbiotic association with pigeonpea.

RevDate: 2023-05-27

Beck A, Casanova-Katny A, J Gerasimova (2023)

Metabarcoding of Antarctic Lichens from Areas with Different Deglaciation Times Reveals a High Diversity of Lichen-Associated Communities.

Genes, 14(5): pii:genes14051019.

Lichens have developed numerous adaptations to optimise their survival under harsh abiotic stress, colonise different substrates, and reach substantial population sizes and high coverage in ice-free Antarctic areas, benefiting from a symbiotic lifestyle. As lichen thalli represent consortia with an unknown number of participants, it is important to know about the accessory organisms and their relationships with various environmental conditions. To this end, we analysed lichen-associated communities from Himantormia lugubris, Placopsis antarctica, P. contortuplicata, and Ramalina terebrata, collected from soils with differing deglaciation times, using a metabarcoding approach. In general, many more Ascomycete taxa are associated with the investigated lichens compared to Basidiomycota. Given our sampling, a consistently higher number of lichen-associated eukaryotes are estimated to be present in areas with deglaciation times of longer than 5000 years compared to more recently deglaciated areas. Thus far, members of Dothideomycetes, Leotiomycetes, and Arthoniomycetes have been restricted to the Placopsis specimens from areas with deglaciation times longer than 5000 years. Striking differences between the associated organisms of R. terebrata and H. lugubris have also been discovered. Thus, a species-specific basidiomycete, Tremella, was revealed for R. terebrata, as was a member of Capnodiales for H. lugubris. Our study provides further understanding of the complex terricolous lichen-associated mycobiome using the metabarcoding approach. It also illustrates the necessity to extend our knowledge of complex lichen symbiosis and further improve the coverage of microbial eukaryotes in DNA barcode libraries, including more extended sampling.

RevDate: 2023-05-27

Duncan SH, Conti E, Ricci L, et al (2023)

Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health.

Biomedicines, 11(5): pii:biomedicines11051338.

A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.

RevDate: 2023-05-27

Ribeiro LEGGT, Batista LDSP, Assis CF, et al (2023)

Potentially Synbiotic Yellow Mombin Beverages: Stability during Refrigerated Storage, Physicochemical Characteristics, and Sensory Properties.

Foods (Basel, Switzerland), 12(10): pii:foods12101994.

This study aimed to develop potentially synbiotic yellow mombin (Spondias mombin L.) beverages added with fructooligosaccharides and Lactiplantibacillus plantarum NRRL B-4496. Six formulations of yellow mombin beverages were prepared to measure the influence of fermentation and pH, which was adjustment to 4.5 for stability and quality parameters. Formulations were evaluated for probiotic survival, pH, titratable acidity, total phenolic compounds (TPC), and antioxidant activity for 28 days at 4 °C. Additionally, the proximate composition, color, sensory aspects, and survival to simulated gastrointestinal conditions were studied. At 21 days of storage, the viability of L. plantarum was 9 CFU/mL for the fermented symbiotic (SYNf) and non-fermented symbiotic with adjusted pH (SYNa) formulations. In addition, the fermented synbiotic with an adjusted pH beverage (SYNfA) showed a count of 8.2 log CFU/mL at 28 days. The formulations showed a high TPC (234-431 mg GAE/L), antioxidant activity (48-75 µM trolox), and a potential use as low-calorie beverages. The SYNf formulation showed an acceptability index higher than 70% and a high purchase intent. The SYNf and SYNa formulations maintained suitable probiotic counts after exposure to the simulated gastrointestinal digestion. Therefore, it was possible to develop a new potentially synbiotic yellow mombin beverage with a high sensory acceptance, supplying the market with a new functional food alternative.

RevDate: 2023-05-27

van Wyk N, Binder J, Ludszuweit M, et al (2023)

The Influence of Pichia kluyveri Addition on the Aroma Profile of a Kombucha Tea Fermentation.

Foods (Basel, Switzerland), 12(10): pii:foods12101938.

Traditional kombucha is a functional tea-based drink that has gained attention as a low or non-alcoholic beverage. The fermentation is conducted by a community of different microorganisms, collectively called SCOBY (Symbiotic Culture of Bacteria and Yeast) and typically consists of different acetic acid bacteria and fermenting yeast, and in some cases lactic acid bacteria that would convert the sugars into organic acids-mostly acetic acid. In this study, the effect of including a Pichia kluyveri starter culture in a kombucha fermentation was investigated. P. kluyveri additions led to a quicker accumulation of acetic acid along with the production of several acetate esters including isoamyl acetate and 2-phenethyl acetate. A subsequent tasting also noted a significant increase in the fruitiness of the kombucha. The significant contribution to the aroma content shows the promise of this yeast in future microbial formulations for kombucha fermentations.

RevDate: 2023-05-27

De Sousa BFS, Domingo-Serrano L, Salinero-Lanzarote A, et al (2023)

The T6SS-Dependent Effector Re78 of Rhizobium etli Mim1 Benefits Bacterial Competition.

Biology, 12(5): pii:biology12050678.

The genes of the type VI secretion system (T6SS) from Rhizobium etli Mim1 (ReMim1) that contain possible effectors can be divided into three modules. The mutants in them indicated that they are not required for effective nodulation with beans. To analyze T6SS expression, a putative promoter region between the tssA and tssH genes was fused in both orientations to a reporter gene. Both fusions are expressed more in free living than in symbiosis. When the module-specific genes were studied using RT-qPCR, a low expression was observed in free living and in symbiosis, which was clearly lower than the structural genes. The secretion of Re78 protein from the T6SS gene cluster was dependent on the presence of an active T6SS. Furthermore, the expression of Re78 and Re79 proteins in E. coli without the ReMim1 nanosyringe revealed that these proteins behave as a toxic effector/immunity protein pair (E/I). The harmful action of Re78, whose mechanism is still unknown, would take place in the periplasmic space of the target cell. The deletion of this ReMim1 E/I pair resulted in reduced competitiveness for bean nodule occupancy and in lower survival in the presence of the wild-type strain.

RevDate: 2023-05-27

Pezzino S, Sofia M, Mazzone C, et al (2023)

Gut Microbiome in the Progression of NAFLD, NASH and Cirrhosis, and Its Connection with Biotics: A Bibliometric Study Using Dimensions Scientific Research Database.

Biology, 12(5): pii:biology12050662.

There is growing evidence that gut microbiota dysbiosis is linked to the etiopathogenesis of nonalcoholic fatty liver disease (NAFLD), from the initial stage of disease until the progressive stage of nonalcoholic steatohepatitis (NASH) and the final stage of cirrhosis. Conversely, probiotics, prebiotics, and synbiotics have shown promise in restoring dysbiosis and lowering clinical indicators of disease in a number of both preclinical and clinical studies. Additionally, postbiotics and parabiotics have recently garnered some attention. The purpose of this bibliometric analysis is to assess recent publishing trends concerning the role of the gut microbiome in the progression of NAFLD, NASH and cirrhosis and its connection with biotics. The free access version of the Dimensions scientific research database was used to find publications in this field from 2002 to 2022. VOSviewer and Dimensions' integrated tools were used to analyze current research trends. Research into the following topics is expected to emerge in this field: (1) evaluation of risk factors which are correlated with the progression of NAFLD, such as obesity and metabolic syndrome; (2) pathogenic mechanisms, such as liver inflammation through toll-like receptors activation, or alteration of short-chain fatty acids metabolisms, which contribute to NAFLD development and its progression in more severe forms, such as cirrhosis; (3) therapy for cirrhosis through dysbiosis reduction, and research on hepatic encephalopathy a common consequence of cirrhosis; (4) evaluation of diversity, and composition of gut microbiome under NAFLD, and as it varies under NASH and cirrhosis by rRNA gene sequencing, a tool which can also be used for the development of new probiotics and explore into the impact of biotics on the gut microbiome; (5) treatments to reduce dysbiosis with new probiotics, such as Akkermansia, or with fecal microbiome transplantation.

RevDate: 2023-05-26

Jeon YJ, Gil CH, Won J, et al (2023)

Symbiotic microbiome Staphylococcus epidermidis restricts IL-33 production in allergic nasal epithelium via limiting the cellular necroptosis.

BMC microbiology, 23(1):154.

BACKGROUND: Allergic rhinitis (AR) is characterized by airway inflammation in nasal mucosa from inhaled allergens and interleukin (IL)-33 is the potent inducer of Th2 inflammation in allergic nasal epithelium. Staphylococcus epidermidis is one of the most abundant colonizers of the healthy human nasal mucosa and might impact the allergen-induced inflammatory responses in the nasal epithelium. Thus, we sought to characterize the mechanism of S. epidermidis regulating Th2 inflammation and IL-33 production in AR nasal mucosa.

RESULTS: The AR symptoms were alleviated and eosinophilic infiltration, serum IgE levels, and Th2 cytokines were significantly decreased in OVA-sensitized AR mice in response to human nasal commensal S. epidermidis. The inoculation of S. epidermidis to normal human nasal epithelial cells reduced IL-33 and GATA3 transcriptions and also reduced IL-33 and GATA3 expression in AR nasal epithelial (ARNE) cells and the nasal mucosa of AR mice. Our data exhibited that the cellular necroptosis of ARNE cells might be involved in IL-33 production and inoculation of S. epidermidis decreased the phosphorylation of necroptosis enzymes in ARNE cells, which was related to the reduction of IL-33 production.

CONCLUSIONS: We present that human nasal commensal S. epidermidis reduces allergic inflammation by suppressing IL-33 production in nasal epithelium. Our findings indicate that S. epidermidis serves a role in blocking allergen-induced cellular necroptosis in allergic nasal epithelium which might be a key mechanism of reduction of IL-33 and Th2 inflammation.

RevDate: 2023-05-26

Chen YP, Li SK, An B, et al (2023)

Effects of arbuscular mycorrhizae and extraradical mycelium of subtropical tree species on soil nitrogen mineralization and enzyme activities.

Ying yong sheng tai xue bao = The journal of applied ecology, 34(5):1235-1243.

Through symbiosis with plants, arbuscular mycorrhizal (AM) fungi effectively improve the availability of soil nitrogen (N). However, the mechanism through which AM and associated extraradical mycelium affect soil N mineralization remains unknow. We carried out an in situ soil culture experiment by using in-growth cores in plantations of three subtropical tree species, Cunninghamia lanceolata, Schima superba, and Liquidambar formosana. We measured soil physical and chemical properties, net N mineralization rate, and the activities of four kinds of hydrolase (leucine aminopeptidase (LAP), β-1,4-N-acetylglucosaminidase (NAG), β-1,4-glucosidase (βG), cellobiohydrolase (CB)) and two kinds of oxidases (polyphenol oxidase (POX) and peroxidase (PER)) involved in soil organic matter (SOM) mineralization in treatments of mycorrhiza (with absorbing roots and hyphae), hyphae (hyphae only), and control (mycorrhiza-free). The results showed that mycorrhizal treatments significantly affected soil total carbon and pH but did not affect N mineralization rates and all enzymatic activities. Tree species significantly affected net ammonification rate, net N mineralization rate and activities of NAG, βG, CB, POX and PER. The net N mineralization rate and enzyme activities in the C. lanceolata stand were significantly higher than that in monoculture broad-leaved stands of either S. superba or L. formosana. There was no interactive effect of mycorrhizal treatment and tree species on any of soil properties, nor on enzymatic activities or net N mineralization rates. Soil pH was negatively and significantly correlated with five kinds of enzymatic activities except for LAP, while net N mineralization rate significantly correlated with ammonium nitrogen content, available phosphorus content, and the activity level of βG, CB, POX, and PER. In conclusion, there was no difference in enzymatic activities and N mineralization rates between rhizosphere and hyphosphere soils of three subtropical tree species in the whole growing season. The activity of particular carbon cycle-related enzymes was closely related to soil N mineralization rate. It is suggested that differences in litter quality and root functional traits among different tree species affect soil enzyme activities and N mineralization rates through organic matter inputs and shaping soil condition.

RevDate: 2023-05-26

Kise H, Nishijima M, Iguchi A, et al (2023)

A new hexactinellid-sponge-associated zoantharian (Porifera, Hexasterophora) from the northwestern Pacific Ocean.

ZooKeys, 1156:71-85 pii:96698.

Symbiotic associations between zoantharians and sponges can be divided into two groups: those that associate with Demospongiae and those that associate with Hexactinellida. Parachurabanashinseimaruae Kise, gen. nov. et sp. nov., a new genus and a new species of Hexactinellida-associated zoantharian from Japanese waters, is described. It is characterized by a combination of the following: i) its host hexactinellid sponge, ii) very flat polyps, iii) cteniform endodermal marginal muscles, and iv) characteristic mutations in three mitochondrial regions (including a unique 26-bp deletion in 16S ribosomal DNA) and three nuclear regions. Parachurabanashinseimaruae Kise, gen. nov. et sp. nov. is the third genus in the family Parazoanthidae that is reported to be associated with Hexasterophora sponges. Although specimens have so far only been collected on Takuyo-Daigo Seamount off Minami-Torishima Island in Japan, unidentified zoantharians of similar description have been reported from the waters around Australia, indicating that the species might be widespread across the Pacific.

RevDate: 2023-05-26

LaPolla JS, SA Schneider (2023)

Trophobiosis between a new species of Acropyga (Hymenoptera, Formicidae) and new Neochavesia (Hemiptera, Xenococcidae) from Peru, and establishment of the Acropygasmithii species-group.

ZooKeys, 1154:1-16 pii:97578.

We describe a new pair of trophobiotic partners from the ant genus Acropyga and the root mealybug genus Neochavesia. A recent field study on Acropyga ants and associated root mealybugs, conducted in the Peruvian Amazon, led to the discovery of Acropygamanuense LaPolla & Schneider, sp. nov. and its root mealybug symbiont Neochavesiapodexuta Schneider & LaPolla, sp. nov. The new root mealybug belongs to the family Xenococcidae, whose members are all obligate associates of Acropyga ants. Providing joint descriptions of new mutualist partners in the same article is a novel approach for this system, and it offers benefits to the ongoing study of mutualism and patterns of association among these symbiotic ants and scales. Here, we also begin to revise the species-group composition of Acropyga by establishing the smithii species-group, and we provide updated information to aid in identifying the new ant species and root mealybug species.

RevDate: 2023-05-26

Ueno Y, S Akimoto (2023)

Long-term light adaptation of light-harvesting and energy-transfer processes in the glaucophyte Cyanophora paradoxa under different light conditions.

Photosynthesis research [Epub ahead of print].

In response to fluctuation in light intensity and quality, oxygenic photosynthetic organisms modify their light-harvesting and excitation energy-transfer processes to maintain optimal photosynthetic activity. Glaucophytes, which are a group of primary symbiotic algae, possess light-harvesting antennas called phycobilisomes (PBSs) consistent with cyanobacteria and red algae. However, compared with cyanobacteria and red algae, glaucophytes are poorly studied and there are few reports on the regulation of photosynthesis in the group. In this study, we examined the long-term light adaptation of light-harvesting functions in a glaucophyte, Cyanophora paradoxa, grown under different light conditions. Compared with cells grown under white light, the relative number of PBSs to photosystems (PSs) increased in blue-light-grown cells and decreased in green-, yellow-, and red-light-grown cells. Moreover, the PBS number increased with increment in the monochromatic light intensity. More energy was transferred from PBSs to PSII than to PSI under blue light, whereas energy transfer from PBSs to PSII was reduced under green and yellow lights, and energy transfer from the PBSs to both PSs decreased under red light. Decoupling of PBSs was induced by intense green, yellow, and red lights. Energy transfer from PSII to PSI (spillover) was observed, but the contribution of the spillover did not distinctly change depending on the culture light intensity and quality. These results suggest that the glaucophyte C. paradoxa modifies the light-harvesting abilities of both PSs and excitation energy-transfer processes between the light-harvesting antennas and both PSs during long-term light adaption.

RevDate: 2023-05-26

D'Agostino PM (2023)

Highlights of biosynthetic enzymes and natural products from symbiotic cyanobacteria.

Natural product reports [Epub ahead of print].

Covering: up to 2023Cyanobacteria have long been known for their intriguing repertoire of natural product scaffolds, which are often distinct from other phyla. Cyanobacteria are ecologically significant organisms that form a myriad of different symbioses including with sponges and ascidians in the marine environment or with plants and fungi, in the form of lichens, in terrestrial environments. Whilst there have been several high-profile discoveries of symbiotic cyanobacterial natural products, genomic data is scarce and discovery efforts have remained limited. However, the rise of (meta-)genomic sequencing has improved these efforts, emphasized by a steep increase in publications in recent years. This highlight focuses on selected examples of symbiotic cyanobacterial-derived natural products and their biosyntheses to link chemistry with corresponding biosynthetic logic. Further highlighted are remaining gaps in knowledge for the formation of characteristic structural motifs. It is anticipated that the continued rise of (meta-)genomic next-generation sequencing of symbiontic cyanobacterial systems will lead to many exciting discoveries in the future.

RevDate: 2023-05-26

Lauritano C, C Galasso (2023)

Microbial Interactions between Marine Microalgae and Fungi: From Chemical Ecology to Biotechnological Possible Applications.

Marine drugs, 21(5): pii:md21050310.

Chemical interactions have been shown to regulate several marine life processes, including selection of food sources, defense, behavior, predation, and mate recognition. These chemical communication signals have effects not only at the individual scale, but also at population and community levels. This review focuses on chemical interactions between marine fungi and microalgae, summarizing studies on compounds synthetized when they are cultured together. In the current study, we also highlight possible biotechnological outcomes of the synthetized metabolites, mainly for human health applications. In addition, we discuss applications for bio-flocculation and bioremediation. Finally, we point out the necessity of further investigating microalgae-fungi chemical interactions because it is a field still less explored compared to microalga-bacteria communication and, considering the promising results obtained until now, it is worthy of further research for scientific advancement in both ecology and biotechnology fields.

RevDate: 2023-05-26

Ahmad N, Ritz M, Calchera A, et al (2023)

Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways.

Journal of fungi (Basel, Switzerland), 9(5): pii:jof9050546.

Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )