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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 20 Jan 2022 at 01:48 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 NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2022-01-19

Jiang W, Yang X, Gu F, et al (2022)

Construction of Synthetic Microbial Ecosystems and the Regulation of Population Proportion.

ACS synthetic biology [Epub ahead of print].

With the development of synthetic biology, the design and application of microbial consortia have received increasing attention. However, the construction of synthetic ecosystems is still hampered by our limited ability to rapidly develop microbial consortia with the required dynamics and functions. By using modular design, we constructed synthetic competitive and symbiotic ecosystems with Escherichia coli. Two ecological relationships were realized by reconfiguring the layout between the communication and effect modules. Furthermore, we designed inducible synthetic ecosystems to regulate subpopulation ratios. With the addition of different inducers, a wide range of strain ratios between subpopulations was achieved. These inducible synthetic ecosystems enabled a larger volume of population regulation and simplified culture conditions. The synthetic ecosystems we constructed combined both basic and applied functionalities and expanded the toolkit of synthetic biology research.

RevDate: 2022-01-19

Arenas F, López-García Á, Berná LM, et al (2022)

Desert truffle mycorrhizosphere harbors organic acid releasing plant growth-promoting rhizobacteria, essentially during the truffle fruiting season.

Mycorrhiza [Epub ahead of print].

Desert truffle is becoming a new crop in semiarid areas. Climatic parameters and the presence of microorganisms influence the host plant physiology and alter desert truffle production. Desert truffle plants present a typical summer deciduous plant phenology divided into four stages: summer dormancy, autumn bud break, winter photosynthetic activity, and spring fruiting. We hypothesize that the bacterial community associated with desert truffle plants will show a seasonal trend linked to their plant growth-promoting rhizobacteria (PGPR) traits. This information will provide us with a better understanding about its potential role in this symbiosis and possible management implementations. Bacteria were isolated from root-adhering soil at the four described seasons. A total of 417 isolated bacteria were phenotypically and biochemically characterized and gathered by molecular analysis into 68 operational taxonomic units (OTUs). They were further characterized for PGPR traits such as indole acetic acid production, siderophore production, calcium phosphate solubilization, and ACCD (1-amino-cyclopropane-1-carboxilatedeaminase) activity. These PGPR traits were used to infer functional PGPR diversity and cultivable bacterial OTU composition at different phenological moments. The different seasons induced shifts in the OTU composition linked to their PGPR traits. Summer was the phenological stage with the lowest microbial diversity and PGPR functions, whereas spring was the most active one. Among the PGPR traits analyzed, P-solubilizing rhizobacteria were harbored in the mycorrhizosphere during desert truffle fruiting in spring.

RevDate: 2022-01-19

Cahanovitc R, Livne-Luzon S, Angel R, et al (2022)

Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks.

The ISME journal [Epub ahead of print].

Inter-kingdom belowground carbon (C) transfer is a significant, yet hidden, biological phenomenon, due to the complexity and highly dynamic nature of soil ecology. Among key biotic agents influencing C allocation belowground are ectomycorrhizal fungi (EMF). EMF symbiosis can extend beyond the single tree-fungus partnership to form common mycorrhizal networks (CMNs). Despite the high prevalence of CMNs in forests, little is known about the identity of the EMF transferring the C and how these in turn affect the dynamics of C transfer. Here, Pinus halepensis and Quercus calliprinos saplings growing in forest soil were labeled using a 13CO2 labeling system. Repeated samplings were applied during 36 days to trace how 13C was distributed along the tree-fungus-tree pathway. To identify the fungal species active in the transfer, mycorrhizal fine root tips were used for DNA-stable isotope probing (SIP) with 13CO2 followed by sequencing of labeled DNA. Assimilated 13CO2 reached tree roots within four days and was then transferred to various EMF species. C was transferred across all four tree species combinations. While Tomentella ellisii was the primary fungal mediator between pines and oaks, Terfezia pini, Pustularia spp., and Tuber oligospermum controlled C transfer among pines. We demonstrate at a high temporal, quantitative, and taxonomic resolution, that C from EMF host trees moved into EMF and that C was transferred further to neighboring trees of similar and distinct phylogenies.

RevDate: 2022-01-19
CmpDate: 2022-01-19

Jiménez NE, Gerdtzen ZP, Olivera-Nappa Á, et al (2021)

Novel Symbiotic Genome-Scale Model Reveals Wolbachia's Arboviral Pathogen Blocking Mechanism in Aedes aegypti.

mBio, 12(5):e0156321.

Wolbachia are endosymbiont bacteria known to infect arthropods causing different effects, such as cytoplasmic incompatibility and pathogen blocking in Aedes aegypti. Although several Wolbachia strains have been studied, there is little knowledge regarding the relationship between this bacterium and their hosts, particularly on their obligate endosymbiont nature and its pathogen blocking ability. Motivated by the potential applications on disease control, we developed a genome-scale model of two Wolbachia strains: wMel and the strongest Dengue blocking strain known to date: wMelPop. The obtained metabolic reconstructions exhibit an energy metabolism relying mainly on amino acids and lipid transport to support cell growth that is consistent with altered lipid and cholesterol metabolism in Wolbachia-infected mosquitoes. The obtained metabolic reconstruction was then coupled with a reconstructed mosquito model to retrieve a symbiotic genome-scale model accounting for 1,636 genes and 6,408 reactions of the Aedes aegypti-Wolbachia interaction system. Simulation of an arboviral infection in the obtained novel symbiotic model represents a metabolic scenario characterized by pathogen blocking in higher titer Wolbachia strains, showing that pathogen blocking by Wolbachia infection is consistent with competition for lipid and amino acid resources between arbovirus and this endosymbiotic bacteria. IMPORTANCE Arboviral diseases such as Zika and Dengue have been on the rise mainly due to climate change, and the development of new treatments and strategies to limit their spreading is needed. The use of Wolbachia as an approach for disease control has motivated new research related to the characterization of the mechanisms that underlie its pathogen-blocking properties. In this work, we propose a new approach for studying the metabolic interactions between Aedes aegypti and Wolbachia using genome-scale models, finding that pathogen blocking is mainly influenced by competition for the resources required for Wolbachia and viral replication.

RevDate: 2022-01-19
CmpDate: 2022-01-19

Lemoine L, Bayrambey D, Roloff A, et al (2021)

Commensal-Related Changes in the Epidermal Barrier Function Lead to Alterations in the Benzo[a]Pyrene Metabolite Profile and Its Distribution in 3D Skin.

mBio, 12(5):e0122321.

Polycyclic aromatic hydrocarbons (PAH) such as benzo[a]pyrene (B[a]P) are among the most abundant environmental pollutants, resulting in continuous exposure of human skin and its microbiota. However, effects of the latter on B[a]P toxicity, absorption, metabolism, and distribution in humans remain unclear. Here, we demonstrate that the skin microbiota does metabolize B[a]P on and in human skin in situ, using a recently developed commensal skin model. In this model, microbial metabolism leads to high concentrations of known microbial B[a]P metabolites on the surface as well as in the epidermal layers. In contrast to what was observed for uncolonized skin, B[a]P and its metabolites were subject to altered rates of skin penetration and diffusion, resulting in up to 58% reduction of metabolites recovered from basal culture medium. The results indicate the reason for this altered behavior to be a microbially induced strengthening of the epidermal barrier. Concomitantly, colonized models showed decreased formation and penetration of the ultimate carcinogen B[a]P-7,8-dihydrodiol-9,10-epoxide (BPDE), leading, in consequence, to fewer BPDE-DNA adducts being formed. Befittingly, transcript and expression levels of key proteins for repairing environmentally induced DNA damage such as xeroderma pigmentosum complementation group C (XPC) were also found to be reduced in the commensal models, as was expression of B[a]P-associated cytochrome P450-dependent monooxygenases (CYPs). The results show that the microbiome can have significant effects on the toxicology of external chemical impacts. The respective effects rely on a complex interplay between microbial and host metabolism and microbe-host interactions, all of which cannot be adequately assessed using single-system studies. IMPORTANCE Exposure to xenobiotics has repeatedly been associated with adverse health effects. While the majority of reported cases relate to direct substance effects, there is increasing evidence that microbiome-dependent metabolism of xenobiotic substances likewise has direct adverse effects on the host. This can be due to microbial biotransformation of compounds, interaction between the microbiota and the host's endogenous detoxification enzymes, or altered xenobiotic bioavailability. However, there are hardly any studies addressing the complex interplay of such interactions in situ and less so in human test systems. Using a recently developed microbially competent three-dimensional (3D) skin model, we show here for the first time how commensal influence on skin physiology and gene transcription paradoxically modulates PAH toxicity.

RevDate: 2022-01-19
CmpDate: 2022-01-19

Anonymous (2021)

Refocusing Human Microbiota Research in Infectious and Immune-mediated Diseases: Advancing to the Next Stage.

The Pediatric infectious disease journal, 40(10):916.

RevDate: 2022-01-18

Zhang M, Zhong X, Li M, et al (2022)

Genome-wide analyses of the Nodulin-like gene family in bread wheat revealed its potential roles during arbuscular mycorrhizal symbiosis.

International journal of biological macromolecules pii:S0141-8130(22)00091-5 [Epub ahead of print].

Nodulin-like (NL) genes are involved in transporting of various substances and may play key roles during the establishment of symbiosis in legumes plants. However, basic biological information of NL genes in the wheat genome is still largely unknown. Here, we identified and characterized NL genes in wheat via integrating genomic information, collinearity analysis, co-expression network analysis (WGCNA) and transcriptome analysis. In addition, we analyzed the polymorphisms and the roles of NL genes during arbuscular mycorrhizal (AM) symbiosis using a large wheat panel consists of 259 wheat genotypes. We identified 181 NL genes in the wheat genome, which were classified into SWEET, Early Nodulin-Like (ENODL), Major Facilitator Superfamily-Nodulin (MFS), Vacuolar Iron Transporter (VIT) and Early nodulin 93 (ENOD93) subfamily. The expansion of NL genes was mainly driven by segmental duplication. The bHLH genes are potential unrecognized transcription factors regulating NL genes. Moreover, two NL genes were more sensitive than other NL genes to AM colonization. The polymorphisms of NL genes are mainly due to random drift, and the natural mutation of NL genes led to significant differences in the mycorrhizal dependence of wheat in phosphorus uptake. The results concluded that NL genes potentially play important roles during AM symbiosis with wheat.

RevDate: 2022-01-18

Ji C, Qiu M, Ruan H, et al (2022)

Transcriptome Analysis Revealed the Symbiosis Niche of 3D Scaffolds to Accelerate Bone Defect Healing.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) [Epub ahead of print].

Three dimension (3D) printed scaffolds have been shown to be superior in promoting tissue repair, but the cell-level specific regulatory network activated by 3D printing scaffolds with different material components to form a symbiosis niche have not been systematically revealed. Here, three typical 3D printed scaffolds, including natural polymer hydrogel (gelatin-methacryloyl, GelMA), synthetic polymer material (polycaprolactone, PCL), and bioceramic (β-tricalcium phosphate, β-TCP), are fabricated to explore the regulating effect of the symbiotic microenvironment during bone healing. Enrichment analysis show that hydrogel promotes tissue regeneration and reconstruction by improving blood vessel generation by enhancing oxygen transport and red blood cell development. The PCL scaffold regulates cell proliferation and differentiation by promoting cellular senescence, cell cycle and deoxyribonucleic acid (DNA) replication pathways, accelerating the process of endochondral ossification, and the formation of callus. The β-TCP scaffold can specifically enhance the expression of osteoclast differentiation and extracellular space pathway genes to promote the differentiation of osteoclasts and promote the process of bone remodeling. In these processes, specific biomaterial properties can be used to guide cell behavior and regulate molecular network in the symbiotic microenvironment to reduce the barriers of regeneration and repair.

RevDate: 2022-01-17

Singh A, P Ravi (2022)

Global Health Diplomacy and Governance: Mapping and Future Trends.

Hospital topics [Epub ahead of print].

This study evaluates global health diplomacy and governance by performing bibliometric analysis to investigate the current publication trends, authors and keywords-based clusters, research trends, author's productivity, and future research areas. The analysis results suggest that global health diplomacy has garnered attention only in developed countries and has been researched negligibly in developing countries. The research in this field increases after the onset of pandemics such as Swine Flu and COVID-19. Authors kickbush and lee are the most influential authors based on their h index. The identified future research areas are "International laws" and "Social Determinants of Health."

RevDate: 2022-01-17

Ndoye MS, Burridge J, Bhosale R, et al (2022)

Root traits for low input agroecosystems in Africa: lessons from three case studies.

Plant, cell & environment [Epub ahead of print].

In Africa, agriculture is largely based on low-input and small-holder farming systems that use little inorganic fertilizers and have limited access to irrigation and mechanization. Improving agricultural practices and developing new cultivars adapted to these environments, where production already suffers from climate change, is a major priority for food security. Here, we illustrate how breeding for specific root traits could improve crop resilience in Africa using three case studies covering very contrasting low-input agroecosystems. We first review how greater basal root whorl number and longer and denser root hairs increased P acquisition efficiency and yield in common bean in South East Africa. We then discuss how water-saving strategies, root hair density and deep root growth could be targeted to improve sorghum and pearl millet yield in West Africa. Finally, we evaluate how breeding for denser root systems in the topsoil and interactions with arbuscular mycorrhizal fungi could be mobilized to optimize water-saving alternate wetting and drying practices in West African rice agroecosystems. We conclude with a discussion on how to evaluate the utility of root traits and how to make root trait selection feasible for breeders so that improved varieties can be made available to farmers through participatory approaches. This article is protected by copyright. All rights reserved.

RevDate: 2022-01-17

Xie X, Lai W, Che X, et al (2022)

A SPX domain-containing phosphate transporter from Rhizophagus irregularis handles phosphate homeostasis at symbiotic interface of arbuscular mycorrhizas.

The New phytologist [Epub ahead of print].

Reciprocal symbiosis of more than 70% of terrestrial vascular plants with arbuscular mycorrhizal (AM) fungi provides the fungi with fatty acids and sugars. In return, AM fungi facilitate plant phosphate (Pi) uptake from soil. However, how AM fungi handle Pi transport and homeostasis at the symbiotic interface of AM symbiosis is poorly understood. Here, we identify a SPX domain-containing phosphate transporter, RiPT7 from Rhizophagus irregularis. To characterize the RiPT7 transporter, we combined subcellular localization and heterologous expression studies in yeasts with reverse genetics approaches during the in planta phase. The results show that RiPT7 is conserved across fungal species and expressed in the intraradical mycelia. It is expressed in the arbuscules, intraradical hyphae and vesicles, independently of Pi availability. The plasma membrane-localized RiPT7 facilitates bidirectional Pi transport, depending on Pi gradient across the plasma membrane, whereas the SPX domain of RiPT7 inhibits Pi transport activity, and mediates the vacuolar targeting of RiPT7 in yeast in response to Pi starvation. Importantly, RiPT7 silencing hampers arbuscule development of R. irregularis and symbiotic Pi delivery during medium-low Pi conditions. Collectively, our findings reveal a role for RiPT7 in fine-tuning of Pi homeostasis across the fungal membrane to maintain the AM development.

RevDate: 2022-01-17

Zhou J, Wilson GWT, Cobb AB, et al (2022)

Mycorrhizal and rhizobial interactions influence model grassland plant community structure and productivity.

Mycorrhiza [Epub ahead of print].

Arbuscular mycorrhizal (AM) fungi and rhizobium are likely important drivers of plant coexistence and grassland productivity due to complementary roles in supplying limiting nutrients. However, the interactive effects of mycorrhizal and rhizobial associations on plant community productivity and competitive dynamics remain unclear. To address this, we conducted a greenhouse experiment to determine the influences of these key microbial functional groups on communities comprising three plant species by comparing plant communities grown with or without each symbiont. We also utilized N-fertilization and clipping treatments to explore potential shifts in mycorrhizal and rhizobial benefits across abiotic and biotic conditions. Our research suggests AM fungi and rhizobium co-inoculation was strongly facilitative for plant community productivity and legume (Medicago sativa) growth and nodulation. Plant competitiveness shifted in the presence of AM fungi and rhizobium, favoring M. sativa over a neighboring C4 grass (Andropogon gerardii) and C3 forb (Ratibida pinnata). This may be due to rhizobial symbiosis as well as the relatively greater mycorrhizal growth response of M. sativa, compared to the other model plants. Clipping and N-fertilization altered relative costs and benefits of both symbioses, presumably by altering host-plant nitrogen and carbon dynamics, leading to a relative decrease in mycorrhizal responsiveness and proportional biomass of M. sativa relative to the total biomass of the entire plant community, with a concomitant relative increase in A. gerardii and R. pinnata proportional biomass. Our results demonstrate a strong influence of both microbial symbioses on host-plant competitiveness and community dynamics across clipping and N-fertilization treatments, suggesting the symbiotic rhizosphere community is critical for legume establishment in grasslands.

RevDate: 2022-01-18
CmpDate: 2022-01-18

Kadam KD, Ahirrao S, K Kotecha (2022)

Efficient Approach towards Detection and Identification of Copy Move and Image Splicing Forgeries Using Mask R-CNN with MobileNet V1.

Computational intelligence and neuroscience, 2022:6845326.

With the technological advancements of the modern era, the easy availability of image editing tools has dramatically minimized the costs, expense, and expertise needed to exploit and perpetuate persuasive visual tampering. With the aid of reputable online platforms such as Facebook, Twitter, and Instagram, manipulated images are distributed worldwide. Users of online platforms may be unaware of the existence and spread of forged images. Such images have a significant impact on society and have the potential to mislead decision-making processes in areas like health care, sports, crime investigation, and so on. In addition, altered images can be used to propagate misleading information which interferes with democratic processes (e.g., elections and government legislation) and crisis situations (e.g., pandemics and natural disasters). Therefore, there is a pressing need for effective methods for the detection and identification of forgeries. Various techniques are currently employed for the identification and detection of these forgeries. Traditional techniques depend on handcrafted or shallow-learning features. In traditional techniques, selecting features from images can be a challenging task, as the researcher has to decide which features are important and which are not. Also, if the number of features to be extracted is quite large, feature extraction using these techniques can become time-consuming and tedious. Deep learning networks have recently shown remarkable performance in extracting complicated statistical characteristics from large input size data, and these techniques efficiently learn underlying hierarchical representations. However, the deep learning networks for handling these forgeries are expensive in terms of the high number of parameters, storage, and computational cost. This research work presents Mask R-CNN with MobileNet, a lightweight model, to detect and identify copy move and image splicing forgeries. We have performed a comparative analysis of the proposed work with ResNet-101 on seven different standard datasets. Our lightweight model outperforms on COVERAGE and MICCF2000 datasets for copy move and on COLUMBIA dataset for image splicing. This research work also provides a forged percentage score for a region in an image.

RevDate: 2022-01-18

Khan F, Y Ali (2022)

Implementation of the circular supply chain management in the pharmaceutical industry.

Environment, development and sustainability [Epub ahead of print].

The ever-increasing levels of pollution and waste creation have subjected industries around the world to incorporate the concept of circular economy (CE) in their supply chains. The amalgamation of the CE approach along with supply chain management is called circular supply chain management (CSCM). Among other industries, the pharmaceutical industry is also involved in damaging the ecosystem. Hence, an effective framework for the adoption of CSCM in a particular industry is very essential. Therefore, this paper aims to devise a model that will help the pharmaceutical industries to adopt CSCM in their organizations. For this purpose, the study in the first phase identifies ten barriers that are working as an impediment in the adoption of the CSCM approach. To counter those barriers, the study in the second phase identifies a set of twelve enablers. To analyse the barriers and enablers, the study uses a new hybrid methodology. For allocating weights and prioritizing the barriers, the fuzzy multi-criteria decision-making (MCDM) technique, i.e. fuzzy full consistency method (F-FUCOM) is used, whereas the total quality management tool, i.e. fuzzy quality function deployment (FQFD) is used to rank the enablers. The results from F-FUCOM suggest "lack of financial resources and funding", "market challenges", and "lack of coordination and collaboration among the entire supply chain network" to be the top-most barriers, respectively, whereas the results achieved from the FQFD suggest "industrial symbiosis", "Reverse Logistic (RL) infrastructure", and "block chain technology" to be the top-ranked enablers, respectively. The provision of a facilitating framework for the adoption of CSCM in the pharmaceutical industry and the newly developed hybrid methodology are both novelties of this study.

RevDate: 2022-01-18

O'Neill B, L Stapleton (2022)

Digital cultural heritage standards: from silo to semantic web.

AI & society [Epub ahead of print].

This paper is a survey of standards being used in the domain of digital cultural heritage with focus on the Metadata Encoding and Transmission Standard (METS) created by the Library of Congress in the United States of America. The process of digitization of cultural heritage requires silo breaking in a number of areas-one area is that of academic disciplines to enable the performance of rich interdisciplinary work. This lays the foundation for the emancipation of the second form of silo which are the silos of knowledge, both traditional and born digital, held in individual institutions, such as galleries, libraries, archives and museums. Disciplinary silo breaking is the key to unlocking these institutional knowledge silos. Interdisciplinary teams, such as developers and librarians, work together to make the data accessible as open data on the "semantic web". Description logic is the area of mathematics which underpins many ontology building applications today. Creating these ontologies requires a human-machine symbiosis. Currently in the cultural heritage domain, the institutions' role is that of provider of this open data to the national aggregator which in turn can make the data available to the trans-European aggregator known as Europeana. Current ingests to the aggregators are in the form of machine readable cataloguing metadata which is limited in the richness it provides to disparate object descriptions. METS can provide this richness.

RevDate: 2022-01-16

Kamisuki S, Shibasaki H, Ashikawa K, et al (2022)

Determining the absolute configuration of vanitaracin A, an anti-hepatitis B virus agent.

The Journal of antibiotics [Epub ahead of print].

Vanitaracin A is an anti-hepatitis B virus (anti-HBV) compound isolated from the culture broth of the fungus Talaromyces sp. Vanitaracin A inhibits the entry of HBV into target cells with sub-micromolar IC50 values. While a structure-activity relationship study is highly desirable, a synthetic approach still needs to be developed, which is difficult because the absolute configurations of the six stereogenic centers in the structure of vanitaracin A have not yet been determined. In the present study, we used the crystalline sponge method to clarify the configuration of the compound after determining the absolute configuration of the secondary alcohol using a modified Mosher ester method. Combining these analyses with the NOESY spectrum of vanitaracin A and NMR analyses of the crude side-chain carboxylic acid obtained by the alkaline hydrolysis of vanitaracin A revealed the absolute configurations of all stereogenic centers in this important compound.

RevDate: 2022-01-16

Zhou Z, Ni X, Chen S, et al (2022)

Ingested microplastics impair the metabolic relationship between the giant clam Tridacna crocea and its symbionts.

Aquatic toxicology (Amsterdam, Netherlands), 243:106075 pii:S0166-445X(22)00002-9 [Epub ahead of print].

Microplastics are emerging as widespread pollutants in coral reef ecosystems worldwide; however, there is limited knowledge regarding their impact on giant clams, which are important reef builders. In the present study, the cytological, physiological, and molecular response of the giant clam Tridacna crocea to a 5 d exposure of microplastics was investigated. The concentration of microplastics in the intestine and outer mantle increased significantly and gradually after the exposure to microplastics. There were no significant changes in the density of symbiotic Symbiodiniaceae throughout the exposure period, but symbiont chlorophyll content increased significantly after 1 d of exposure. There was a significant increase in symbiont superoxide dismutase (SOD) activity, but a decrease in giant clam SOD activity and symbiont glutathione S-transferase (GST) activity. No significant changes in catalase (CAT) activity and caspase3 activation level were observed in the two symbiotic partners. Transcriptomic analysis of the giant clam revealed 138 significantly upregulated and 1390 significantly downregulated genes after 5 d of microplastic exposure. The top 20 GO terms overrepresented by these significantly downregulated genes were related to primary metabolic processes and cellular metabolic processes. No significantly upregulated genes were observed in symbionts, but 28 genes were significantly downregulated, including chloroplast oxygen-evolving enhancer, photosystem I reaction center subunit II, peptide/nitrate transporter, sodium-coupled neutral amino acid transporter, beta-glucosidase, and TPA: lipase. These results suggest that T. crocea ingests microplastics through the outer mantle and intestine, and these microplastics can suppress the photosynthesis, organic nutrient transportation, and detoxification ability of the symbionts, as well as the primary metabolism of the giant clam. This eventually could threaten their metabolic relationship and long-term survival.

RevDate: 2022-01-17
CmpDate: 2022-01-17

Ren Z, Huo Y, Zhang Q, et al (2021)

Protective Effect of Lactiplantibacillus plantarum 1201 Combined with Galactooligosaccharide on Carbon Tetrachloride-Induced Acute Liver Injury in Mice.

Nutrients, 13(12):.

Acute liver injury (ALI) has a high mortality rate of approximately 20-40%, and it is imperative to find complementary and alternative drugs for treating ALI. A carbon tetrachloride (CCl4)-induced ALI mouse model was established to explore whether dietary intervention can alleviate ALI in mice. Intestinal flora, intestinal integrity, biomarkers of hepatic function, systemic inflammation, autophagy, and apoptosis signals were detected through a real-time PCR, hematoxylin-eosin staining, 16S rRNA gene sequencing, and so on. The results showed that Lactiplantibacillus plantarum 1201 had a strongly antioxidant ability, and galactooligosaccharide (GOS) could boost its growth. Based on these findings, the combination of L. plantarum 1201 and GOS, the synbiotic, was applied to prevent CCl4-induced ALI in mice. The current research proved that GOS promoted the intestinal colonization of L. plantarum 1201, and the synbiotic improved the antioxidant capacity of the host, regulated the intestinal flora, repaired the intestinal barrier, inhibited the activation of the MAPK/NF-κB pathway, and then inhibited the apoptosis and autophagy pathways, relieving inflammation and liver oxidation; thereby, the ALI of mice was alleviated. These results suggest that synbiotics may become a new research direction for liver-protecting drugs.

RevDate: 2022-01-17
CmpDate: 2022-01-17

Zhang Q, Wang S, Zhang X, et al (2021)

Enterobacter hormaechei in the intestines of housefly larvae promotes host growth by inhibiting harmful intestinal bacteria.

Parasites & vectors, 14(1):598.

BACKGROUND: As a pervasive insect that transmits a variety of pathogens to humans and animals, the housefly has abundant and diverse microbial communities in its intestines. These gut microbes play an important role in the biology of insects and form a symbiotic relationship with the host insect. Alterations in the structure of the gut microbial community would affect larval development. Therefore, it is important to understand the mechanism regulating the influence of specific bacteria on the development of housefly larvae.

METHODS: For this study we selected the intestinal symbiotic bacterium Enterobacter hormaechei, which is beneficial to the growth and development of housefly larvae, and used it as a probiotic supplement in larval feed. 16S rRNA gene sequencing technology was used to explore the effect of E. hormaechei on the intestinal flora of housefly larvae, and plate confrontation experiments were performed to study the interaction between E. hormaechei and intestinal microorganisms.

RESULTS: The composition of the gut microflora of the larvae changed after the larvae were fed E. hormaechei, with the abundance of Pseudochrobactrum, Enterobacter and Vagococcus increasing and that of Klebsiella and Bacillus decreasing. Analysis of the structure and interaction of larval intestinal flora revealed that E. hormaechei inhibited the growth of harmful bacteria, such as Pseudomonas aeruginosa, Providencia stuartii and Providencia vermicola, and promoted the reproduction of beneficial bacteria.

CONCLUSIONS: Our study has explored the influence of specific beneficial bacteria on the intestinal flora of houseflies. The results of this study reveal the important role played by specific beneficial bacteria on the development of housefly larvae and provide insight for the development of sustained biological agents for housefly control through interference of gut microbiota.

RevDate: 2022-01-18
CmpDate: 2022-01-18

Wolinska KW, Vannier N, Thiergart T, et al (2021)

Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots.

Proceedings of the National Academy of Sciences of the United States of America, 118(49):.

In nature, roots of healthy plants are colonized by multikingdom microbial communities that include bacteria, fungi, and oomycetes. A key question is how plants control the assembly of these diverse microbes in roots to maintain host-microbe homeostasis and health. Using microbiota reconstitution experiments with a set of immunocompromised Arabidopsis thaliana mutants and a multikingdom synthetic microbial community (SynCom) representative of the natural A. thaliana root microbiota, we observed that microbiota-mediated plant growth promotion was abolished in most of the tested immunocompromised mutants. Notably, more than 40% of between-genotype variation in these microbiota-induced growth differences was explained by fungal but not bacterial or oomycete load in roots. Extensive fungal overgrowth in roots and altered plant growth was evident at both vegetative and reproductive stages for a mutant impaired in the production of tryptophan-derived, specialized metabolites (cyp79b2/b3). Microbiota manipulation experiments with single- and multikingdom microbial SynComs further demonstrated that 1) the presence of fungi in the multikingdom SynCom was the direct cause of the dysbiotic phenotype in the cyp79b2/b3 mutant and 2) bacterial commensals and host tryptophan metabolism are both necessary to control fungal load, thereby promoting A. thaliana growth and survival. Our results indicate that protective activities of bacterial root commensals are as critical as the host tryptophan metabolic pathway in preventing fungal dysbiosis in the A. thaliana root endosphere.

RevDate: 2022-01-18
CmpDate: 2022-01-18

Mousavi SA, Gao Y, Penttinen P, et al (2022)

Using amplicon sequencing of rpoB for identification of inoculant rhizobia from peanut nodules.

Letters in applied microbiology, 74(2):204-211.

To improve the nitrogen fixation, legume crops are often inoculated with selected effective rhizobia. However, there is large variation in how well the inoculant strains compete with the indigenous microflora in soil. To assess the success of the inoculant, it is necessary to distinguish it from other, closely related strains. Methods used until now have generally been based either on fingerprinting methods or on the use of reporter genes. Nevertheless, these methods have their shortcomings, either because they do not provide sufficiently specific information on the identity of the inoculant strain, or because they use genetically modified organisms that need prior authorization to be applied in the field or other uncontained environments. Another possibility is to target a gene that is naturally present in the bacterial genomes. Here we have developed a method that is based on amplicon sequencing of the bacterial housekeeping gene rpoB, encoding the beta-subunit of the RNA polymerase, which has been proposed as an alternative to the 16S rRNA gene to study the diversity of rhizobial populations in soils. We evaluated the method under laboratory and field conditions. Peanut seeds were inoculated with various Bradyrhizobium strains. After nodule development, DNA was extracted from selected nodules and the nodulating rhizobia were analysed by amplicon sequencing of the rpoB gene. The analyses of the sequence data showed that the method reliably identified bradyrhizobial strains in nodules, at least at the species level, and could be used to assess the competitiveness of the inoculant compared to other bradyrhizobia.

RevDate: 2022-01-18
CmpDate: 2022-01-18

Woo V, Eshleman EM, Hashimoto-Hill S, et al (2021)

Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection.

Cell host & microbe, 29(12):1744-1756.e5.

Interactions between the microbiota and mammalian host are essential for defense against infection, but the microbial-derived cues that mediate this relationship remain unclear. Here, we find that intestinal epithelial cell (IEC)-associated commensal bacteria, segmented filamentous bacteria (SFB), promote early protection against the pathogen Citrobacter rodentium, independent of CD4+ T cells. SFB induced histone modifications in IECs at sites enriched for retinoic acid receptor motifs, suggesting that SFB may enhance defense through retinoic acid (RA). Consistent with this, inhibiting RA signaling suppressed SFB-induced protection. Intestinal RA levels were elevated in SFB mice, despite the inhibition of mammalian RA production, indicating that SFB directly modulate RA. Interestingly, RA was produced by intestinal bacteria, and the loss of bacterial-intrinsic aldehyde dehydrogenase activity decreased the RA levels and increased infection. These data reveal RA as an unexpected microbiota-derived metabolite that primes innate defense and suggests that pre- and probiotic approaches to elevate RA could prevent or combat infections.

RevDate: 2022-01-17
CmpDate: 2022-01-17

Zhu L, Zhang Y, Cui X, et al (2021)

Host Bias in Diet-Source Microbiome Transmission in Wild Cohabitating Herbivores: New Knowledge for the Evolution of Herbivory and Plant Defense.

Microbiology spectrum, 9(1):e0075621.

It is commonly understood that dietary nutrition will influence the composition and function of the animal gut microbiome. However, the transmission of organisms from the diet-source microbiome to the animal gut microbiome in the natural environment remains poorly understood, and elucidating this process may help in understanding the evolution of herbivores and plant defenses. Here, we investigated diet-source microbiome transmission across a range of herbivores (insects and mammals) living in both captive and wild environments. We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. IMPORTANCE We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. This study shed new light on the coevolution of herbivory and plant defense.

RevDate: 2022-01-17
CmpDate: 2022-01-17

Zhang X, Wang S, Li T, et al (2021)

Bacteriophage: A Useful Tool for Studying Gut Bacteria Function of Housefly Larvae, Musca domestica.

Microbiology spectrum, 9(1):e0059921.

Beneficial symbiotic bacteria have positive effects on some insects' (such as mosquitoes, cockroaches, and flies) biological activities. However, the effects of a lack of one specific symbiotic bacterium on the life activities of some insects and their natural gut microbiota composition remain unclear. Bacteriophages are viruses that specifically target and kill bacteria and have the potential to shape gut bacterial communities. In previous work, Pseudomonas aeruginosa that naturally colonized the intestines of housefly larvae was shown to be essential to protect housefly larvae from entomopathogenic fungal infections, leading us to test whether a deficiency in Pseudomonas aeruginosa strains in housefly larvae that was specifically caused using bacteriophages could remold the composition of the intestinal bacteria and affect the development of housefly larvae. Our research revealed that the phage, with a titer of 108 PFU/ml, can remove 90% of Pseudomonas aeruginosa in the gut. A single feeding of low-dose phage had no effect on the health of housefly larvae. However, the health of housefly larvae was affected by treatment with phage every 24 h. Additionally, treating housefly larvae with bacteriophages every 24 h led to bacterial composition changes in the gut. Collectively, the results revealed that deficiency in one symbiotic gut bacteria mediated by precise targeting using bacteriophages indirectly influences the intestinal microbial composition of housefly larvae and has negative effects on the development of the host insect. Our results indicated the important role of symbiotic gut bacteria in shaping the normal gut microbiota composition in insects. IMPORTANCE The well-balanced gut microbiota ensures appropriate development of the host insect, such as mosquitoes, cockroaches, and flies. Various intestinal symbiotic bacteria have different influences on the host gut community structure and thus exert different effects on host health. Therefore, it is of great importance to understand the contributions of one specific bacterial symbiont to the gut microbiota community structure and insect health. Bacteriophages that target certain bacteria are effective tools that can be used to analyze gut bacterial symbionts. However, experimental evidence for phage efficacy in regulating insect intestinal bacteria has been little reported. In this study, we used phages as precision tools to regulate a bacterial community and analyzed the influence on host health after certain bacteria were inhibited by bacteriophage. The ability of phages to target intestinal-specific bacteria in housefly larvae and reduce the levels of target bacteria makes them an effective tool for studying the function of gut bacteria.

RevDate: 2022-01-17
CmpDate: 2022-01-17

Kodama Y, H Sumita (2022)

The ciliate Paramecium bursaria allows budding of symbiotic Chlorella variabilis cells singly from the digestive vacuole membrane into the cytoplasm during algal reinfection.

Protoplasma, 259(1):117-125.

The ciliate Paramecium bursaria harbors several hundred symbiotic Chlorella spp. cells in the cytoplasm. Algal re-endosymbiosis can be artificially induced using alga-removed P. bursaria. During algal re-endosymbiosis, algae ingested into the host digestive vacuoles (DVs) avoid digestion by the host lysosomal enzymes and then escape into the cytoplasm by budding off of the DV membrane. The budded alga-enclosing DV membrane then differentiates into the symbiosome or perialgal vacuole (PV) membrane and is localized beneath the host cell cortex. In this study, we determined whether the PV membrane has the ability to recognize the symbiotic alga singly by eliminating other small microspheres in the same DV. To clarify the accuracy of the budding process, we mixed fluorescent-labeled microspheres of diameter 0.20 µm with isolated symbiotic algae during algal re-endosymbiosis. No fluorescence was observed from the PV membrane, as expected, and the budding DVs that enclosed both undigested and digested algae. Additionally, the algal re-endosymbiosis rate was significantly reduced in the presence of microspheres. These observations showed that the host P. bursaria allowed budding of the algae singly from the membranes of DVs without microspheres and this process required close contact between the DV membrane and the algal cell wall.

RevDate: 2021-12-28
CmpDate: 2021-12-28

Kapantaidaki DE, Antonatos S, Evangelou V, et al (2021)

Genetic and endosymbiotic diversity of Greek populations of Philaenus spumarius, Philaenus signatus and Neophilaenus campestris, vectors of Xylella fastidiosa.

Scientific reports, 11(1):3752.

The plant-pathogenic bacterium Xylella fastidiosa which causes significant diseases to various plant species worldwide, is exclusively transmitted by xylem sap-feeding insects. Given the fact that X. fastidiosa poses a serious potential threat for olive cultivation in Greece, the main aim of this study was to investigate the genetic variation of Greek populations of three spittlebug species (Philaenus spumarius, P. signatus and Neophilaenus campestris), by examining the molecular markers Cytochrome Oxidase I, cytochrome b and Internal Transcribed Spacer. Moreover, the infection status of the secondary endosymbionts Wolbachia, Arsenophonus, Hamiltonella, Cardinium and Rickettsia, among these populations, was determined. According to the results, the ITS2 region was the less polymorphic, while the analyzed fragments of COI and cytb genes, displayed high genetic diversity. The phylogenetic analysis placed the Greek populations of P. spumarius into the previously obtained Southwest clade in Europe. The analysis of the bacterial diversity revealed a diverse infection status. Rickettsia was the most predominant endosymbiont while Cardinium was totally absent from all examined populations. Philaenus spumarius harbored Rickettsia, Arsenophonus, Hamiltonella and Wolbachia, N. campestris carried Rickettsia, Hamiltonella and Wolbachia while P. signatus was infected only by Rickettsia. The results of this study will provide an important knowledge resource for understanding the population dynamics of vectors of X. fastidiosa with a view to formulate effective management strategies towards the bacterium.

RevDate: 2022-01-18
CmpDate: 2022-01-18

Jawale CV, Li DD, Ramani K, et al (2021)

Uremia Coupled with Mucosal Damage Predisposes Mice with Kidney Disease to Systemic Infection by Commensal Candida albicans.

ImmunoHorizons, 5(1):16-24.

Infections are the second major cause of mortality in patients with kidney disease and accompanying uremia. Both vascular access and non-access-related infections contribute equally to the infection-related deaths in patients with kidney disease. Dialysis is the most common cause of systemic infection by Candida albicans in these patients. C albicans also reside in the gastrointestinal tract as a commensal fungus. However, the contribution of gut-derived C albicans in non-access-related infections in kidney disease is unknown. Using a mouse model of kidney disease, we demonstrate that uremic animals showed increased gut barrier permeability, impaired mucosal defense, and dysbiosis. The disturbance in gut homeostasis is sufficient to drive the translocation of microbiota and intestinal pathogen Citrobacter rodentium to extraintestinal sites but not C albicans Interestingly, a majority of uremic animals showed fungal translocation only when the gut barrier integrity is disrupted. Our data demonstrate that uremia coupled with gut mucosal damage may aid in the translocation of C. albicans and cause systemic infection in kidney disease. Because most of the individuals with kidney disease suffer from some form of gut mucosal damage, these results have important implications in the risk stratification and control of non-access-related opportunistic fungal infections in these patients.

RevDate: 2022-01-15

Černajová I, Schiefelbein U, P Škaloud (2022)

Lichens from the littoral zone host diverse ulvophycean photobionts.

Journal of phycology [Epub ahead of print].

Crustose Verrucariaceae lichens form a distinctive black belt on seashores all over the world. This lifestyle is apparently enabled by a specific set of photobionts. However, their diversity is understudied. We sampled these lichens from the northern Patagonian Pacific coast of Chile. Using molecular markers, we identified both mycobionts and photobionts. The lichens, belonging to the genus Hydropunctaria and Wahlenbergiella group, hosted solely Ulvophycean photobionts. Pseudendoclonium submarinum (Kornmanniaceae, Ulvales) was the most common, but representatives of other closely related, yet undescribed, lineages were also found. Undulifilum symbioticum gen. et sp. nov. is described within the Kornmanniaceae based on culture morphology and DNA sequence data. Furthermore, the free-living macroscopic genus Urospora (Acrosiphoniaceae, Ulotrichales) is reported as a lichen photobiont for the first time and is the first of its kind in the order. These results indicate that undescribed algal diversity is waiting to be uncovered in seashore lichens.

RevDate: 2022-01-15

Schultz CJ, Wu Y, U Baumann (2022)

A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to Glomeromycotina.

Mycorrhiza [Epub ahead of print].

Diversity in arbuscular mycorrhizal fungi (AMF) contributes to biodiversity and resilience in natural environments and healthy agricultural systems. Functional complementarity exists among species of AMF in symbiosis with their plant hosts, but the molecular basis of this is not known. We hypothesise this is in part due to the difficulties that current sequence assembly methodologies have assembling sequences for intrinsically disordered proteins (IDPs) due to their low sequence complexity. IDPs are potential candidates for functional complementarity because they often exist as extended (non-globular) proteins providing additional amino acids for molecular interactions. Rhizophagus irregularis arabinogalactan-protein-like proteins (AGLs) are small secreted IDPs with no known orthologues in AMF or other fungi. We developed a targeted bioinformatics approach to identify highly variable AGLs/IDPs in RNA-sequence datasets. The approach includes a modified multiple k-mer assembly approach (Oases) to identify candidate sequences, followed by targeted sequence capture and assembly (mirabait-mira). All AMF species analysed, including the ancestral family Paraglomeraceae, have small families of proteins rich in disorder promoting amino acids such as proline and glycine, or glycine and asparagine. Glycine- and asparagine-rich proteins also were found in Geosiphon pyriformis (an obligate symbiont of a cyanobacterium), from the same subphylum (Glomeromycotina) as AMF. The sequence diversity of AGLs likely translates to functional diversity, based on predicted physical properties of tandem repeats (elastic, amyloid, or interchangeable) and their broad pI ranges. We envisage that AGLs/IDPs could contribute to functional complementarity in AMF through processes such as self-recognition, retention of nutrients, soil stability, and water movement.

RevDate: 2022-01-14

Weiner AKM, Cullison B, Date SV, et al (2021)

Examining the Relationship Between the Testate Amoeba Hyalosphenia papilio (Arcellinida, Amoebozoa) and its Associated Intracellular Microalgae Using Molecular and Microscopic Methods.

Protist, 173(1):125853 pii:S1434-4610(21)00063-8 [Epub ahead of print].

Symbiotic relationships between heterotrophic and phototrophic partners are common in microbial eukaryotes. Among Arcellinida (Amoebozoa) several species are associated with microalgae of the genus Chlorella (Archaeplastida). So far, these symbioses were assumed to be stable and mutualistic, yet details of the interactions are limited. Here, we analyzed 22 single-cell transcriptomes and 36 partially-sequenced genomes of the Arcellinida morphospecies Hyalosphenia papilio, which contains Chlorella algae, to shed light on the amoeba-algae association. By characterizing the genetic diversity of associated Chlorella, we detected two distinct clades that can be linked to host genetic diversity, yet at the same time show a biogeographic signal across sampling sites. Fluorescence and transmission electron microscopy showed the presence of intact algae cells within the amoeba cell. Yet analysis of transcriptome data suggested that the algal nuclei are inactive, implying that instead of a stable, mutualistic relationship, the algae may be temporarily exploited for photosynthetic activity before being digested. Differences in gene expression of H. papilio and Hyalosphenia elegans demonstrated increased expression of genes related to oxidative stress. Together, our analyses increase knowledge of this host-symbiont association and reveal 1) higher diversity of associated algae than previously characterized, 2) a transient association between H. papilio and Chlorella with unclear benefits for the algae, 3) algal-induced gene expression changes in the host.

RevDate: 2022-01-14

Sebestyén A, Dankó T, Sztankovics D, et al (2022)

The role of metabolic ecosystem in cancer progression - metabolic plasticity and mTOR hyperactivity in tumor tissues.

Cancer metastasis reviews [Epub ahead of print].

Despite advancements in cancer management, tumor relapse and metastasis are associated with poor outcomes in many cancers. Over the past decade, oncogene-driven carcinogenesis, dysregulated cellular signaling networks, dynamic changes in the tissue microenvironment, epithelial-mesenchymal transitions, protein expression within regulatory pathways, and their part in tumor progression are described in several studies. However, the complexity of metabolic enzyme expression is considerably under evaluated. Alterations in cellular metabolism determine the individual phenotype and behavior of cells, which is a well-recognized hallmark of cancer progression, especially in the adaptation mechanisms underlying therapy resistance. In metabolic symbiosis, cells compete, communicate, and even feed each other, supervised by tumor cells. Metabolic reprogramming forms a unique fingerprint for each tumor tissue, depending on the cellular content and genetic, epigenetic, and microenvironmental alterations of the developing cancer. Based on its sensing and effector functions, the mechanistic target of rapamycin (mTOR) kinase is considered the master regulator of metabolic adaptation. Moreover, mTOR kinase hyperactivity is associated with poor prognosis in various tumor types. In situ metabolic phenotyping in recent studies highlights the importance of metabolic plasticity, mTOR hyperactivity, and their role in tumor progression. In this review, we update recent developments in metabolic phenotyping of the cancer ecosystem, metabolic symbiosis, and plasticity which could provide new research directions in tumor biology. In addition, we suggest pathomorphological and analytical studies relating to metabolic alterations, mTOR activity, and their associations which are necessary to improve understanding of tumor heterogeneity and expand the therapeutic management of cancer.

RevDate: 2022-01-14

Vohník M, Figura T, M Réblová (2022)

Hyaloscypha gabretae and Hyaloscypha gryndleri spp. nov. (Hyaloscyphaceae, Helotiales), two new mycobionts colonizing conifer, ericaceous and orchid roots.

Mycorrhiza [Epub ahead of print].

Historically, Hyaloscypha s. lat. (Hyaloscyphaceae, Helotiales) included various saprobes with small apothecia formed on decaying plant matter, usually wood, that were defined by chemical and (ultra)structural aspects. However, recent molecular phylogenetic and resynthesis studies have narrowed the concept of the genus and shown that it contains several widely distributed species with unknown sexual morphs that form ectomycorrhizae, ericoid mycorrhizae, and mycothalli and also grow endophytically in plant roots and hypogeous ectomycorrhizal (EcM) fruitbodies (i.e., the historical Hymenoscyphus ericae aggregate). Hence, some of the sexually reproducing saprobic Hyaloscypha s. lat. and the symbionts belong to the monophyletic Hyaloscypha s. str. Here, we introduce two new root-symbiotic Hyaloscypha s. str. species, i.e., H. gabretae and H. gryndleri spp. nov. While the former was isolated only from ericaceous hosts (Vaccinium myrtillus from Southern Bohemia, Czechia and Calluna vulgaris from England, UK), the latter was obtained from a basidiomycetous EcM root tip of Picea abies (Pinaceae), roots of Pseudorchis albida (Orchidaceae), and hair roots of V. myrtillus from Southern Bohemia and C. vulgaris from England. Hyaloscypha gryndleri comprises two closely related lineages, suggesting ongoing speciation, possibly connected with the root-symbiotic life-style. Fungal isolates from ericaceous roots with sequences similar to H. gabretae and H. gryndleri have been obtained in Japan and in Canada and Norway, respectively, suggesting a wide and scattered distribution across the Northern Hemisphere. In a series of in vitro experiments, both new species failed to form orchid mycorrhizal structures in roots of P. albida and H. gryndleri repeatedly formed what morphologically corresponds to the ericoid mycorrhizal (ErM) symbiosis in hair roots of V. myrtillus, whereas the ErM potential of H. gabretae remained unresolved. Our results highlight the symbiotic plasticity of root-associated hyaloscyphoid mycobionts as well as our limited knowledge of their diversity and distribution, warranting further ecophysiological and taxonomic research of these important and widespread fungi.

RevDate: 2022-01-14

Muñoz-Gómez SA, Susko E, Williamson K, et al (2022)

Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria.

Nature ecology & evolution [Epub ahead of print].

Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.

RevDate: 2022-01-14
CmpDate: 2022-01-14

Tao L, Qiuhong L, Fuqiang Y, et al (2021)

Plant growth-promoting activities of bacterial endophytes isolated from the medicinal plant Pairs polyphylla var. yunnanensis.

World journal of microbiology & biotechnology, 38(1):15.

Pairs polyphylla var. yunnanensis (Paris L.) is a valuable medicinal plant used in traditional Chinese medicine. The market demand for P. polyphylla has increased over time, but it has slow growth and a low natural propagation rate. Endophytic bacteria are bioactive microorganisms that form a mutualistic relationship with host plants in long-term coordinated evolution, and they can promote the growth and accumulation of effective components in host plants. The aims of this study were to identify endophytic bacteria of P. polyphylla and to characterize their properties in promoting plant growth. A total of 10 endophytic bacteria were isolated from rhizomes of P. polyphylla. The isolated endophytes exhibited a variable capacity for indole acetic acid production, phosphate solubilization and nitrogen fixation. To investigate the effects of the endophytes on plant growth, four endophyte strains, G5, J2, G20, and Y2, were selected to compare their ability to promote plant growth. The results indicated that microbial endophytes isolated from P. polyphylla rhizomes play a vital role in improving P. polyphylla plant growth and could be used as inoculants to establish a sustainable crop production system.

RevDate: 2022-01-14
CmpDate: 2022-01-14

Oh SF, Praveena T, Song H, et al (2021)

Host immunomodulatory lipids created by symbionts from dietary amino acids.

Nature, 600(7888):302-307.

Small molecules derived from symbiotic microbiota critically contribute to intestinal immune maturation and regulation1. However, little is known about the molecular mechanisms that control immune development in the host-microbiota environment. Here, using a targeted lipidomic analysis and synthetic approach, we carried out a multifaceted investigation of immunomodulatory α-galactosylceramides from the human symbiont Bacteroides fragilis (BfaGCs). The characteristic terminal branching of BfaGCs is the result of incorporation of branched-chain amino acids taken up in the host gut by B. fragilis. A B. fragilis knockout strain that cannot metabolize branched-chain amino acids showed reduced branching in BfaGCs, and mice monocolonized with this mutant strain had impaired colonic natural killer T (NKT) cell regulation, implying structure-specific immunomodulatory activity. The sphinganine chain branching of BfaGCs is a critical determinant of NKT cell activation, which induces specific immunomodulatory gene expression signatures and effector functions. Co-crystal structure and affinity analyses of CD1d-BfaGC-NKT cell receptor complexes confirmed the interaction of BfaGCs as CD1d-restricted ligands. We present a structural and molecular-level paradigm of immunomodulatory control by interactions of endobiotic metabolites with diet, microbiota and the immune system.

RevDate: 2022-01-14
CmpDate: 2022-01-14

Maier L, Goemans CV, Wirbel J, et al (2021)

Unravelling the collateral damage of antibiotics on gut bacteria.

Nature, 599(7883):120-124.

Antibiotics are used to fight pathogens but also target commensal bacteria, disturbing the composition of gut microbiota and causing dysbiosis and disease1. Despite this well-known collateral damage, the activity spectrum of different antibiotic classes on gut bacteria remains poorly characterized. Here we characterize further 144 antibiotics from a previous screen of more than 1,000 drugs on 38 representative human gut microbiome species2. Antibiotic classes exhibited distinct inhibition spectra, including generation dependence for quinolones and phylogeny independence for β-lactams. Macrolides and tetracyclines, both prototypic bacteriostatic protein synthesis inhibitors, inhibited nearly all commensals tested but also killed several species. Killed bacteria were more readily eliminated from in vitro communities than those inhibited. This species-specific killing activity challenges the long-standing distinction between bactericidal and bacteriostatic antibiotic classes and provides a possible explanation for the strong effect of macrolides on animal3-5 and human6,7 gut microbiomes. To mitigate this collateral damage of macrolides and tetracyclines, we screened for drugs that specifically antagonized the antibiotic activity against abundant Bacteroides species but not against relevant pathogens. Such antidotes selectively protected Bacteroides species from erythromycin treatment in human-stool-derived communities and gnotobiotic mice. These findings illluminate the activity spectra of antibiotics in commensal bacteria and suggest strategies to circumvent their adverse effects on the gut microbiota.

RevDate: 2022-01-13

Goto Y (2022)

Unique symbiont-derived sphingolipids: Dietary amino acids source branch formation.

Cell host & microbe, 30(1):3-5.

Metabolites derived from symbionts have the potential to regulate host pathophysiological conditions, especially in the gut. In a recent issue of Nature, Oh et al. clarify unique molecular structures of α-galactosylceramides derived from B. fragilis and their immune-modulatory functions against host natural killer T (NKT) cells.

RevDate: 2022-01-13

Jiang D, Lin R, Tan M, et al (2021)

The mycorrhizal-induced growth promotion and insect resistance reduction in Populus alba × P. berolinensis seedlings: a multi-omics study.

Tree physiology pii:6431951 [Epub ahead of print].

Arbuscular mycorrhizal (AM) fungi are an alternative to chemical insecticides or fertilizers, and there is an urgent need to extend the application of AM fungi to woody plants. This study aims to investigate the growth and resistance against the gypsy moth larvae (Lymantria dispar) in Glomus intraradices-colonized Populus alba × P. berolinensis seedlings, and to unravel the transcriptome and metabolome phenotypes recruited by AM fungus colonization that affect plant growth and insect resistance. Our results showed a positive mycorrhizal growth response, i.e., growth and biomass of mycorrhizal seedlings were enhanced. However, AM fungus inoculation reduced the resistance of poplar to gypsy moth larvae, as evidenced by the decreased carbon/nitrogen ratio in leaves, as well as the increased larval growth and shortened larval developmental duration. Transcriptome analysis revealed that in both auxin and gibberellin signaling transductions, all nodes were responsive to AM symbiosis and most differentially expressed genes belonging to effectors were up-regulated in mycorrhizal seedlings. Furthermore, the two key enzymes (4-coumarate-CoA ligase and trans-cinnamate 4-monooxygenase) involved in the synthesis of p-Coumaroyl-CoA, an initial metabolite in flavonoid biosynthesis and the first rate-limiting enzyme (chalcone synthase) in flavonoid biosynthesis, were down-regulated at the transcriptional level. Consistent with the transcriptome results, metabolome analysis found that the amounts of all differentially accumulated flavonoid compounds (e.g., catechin and quercetin) identified in mycorrhizal seedlings were decreased. Taken together, these findings highlight the diverse outcomes of AM fungi-host plant-insect interaction and reveal the regulatory network of the positive mycorrhizal growth response and mycorrhizal-induced reduction of insect resistance in poplar.

RevDate: 2022-01-13

Tanaka S, Hashimoto K, Kobayashi Y, et al (2022)

Asymbiotic mass production of the arbuscular mycorrhizal fungus Rhizophagus clarus.

Communications biology, 5(1):43.

Arbuscular mycorrhizal (AM) symbiosis is a mutually beneficial interaction between fungi and land plants and promotes global phosphate cycling in terrestrial ecosystems. AM fungi are recognised as obligate symbionts that require root colonisation to complete a life cycle involving the production of propagules, asexual spores. Recently, it has been shown that Rhizophagus irregularis can produce infection-competent secondary spores asymbiotically by adding a fatty acid, palmitoleic acid. Furthermore, asymbiotic growth can be supported using myristate as a carbon and energy source for their asymbiotic growth to increase fungal biomass. However, the spore production and the ability of these spores to colonise host roots were still limited compared to the co-culture of the fungus with plant roots. Here we show that a combination of two plant hormones, strigolactone and jasmonate, induces the production of a large number of infection-competent spores in asymbiotic cultures of Rhizophagus clarus HR1 in the presence of myristate and organic nitrogen. Inoculation of asymbiotically-generated spores promoted the growth of host plants, as observed for spores produced by symbiotic culture system. Our findings provide a foundation for the elucidation of hormonal control of the fungal life cycle and the development of inoculum production schemes.

RevDate: 2022-01-13
CmpDate: 2022-01-13

Aparicio A, Velasco-Hernández JX, Moog CH, et al (2021)

Structure-based identification of sensor species for anticipating critical transitions.

Proceedings of the National Academy of Sciences of the United States of America, 118(51):.

Ecological systems can undergo sudden, catastrophic changes known as critical transitions. Anticipating these critical transitions remains challenging in systems with many species because the associated early warning signals can be weakly present or even absent in some species, depending on the system dynamics. Therefore, our limited knowledge of ecological dynamics may suggest that it is hard to identify those species in the system that display early warning signals. Here, we show that, in mutualistic ecological systems, it is possible to identify species that early anticipate critical transitions by knowing only the system structure-that is, the network topology of plant-animal interactions. Specifically, we leverage the mathematical theory of structural observability of dynamical systems to identify a minimum set of "sensor species," whose measurement guarantees that we can infer changes in the abundance of all other species. Importantly, such a minimum set of sensor species can be identified by using the system structure only. We analyzed the performance of such minimum sets of sensor species for detecting early warnings using a large dataset of empirical plant-pollinator and seed-dispersal networks. We found that species that are more likely to be sensors tend to anticipate earlier critical transitions than other species. Our results underscore how knowing the structure of multispecies systems can improve our ability to anticipate critical transitions.

RevDate: 2022-01-13
CmpDate: 2022-01-13

Liu D, Pérez-Moreno J, He X, et al (2021)

Truffle Microbiome Is Driven by Fruit Body Compartmentalization Rather than Soils Conditioned by Different Host Trees.

mSphere, 6(4):e0003921.

Truffles are among the most expensive edible mushrooms; their value is worth billions of U.S. dollars annually in international markets. They establish ectomycorrhizal symbiotic relationships with diverse host tree roots and produce hypogeous ascomata. Their whole life cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host tree rhizospheres are the vital driver for truffle ascomata microbiome is unclear. To identify and compare fungal and bacterial communities in four truffle-associated compartments (Tuber indicum: bulk soil, adhering soil to peridium, peridium, and gleba) from three host trees, we sequenced their ITS (fungal) and 16S (bacterial) ribosomal DNA using the Illumina MiSeq high-throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Tuber indicum microbiome composition was strongly driven by its associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex interacting network compared to that of the fungal community. The core fungal community changed from Basidiomycota dominated (bulk soil) to Rozellomycota dominated (interphase soil); the core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. Especially, at the truffle and soil interphase, the niche-based selection of truffle microbiome was verified by (i) a clear exclusion of four bacterial phyla (Rokubacteria, Nitrospirae, Chloroflexi, and Planctomycetes) in gleba; (ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon, and Simpson indices); and (iii) the complexity of the network substantially decreased from bulk soil to soil-truffle interphase and further to the peridium and gleba. The network analysis of microbiome showed that the microbial positive interactions were higher in truffle tissues than in both bulk soil and peridium-adhering soil and that Cupriavidus, Bradyrhizobium, Aminobacter, and Mesorhizobium spp. were the keystone network hubs in the truffle gleba. This study provides insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components. IMPORTANCE Currently, the factors that drive the microbiome associated with truffles, the most highly prized fungi in the world, are largely unknown. We demonstrate for the first time here that truffle microbiome composition is strongly driven by associated compartments rather than by symbiotic host trees. The truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex (with the higher numbers of nodes, links, and modules) interacting network compared to that of the fungal community. Network analysis showed a higher number of positive microbial interactions with each other in truffle tissues than in both bulk soil and peridium-adhering soil. For the first time, the fungal community structure associated with truffles using high-throughput sequencing, microbial networks, and keystone species analyses is presented. This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing that they are more complex than previously thought.

RevDate: 2022-01-13
CmpDate: 2022-01-13

Konstantinidis D, Pereira F, Geissen EM, et al (2021)

Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion.

Molecular systems biology, 17(8):e10189.

Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutualistic communities for improving secretion of fitness-costly metabolites through natural selection. In this strategy, metabolic cross-feeding connects secretion of the target metabolite, despite its cost to the secretor, to the survival and proliferation of the entire community. We thus co-evolved wild-type lactic acid bacteria and engineered auxotrophic Saccharomyces cerevisiae in a synthetic growth medium leading to bacterial isolates with enhanced secretion of two B-group vitamins, viz., riboflavin and folate. The increased production was specific to the targeted vitamin, and evident also in milk, a more complex nutrient environment that naturally contains vitamins. Genomic, proteomic and metabolomic analyses of the evolved lactic acid bacteria, in combination with flux balance analysis, showed altered metabolic regulation towards increased supply of the vitamin precursors. Together, our findings demonstrate how microbial metabolism adapts to mutualistic lifestyle through enhanced metabolite exchange.

RevDate: 2022-01-12

Bell CA, Magkourilou E, Urwin PE, et al (2022)

Disruption of carbon for nutrient exchange between potato and arbuscular mycorrhizal fungi enhanced cyst nematode fitness and host pest tolerance.

The New phytologist [Epub ahead of print].

▪Plants simultaneously interact with a range of biotrophic symbionts, ranging from mutualists such as arbuscular mycorrhizal fungi (AMF), to parasites such as the potato cyst nematode (PCN). The exchange of mycorrhizal-acquired nutrients for plant-fixed carbon is well-studied, however the impact of competing symbionts remains under-explored. ▪In this study, we examined mycorrhizal nutrient and host resource allocation in potato with and without AMF and PCN using radioisotope tracing, whilst determining the consequences of such allocation. ▪The presence of PCN disrupted carbon for nutrient exchange between plants and AMF, with plant-C overwhelmingly obtained by the nematodes. Despite this, AMF maintained transfer of nutrients on PCN-infected potato, ultimately losing out in their carbon for nutrient exchange with the host. Whilst PCN exploited the greater nutrient reserves to drive population growth on AMF-potato, the fungus imparted tolerance to allow the host to bear the parasitic burden. ▪Our findings provide important insights into the below-ground dynamics of plant-AMF symbioses, where simultaneous nutritional and non-nutritional benefits conferred by AMF to hosts and their parasites are seldom considered in plant community dynamics. Our findings suggest this may be a critical oversight, particularly in the consideration of carbon and nutrient flows in plant and soil communities.

RevDate: 2022-01-12

Cibichakravarthy B, Oses-Prieto JA, Ben-Yosef M, et al (2022)

Comparative Proteomics of Coxiella like Endosymbionts (CLEs) in the Symbiotic Organs of Rhipicephalus sanguineus Ticks.

Microbiology spectrum [Epub ahead of print].

Maternally transmitted obligatory endosymbionts are found in the female gonads as well as in somatic tissue and are expected to provide missing metabolite to their hosts. These deficiencies are presumably complemented through specific symbiotic microorganisms such as Coxiella-like endosymbionts (CLEs) of Rhipicephalus ticks. CLEs are localized in specialized host tissue cells within the Malpighian tubules (Mt) and the ovaries (Ov) from which they are maternally transmitted to developing oocytes. These two organs differ in function and cell types, but the role of CLEs in these tissues is unknown. To probe possible functions of CLEs, comparative proteomics was performed between Mt and Ov of R. sanguineus ticks. Altogether, a total of 580 and 614 CLE proteins were identified in Mt and Ov, respectively. Of these, 276 CLE proteins were more abundant in Mt, of which 12 were significantly differentially abundant. In Ov, 290 CLE proteins were more abundant, of which 16 were significantly differentially abundant. Gene Ontology analysis revealed that most of the proteins enriched in Mt are related to cellular metabolic functions and stress responses, whereas in Ov, the majority were related to cell proliferation suggesting CLEs function differentially and interdependently with host requirements specific to each organ. The results suggest Mt CLEs provide essential nutrients to its host and Ov CLEs promote proliferation and vertical transmission to tick progeny. IMPORTANCE Here we compare the Coxiella-like endosymbionts (CLEs) proteomes from Malpighian tubule (Mt) and the ovaries (Ov) of the brown dog tick Rhipicephalus sanguineus. Our results support the hypothesis that CLEs function interdependently with host requirements in each of the organs. The different functional specificity of CLE in the same host suggest that metabolic capabilities evolved according to the constrains imposed by the specific organ function and requirements. Our findings provide specific CLE protein targets that can be useful for future studies of CLE biology with a focus on tick population control.

RevDate: 2022-01-12

Li Y, Cao P, Wang S, et al (2022)

Research on the treatment mechanism of anthraquinone dye wastewater by algal-bacterial symbiotic system.

Bioresource technology pii:S0960-8524(22)00020-7 [Epub ahead of print].

This study analyzed the role of algae and bacteria in algal-bacterial symbiotic systems for the treatment of dyeing wastewater. The mechanism was investigated by constructing an algae-bacteria tandem system (A system) and a bacteria-algae tandem system (B system). The results showed that the chemical oxygen demand (COD) removal and decolorization rates of A system reached 91% and 90%, respectively, under optimal conditions, which were higher than that of B system. The degradation pathways of A and B systems differed according the degradation product analysis. High-throughput sequencing analysis revealed that Proteobacteria were the dominant bacteria in A and B systems. Armatimonadetes increased considerably in A system. These results show that algae mainly contributed to the preliminary degradation of anthraquinone dye, and resulting products were easily degraded by bacteria. This study provides guidance on the optimization of the system. It can be better adapted to the actual needs of wastewater treatment plants.

RevDate: 2022-01-12
CmpDate: 2022-01-12

Moon EK, Kim MJ, Lee HA, et al (2022)

Comparative analysis of differentially expressed genes in Acanthamoeba after ingestion of Legionella pneumophila and Escherichia coli.

Experimental parasitology, 232:108188.

Acanthamoeba spp. feeds on bacteria, fungi, and algae to obtain nutrients from the environment. However, several pathogens can survive and multiply in Acanthamoeba. Mechanisms necessary for the survival and proliferation of microorganisms in Acanthamoeba remain unclear. The object of this study was to identify effective factors for the survival of microorganisms in Acanthamoeba. Differentially expressed genes (DEGs) in A. castellanii infected by Legionella pneumophila or Escherichia coli were identified based on mRNA sequencing. A total of 2342 and 1878 DEGs were identified in Acanthamoeba with L. pneumophila and E. coli, respectively. Among these DEGs, 502 were up-regulated and 116 were down-regulated in Acanthamoeba infected by L. pneumophila compared to those in Acanthamoeba feed on E. coli. Gene ontology analysis showed that the genes encoded small GTPase-mediated signal transduction proteins in the biological process domain, intracellular proteins in the cellular component domain, and ATP binding proteins in the molecular function domain were up-regulated while integral components of membrane proteins in the cellular component domain were down-regulated in Acanthamoeba infected by Legionella compared to those in Acanthamoeba feed on E. coli. During endosymbiosis with Legionella, Acanthamoeba showed various changes in the expression of genes supposed to be involved in phagosomal maturation. Acanthamoeba infected by Legionella also showed high expression levels of aminotransferase, methyltransferase, and cysteine proteinase but low expression levels of RNA pseudouridine synthase superfamily protein and 2OG-Fe(II) oxygenase superfamily. These results provide directions for further research to understand the survival strategy of L. pneumophila in A. castellanii.

RevDate: 2022-01-12
CmpDate: 2022-01-12

Hamlili FZ, Bérenger JM, Diarra AZ, et al (2021)

Molecular and MALDI-TOF MS identification of swallow bugs Cimex hirundinis (Heteroptera: Cimicidae) and endosymbionts in France.

Parasites & vectors, 14(1):587.

BACKGROUND: The Cimicidae are obligatory blood-feeding ectoparasites of medical and veterinary importance. We aim in the current study to assess the ability of MALDI-TOF MS to identify Cimex hirundinis swallow bugs collected in house martin nests.

METHODS: Swallow bugs were picked out from abandoned nests of house martin swallows and identified morphologically to the species level. The bugs were randomly selected, dissected and then subjected to MALDI-TOF MS and molecular analyses.

RESULTS: A total of 65 adults and 50 nymphs were used in the attempt to determine whether this tool could identify the bug species and discriminate their developmental stages. Five adults and four nymphs of C. hirundinis specimens were molecularly identified to update our MS homemade arthropod database. BLAST analysis of COI gene sequences from these C. hirundinis revealed 98.66-99.12% identity with the corresponding sequences of C. hirundinis of the GenBank. The blind test against the database supplemented with MS reference spectra showed 100% (57/57) C. hirundinis adults and 100% (46/46) C. hirundinis nymphs were reliably identified and in agreement with morphological identification with logarithmic score values between 1.922 and 2.665. Ninety-nine percent of C. hirundinis specimens tested were positive for Wolbachia spp. The sequencing results revealed that they were identical to Wolbachia massiliensis, belonging to the new T-supergroup strain and previously isolated from C. hemipterus.

CONCLUSIONS: We report for the first time to our knowledge a case of human infestation by swallow bugs (C. hirundinis) in France. We also show the usefulness of MALDI-TOF MS in the rapid identification of C. hirundinis specimens and nymphs with minimal sample requirements. We phylogenetically characterized the novel Wolbachia strain (W. massiliensis) infecting C. hirundinis and compared it to other recognized Wolbachia clades.

RevDate: 2022-01-12
CmpDate: 2022-01-12

da Silva Reis A, de Almeida Zampaulo R, Dornelles GDP, et al (2022)

Variation of dipteran ectoparasites (Streblidae) on Anoura geoffroyi Gray, 1838 (Phyllostomidae) in two caves in southeastern Brazil.

Parasitology research, 121(1):255-265.

Bats are parasitized by many different arthropods, among which the dipteran families Nycteribiidae and Streblidae are exclusive to bats. Researches that relate the ecology of ectoparasites with their hosts are fundamental for understanding issues related to the interactions between these two groups, in addition to epidemiological aspects of pathogen transmission. The present study evaluated the rate of infestation by dipteran (Streblidae) ectoparasites in two colonies of Anoura geoffroyi associated with caves in the southeastern Brazil. It also evaluated whether parasitological indices differ significantly with regard to host sex and reproductive condition. A total of 1377 bats were captured, of which 84% were parasitized. From these, a total of 5047 streblid bat flies belonging to three species of three genera were collected and identified. The most abundant was Exastinion clovisi (57%), followed by Anastrebla modestini (30%) and Trichobius propinquus (13%). In general, the populations of ectoparasites fluctuated throughout the year, with peaks of abundance during the rainy season. The sex ratios for the species of ectoparasites were close to one, which differs from what is reported in the literature. In addition, there were significant differences in parasitism rates in relation to host sex and reproductive condition. In both populations, ectoparasite infestation of pregnant or lactating females was significantly higher than for non-reproductive females. New studies aimed at assessing whether these higher rates of infestation have any effect on female bat reproduction are needed.

RevDate: 2022-01-12
CmpDate: 2022-01-12

Oborník M, Z Füssy (2021)

Evolutionary and Molecular Aspects of Plastid Endosymbioses.

Biomolecules, 11(11):.

Plastids are membrane-bound organelles that bestow phototrophic abilities to eukaryotes [...].

RevDate: 2022-01-12
CmpDate: 2022-01-12

Maresca M, Alatou R, Pujol A, et al (2021)

RadA, a MSCRAMM Adhesin of the Dominant Symbiote Ruminococcus gnavus E1, Binds Human Immunoglobulins and Intestinal Mucins.

Biomolecules, 11(11):.

Adhesion to the digestive mucosa is considered a key factor for bacterial persistence within the gut. In this study, we show that Ruminococcus gnavus E1 can express the radA gene, which encodes an adhesin of the MSCRAMMs family, only when it colonizes the gut. The RadA N-terminal region contains an all-β bacterial Ig-like domain known to interact with collagens. We observed that it preferentially binds human immunoglobulins (IgA and IgG) and intestinal mucins. Using deglycosylated substrates, we also showed that the RadA N-terminal region recognizes two different types of motifs, the protein backbone of human IgG and the glycan structure of mucins. Finally, competition assays with lectins and free monosaccharides identified Galactose and N-Acetyl-Galactosamine motifs as specific targets for the binding of RadA to mucins and the surface of human epithelial cells.

RevDate: 2022-01-12
CmpDate: 2022-01-12

Andeweg SP, Keşmir C, BE Dutilh (2021)

Quantifying the Impact of Human Leukocyte Antigen on the Human Gut Microbiota.

mSphere, 6(4):e0047621.

The composition of the gut microbiota is affected by a number of factors, including the innate and adaptive immune system. The major histocompatibility complex (MHC), or the human leukocyte antigen (HLA) in humans, performs an essential role in vertebrate immunity and is very polymorphic in different populations. HLA determines the specificity of T lymphocyte and natural killer (NK) cell responses, including those against the commensal bacteria present in the human gut. Thus, it is likely that our HLA molecules, and thereby the adaptive immune response, can shape the composition of our microbiota. Here, we investigated the effect of HLA haplotype on the microbiota composition. We performed HLA typing and microbiota composition analyses on 3,002 public human gut microbiome data sets. We found that individuals with functionally similar HLA molecules are also similar in their microbiota composition. Our results show a statistical association between host HLA haplotype and gut microbiota composition. Because the HLA haplotype is a readily measurable parameter of the human immune system, these results open the door to incorporating the genetics of the immune system into predictive microbiome models. IMPORTANCE The microorganisms that live in the digestive tracts of humans, known as the gut microbiota, are essential for hosts' survival, as they support crucial functions. For example, they support the host in facilitating the uptake of nutrients and give colonization resistance against pathogens. The composition of the gut microbiota varies among humans. Studies have proposed multiple factors driving the observed variation, including diet, lifestyle, and health condition. Another major influence on the microbiota is the host's genetic background. We hypothesized the immune system to be one of the most important genetic factors driving the differences observed between gut microbiotas. Therefore, we searched for a link between the polymorphic molecules that shape human immune responses and the composition of the microbiota. HLA molecules are the most polymorphic molecules in our genome and therefore makes an excellent candidate to test such an association. To our knowledge for the first time, our results indicate a significant impact of the HLA on the human gut microbiota.

RevDate: 2022-01-11

Jarratt-Barnham E, Zarrabian D, GED Oldroyd (2022)

Symbiotic regulation: How plants seek salvation in starvation.

Current biology : CB, 32(1):R46-R48.

When plants are starved of phosphate, many rely on an ancient symbiosis with arbuscular mycorrhizal fungi to secure a critical supply. A new study demonstrates a molecular basis for the regulation of symbiosis by phosphate starvation.

RevDate: 2022-01-11

Coelho JC, Calhoun ED, Calhoun GN, et al (2022)

Patchy Distribution of GTPases of Immunity Associated Proteins (GIMAP) within Cnidarians and Dinoflagellates Suggests a Complex Evolutionary History.

Genome biology and evolution pii:6500283 [Epub ahead of print].

GTPases of Immunity Associated Proteins (GIMAP) are a group of small GTP binding proteins found in a variety of organisms, including vertebrates, invertebrates, and plants. These proteins are characterized by the highly conserved AIG1 domain, and in vertebrates, have been implicated in regulation of the immune system as well as apoptosis and autophagy, though their exact mechanism of action remains unclear. Recent work on cnidarian GIMAPs suggests a conserved role in immunity, apoptosis, and autophagy- three processes involved in coral bleaching, or the breakdown of cnidarian-dinoflagellate symbiosis. Therefore, to further understand the evolution of GIMAPs in this group of organisms, the purpose of this study was to characterize GIMAP or GIMAP-like sequences utilizing publicly available genomic and transcriptomic data in species across the cnidarian phylogeny. The results revealed a patchy distribution of GIMAPs in cnidarians, with three distinct types referred to as L-GIMAP, S-GIMAP, and GIMAP-like. Additionally, GIMAPs were present in most dinoflagellate species and formed seven well-supported clades. Overall, these results elucidate the distribution of GIMAPs within two distantly related eukaryotic groups and represents the first in-depth investigation on the evolution of these proteins within both protists and basal metazoans.

RevDate: 2022-01-11

Schulte CCM, Ramachandran VK, Papachristodoulou A, et al (2022)

Genome-Scale Metabolic Modelling of Lifestyle Changes in Rhizobium leguminosarum.

mSystems [Epub ahead of print].

Biological nitrogen fixation in rhizobium-legume symbioses is of major importance for sustainable agricultural practices. To establish a mutualistic relationship with their plant host, rhizobia transition from free-living bacteria in soil to growth down infection threads inside plant roots and finally differentiate into nitrogen-fixing bacteroids. We reconstructed a genome-scale metabolic model for Rhizobium leguminosarum and integrated the model with transcriptome, proteome, metabolome, and gene essentiality data to investigate nutrient uptake and metabolic fluxes characteristic of these different lifestyles. Synthesis of leucine, polyphosphate, and AICAR is predicted to be important in the rhizosphere, while myo-inositol catabolism is active in undifferentiated nodule bacteria in agreement with experimental evidence. The model indicates that bacteroids utilize xylose and glycolate in addition to dicarboxylates, which could explain previously described gene expression patterns. Histidine is predicted to be actively synthesized in bacteroids, consistent with transcriptome and proteome data for several rhizobial species. These results provide the basis for targeted experimental investigation of metabolic processes specific to the different stages of the rhizobium-legume symbioses. IMPORTANCE Rhizobia are soil bacteria that induce nodule formation on plant roots and differentiate into nitrogen-fixing bacteroids. A detailed understanding of this complex symbiosis is essential for advancing ongoing efforts to engineer novel symbioses with cereal crops for sustainable agriculture. Here, we reconstruct and validate a genome-scale metabolic model for Rhizobium leguminosarum bv. viciae 3841. By integrating the model with various experimental data sets specific to different stages of symbiosis formation, we elucidate the metabolic characteristics of rhizosphere bacteria, undifferentiated bacteria inside root nodules, and nitrogen-fixing bacteroids. Our model predicts metabolic flux patterns for these three distinct lifestyles, thus providing a framework for the interpretation of genome-scale experimental data sets and identifying targets for future experimental studies.

RevDate: 2022-01-11

Kreuzenbeck NB, Seibel E, Schwitalla JW, et al (2022)

Comparative Genomic and Metabolomic Analysis of Termitomyces Species Provides Insights into the Terpenome of the Fungal Cultivar and the Characteristic Odor of the Fungus Garden of Macrotermes natalensis Termites.

mSystems [Epub ahead of print].

Macrotermitinae termites have domesticated fungi of the genus Termitomyces as food for their colony, analogously to human farmers growing crops. Termites propagate the fungus by continuously blending foraged and predigested plant material with fungal mycelium and spores (fungus comb) within designated subterranean chambers. To test the hypothesis that the obligate fungal symbiont emits specific volatiles (odor) to orchestrate its life cycle and symbiotic relations, we determined the typical volatile emission of fungus comb biomass and Termitomyces nodules, revealing α-pinene, camphene, and d-limonene as the most abundant terpenes. Genome mining of Termitomyces followed by gene expression studies and phylogenetic analysis of putative enzymes related to secondary metabolite production encoded by the genomes uncovered a conserved and specific biosynthetic repertoire across strains. Finally, we proved by heterologous expression and in vitro enzymatic assays that a highly expressed gene sequence encodes a rare bifunctional mono-/sesquiterpene cyclase able to produce the abundant comb volatiles camphene and d-limonene. IMPORTANCE The symbiosis between macrotermitinae termites and Termitomyces is obligate for both partners and is one of the most important contributors to biomass conversion in the Old World tropic's ecosystems. To date, research efforts have dominantly focused on acquiring a better understanding of the degradative capabilities of Termitomyces to sustain the obligate nutritional symbiosis, but our knowledge of the small-molecule repertoire of the fungal cultivar mediating interspecies and interkingdom interactions has remained fragmented. Our omics-driven chemical, genomic, and phylogenetic study provides new insights into the volatilome and biosynthetic capabilities of the evolutionarily conserved fungal genus Termitomyces, which allows matching metabolites to genes and enzymes and, thus, opens a new source of unique and rare enzymatic transformations.

RevDate: 2022-01-11

Ortiz-Barbosa GS, Torres-Martínez L, Manci A, et al (2022)

No disruption of rhizobial symbiosis during early stages of cowpea domestication.

Evolution; international journal of organic evolution [Epub ahead of print].

Modern agriculture intensely selects aboveground plant structures, while often neglecting belowground features, and evolutionary tradeoffs between these traits are predicted to disrupt host control over microbiota. Moreover, drift, inbreeding, and relaxed selection for symbiosis in crops might degrade plant mechanisms that support beneficial microbes. We studied the impact of domestication on the nitrogen fixing symbiosis between cowpea and root-nodulating Bradyrhizobium. We combined genome-wide analyses with a greenhouse inoculation study to investigate genomic diversity, heritability, and symbiosis trait variation among wild and early-domesticated cowpea genotypes. Cowpeas experienced modest decreases in genome-wide diversity during early domestication. Nonetheless, domesticated cowpeas responded efficiently to variation in symbiotic effectiveness, by forming more root nodules with nitrogen-fixing rhizobia and sanctioning non-fixing strains. Domesticated populations invested a larger proportion of host tissues into root nodules than wild cowpeas. Unlike soybean and wheat, cowpea showed no compelling evidence for degradation of symbiosis during domestication. Domesticated cowpeas experienced a less severe bottleneck than these crops and the low nutrient conditions in Africa where cowpea landraces were developed likely favored plant genotypes that gain substantial benefits from symbiosis. Breeders have largely neglected symbiosis traits, but artificial selection for improved plant responses to microbiota could increase plant performance and sustainability. This article is protected by copyright. All rights reserved.

RevDate: 2022-01-11

Das S, Das S, MM Ghangrekar (2022)

Efficacious bioremediation of heavy metals and radionuclides from wastewater employing aquatic macro- and microphytes.

Journal of basic microbiology [Epub ahead of print].

Cytotoxic, mutagenic, and carcinogenic contaminants, such as heavy metals and radionuclides, have become an alarming environmental concern globally, especially for developed and developing nations. Moreover, inefficient prevalent wastewater treatment technologies combined with increased industrial activity and modernization has led to increase in the concentration of toxic metals and radioactive components in the natural water bodies. However, for the improvement of ecosystem of rivers, lakes, and other water sources different physicochemical methods such as membrane filtration, reverse osmosis, activated carbon adsorption, electrocoagulation, and other electrochemical treatment are employed, which are uneconomical and insufficient for the complete abatement of these emerging pollutants. Therefore, the application of bioremediation employing aquatic macrophytes and microphytes have gained considerable importance owing to the benefits of cost-effectiveness, eco-friendly, and higher energy efficiency. Thus, the present review aims to enlighten the readers on the potential application of algae, cyanobacteria, plant, and other aquatic micro- and macrophytes for the elimination of carcinogenic metals and radioactive isotopes from wastewater. Additionally, the use of transgenic plants, genetically modified species, algal-bacterial symbiosis for the enhancement of removal efficiency of mutagenic contaminants are also highlighted. Furthermore, species selection based on robustness, mechanism of different pathways for heavy metal and radionuclide detoxification are elucidated in this review article.

RevDate: 2022-01-11

Wong-Bajracharya J, Singan VR, Monti R, et al (2022)

The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis.

Proceedings of the National Academy of Sciences of the United States of America, 119(3):.

Small RNAs (sRNAs) are known to regulate pathogenic plant-microbe interactions. Emerging evidence from the study of these model systems suggests that microRNAs (miRNAs) can be translocated between microbes and plants to facilitate symbiosis. The roles of sRNAs in mutualistic mycorrhizal fungal interactions, however, are largely unknown. In this study, we characterized miRNAs encoded by the ectomycorrhizal fungus Pisolithus microcarpus and investigated their expression during mutualistic interaction with Eucalyptus grandis. Using sRNA sequencing data and in situ miRNA detection, a novel fungal miRNA, Pmic_miR-8, was found to be transported into E. grandis roots after interaction with P. microcarpus Further characterization experiments demonstrate that inhibition of Pmic_miR-8 negatively impacts the maintenance of mycorrhizal roots in E. grandis, while supplementation of Pmic_miR-8 led to deeper integration of the fungus into plant tissues. Target prediction and experimental testing suggest that Pmic_miR-8 may target the host NB-ARC domain containing transcripts, suggesting a potential role for this miRNA in subverting host signaling to stabilize the symbiotic interaction. Altogether, we provide evidence of previously undescribed cross-kingdom sRNA transfer from ectomycorrhizal fungi to plant roots, shedding light onto the involvement of miRNAs during the developmental process of mutualistic symbioses.

RevDate: 2022-01-11

Abedi A, Hajiahmadi Z, Kordrostami M, et al (2021)

Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study.

Cells, 11(1): pii:cells11010037.

The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes' function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.

RevDate: 2022-01-11

Shin D, Kim HU, Kulkarni A, et al (2021)

Development of Force Sensor System Based on Tri-Axial Fiber Bragg Grating with Flexure Structure.

Sensors (Basel, Switzerland), 22(1): pii:s22010016.

Fiber Bragg grating (FBG) sensors have an advantage over optical sensors in that they are lightweight, easy to terminate, and have a high flexibility and a low cost. Additionally, FBG is highly sensitive to strain and temperature, which is why it has been used in FBG force sensor systems for cardiac catheterization. When manually inserting the catheter, the physician should sense the force at the catheter tip under the limitation of power (<0.5 N). The FBG force sensor can be optimal for a catheter as it can be small, low-cost, easy to manufacture, free of electromagnetic interference, and is materially biocompatible with humans. In this study, FBG fibers mounted on two different flexure structures were designed and simulated using ANSYS simulation software to verify their sensitivity and durability for use in a catheter tip. The selected flexure was combined with three FBGs and an interrogator to obtain the wavelength signals. To obtain a calibration curve, the FBG sensor obtained data on the change in wavelength with force at a high resolution of 0.01 N within the 0.1-0.5 N range. The calibration curve was used in the force sensor system by the LabVIEW program to measure the unknown force values in real time.

RevDate: 2022-01-11

Corcoz L, Păcurar F, Pop-Moldovan V, et al (2021)

Mycorrhizal Patterns in the Roots of Dominant Festuca rubra in a High-Natural-Value Grassland.

Plants (Basel, Switzerland), 11(1): pii:plants11010112.

Grassland ecosystems occupy significant areas worldwide and represent a reservoir for biodiversity. These areas are characterized by oligotrophic conditions that stimulate mycorrhizal symbiotic partnerships to meet nutritional requirements. In this study, we selected Festuca rubra for its dominance in the studied mountain grassland, based on the fact that grasses more easily accept a symbiotic partner. Quantification of the entire symbiosis process, both the degree of colonization and the presence of a fungal structure, was performed using the root mycorrhizal pattern method. Analysis of data normality indicated colonization frequency as the best parameter for assessing the entire mycorrhizal mechanism, with five equal levels, each of 20%. Most of the root samples showed an intensity of colonization between 0 and 20% and a maximum of arbuscules of about 5%. The colonization degree had an average value of 35%, which indicated a medium permissiveness of roots for mycorrhizal partners. Based on frequency regression models, the intensity of colonization presented high fluctuations at 50% frequency, while the arbuscule development potential was set to a maximum of 5% in mycorrhized areas. Arbuscules were limited due to the unbalanced and unequal root development and their colonizing hyphal networks. The general regression model indicated that only 20% of intra-radicular hyphae have the potential to form arbuscules. The colonization patterns of dominant species in mountain grasslands represent a necessary step for improved understanding of the symbiont strategies that sustain the stability and persistence of these species.

RevDate: 2022-01-11

Wagle SA, Harikrishnan R, Ali SHM, et al (2021)

Classification of Plant Leaves Using New Compact Convolutional Neural Network Models.

Plants (Basel, Switzerland), 11(1): pii:plants11010024.

Precision crop safety relies on automated systems for detecting and classifying plants. This work proposes the detection and classification of nine species of plants of the PlantVillage dataset using the proposed developed compact convolutional neural networks and AlexNet with transfer learning. The models are trained using plant leaf data with different data augmentations. The data augmentation shows a significant improvement in classification accuracy. The proposed models are also used for the classification of 32 classes of the Flavia dataset. The proposed developed N1 model has a classification accuracy of 99.45%, N2 model has a classification accuracy of 99.65%, N3 model has a classification accuracy of 99.55%, and AlexNet has a classification accuracy of 99.73% for the PlantVillage dataset. In comparison to AlexNet, the proposed models are compact and need less training time. The proposed N1 model takes 34.58%, the proposed N2 model takes 18.25%, and the N3 model takes 20.23% less training time than AlexNet. The N1 model and N3 models are size 14.8 MB making it 92.67% compact, and the N2 model is 29.7 MB which makes it 85.29% compact as compared to AlexNet. The proposed models are giving good accuracy in classifying plant leaf, as well as diseases in tomato plant leaves.

RevDate: 2022-01-11

Mendiola SY, Stoy KS, DiSalvo S, et al (2022)

Competitive Exclusion of Phytopathogenic Serratia marcescens from Squash Bug Vectors by the Gut Endosymbiont Caballeronia.

Applied and environmental microbiology, 88(1):e0155021.

Many insects harbor microbial symbiotic partners that offer protection against pathogens, parasitoids, and other natural enemies. Mounting evidence suggests that these symbiotic microbes can play key roles in determining infection outcomes in insect vectors, making them important players in the quest to develop novel vector control strategies. Using the squash bug Anasa tristis, we investigated how the presence of Caballeronia symbionts affected the persistence and intensity of phytopathogenic Serratia marcescens within the insect vector. We reared insects aposymbiotically and with different Caballeronia isolates, infected them with S. marcescens, and then sampled the insects periodically to assess the intensity and persistence of pathogen infection. Squash bugs harboring Caballeronia consistently had much lower-intensity infections and cleared S. marcescens significantly faster than their aposymbiotic counterparts. These patterns held even when we reversed the timing of exposure to symbiont and pathogen. Taken together, these results indicate that Caballeronia symbionts play an essential role in S. marcescens infection outcomes in squash bugs and could be used to alter vector competence to enhance agricultural productivity in the future. IMPORTANCE Insect-microbe symbioses have repeatedly been shown to profoundly impact an insect's ability to vector pathogens to other hosts. The use of symbiotic microbes to control insect vector populations is of growing interest in agricultural settings. Our study examines how symbiotic microbes affect the dynamics of a plant pathogen infection within the squash bug vector Anasa tristis, a well-documented pest of squash and other cucurbit plants and a vector of Serratia marcescens, the causative agent of cucurbit yellow vine disease. We provide evidence that the symbiont Caballeronia prevents successful, long-term establishment of S. marcescens in the squash bug. These findings give us insight into symbiont-pathogen dynamics within the squash bug that could ultimately determine its ability to transmit pathogens and be leveraged to interrupt disease transmission in this system.

RevDate: 2022-01-11
CmpDate: 2022-01-11

Esposito R, Ruocco N, Viel T, et al (2021)

Sponges and Their Symbionts as a Source of Valuable Compounds in Cosmeceutical Field.

Marine drugs, 19(8):.

In the last decades, the marine environment was discovered as a huge reservoir of novel bioactive compounds, useful for medicinal treatments improving human health and well-being. Among several marine organisms exhibiting biotechnological potential, sponges were highlighted as one of the most interesting phyla according to a wide literature describing new molecules every year. Not surprisingly, the first marine drugs approved for medical purposes were isolated from a marine sponge and are now used as anti-cancer and anti-viral agents. In most cases, experimental evidence reported that very often associated and/or symbiotic communities produced these bioactive compounds for a mutual benefit. Nowadays, beauty treatments are formulated taking advantage of the beneficial properties exerted by marine novel compounds. In fact, several biological activities suitable for cosmetic treatments were recorded, such as anti-oxidant, anti-aging, skin whitening, and emulsifying activities, among others. Here, we collected and discussed several scientific contributions reporting the cosmeceutical potential of marine sponge symbionts, which were exclusively represented by fungi and bacteria. Bioactive compounds specifically indicated as products of the sponge metabolism were also included. However, the origin of sponge metabolites is dubious, and the role of the associated biota cannot be excluded, considering that the isolation of symbionts represents a hard challenge due to their uncultivable features.

RevDate: 2022-01-11
CmpDate: 2022-01-11

Takeuchi T, Miyauchi E, Kanaya T, et al (2021)

Acetate differentially regulates IgA reactivity to commensal bacteria.

Nature, 595(7868):560-564.

The balance between bacterial colonization and its containment in the intestine is indispensable for the symbiotic relationship between humans and their bacteria. One component to maintain homeostasis at the mucosal surfaces is immunoglobulin A (IgA), the most abundant immunoglobulin in mammals1,2. Several studies have revealed important characteristics of poly-reactive IgA3,4, which is produced naturally without commensal bacteria. Considering the dynamic changes within the gut environment, however, it remains uncertain how the commensal-reactive IgA pool is shaped and how such IgA affects the microbial community. Here we show that acetate-one of the major gut microbial metabolites-not only increases the production of IgA in the colon, but also alters the capacity of the IgA pool to bind to specific microorganisms including Enterobacterales. Induction of commensal-reactive IgA and changes in the IgA repertoire by acetate were observed in mice monocolonized with Escherichia coli, which belongs to Enterobacterales, but not with the major commensal Bacteroides thetaiotaomicron, which suggests that acetate directs selective IgA binding to certain microorganisms. Mechanistically, acetate orchestrated the interactions between epithelial and immune cells, induced microbially stimulated CD4 T cells to support T-cell-dependent IgA production and, as a consequence, altered the localization of these bacteria within the colon. Collectively, we identified a role for gut microbial metabolites in the regulation of differential IgA production to maintain mucosal homeostasis.

RevDate: 2022-01-10

Tran CTK, Watts-Williams SJ, Smernik RJ, et al (2022)

Arbuscular mycorrhizas increased tomato biomass and nutrition but did not affect local soil P availability or 16S bacterial community in the field.

The Science of the total environment pii:S0048-9697(21)07698-1 [Epub ahead of print].

While interest in arbuscular mycorrhizal (AM) fungal effects on soil phosphorus (P) have recently increased, field experiments on this topic are lacking. While microcosm studies provided valuable insights, the lack of field studies represents a knowledge gap. Here, we present a field study in which we grew a mycorrhiza-defective tomato (Solanum lycopersicum L.) genotype (named rmc) and its mycorrhizal wild-type progenitor (named 76R) with and without additional fertiliser, using a drip-irrigation system to examine the impacts of the AM symbiosis on soil P availability and plant growth and nutrition. AM effects on fruit biomass and nutrients, soil nutrient availability, soil moisture and the soil bacterial community were examined. At the time of harvest, the AM tomato plants without fertiliser had the same early season fruit biomass and fruit nutrient concentrations as plants that received fertiliser. The presence of roots reduced the concentration of available soil P, ammonium and soil moisture in the top 10 cm soil layer. Arbuscular mycorrhizas did not significantly affect soil P availability, soil moisture, or 16S bacterial community composition. These findings suggest an indirect role for AM fungi for tomato production but not necessarily a direct role in determining soil physicochemical traits, during the one season that this experiment was conducted. While longer-term field studies may be required in the future, the present study provides new insights into impacts of AM on P availability and uptake in a field soil system, in a single growing season.

RevDate: 2022-01-10

Fokin SI, V Serra (2022)

Bacterial Symbiosis in Ciliates (Alveolata, Ciliophora): Roads Traveled and Those Still to be Taken.

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

The diversity of prokaryotic symbionts in Ciliophora and other protists is fascinatingly rich; they may even include some potentially pathogenic bacteria. In this review, we summarize currently available data on biodiversity and some morphological and biological peculiarities of prokaryotic symbionts mainly within the genera Paramecium and Euplotes. Another direction of ciliates symbiology, neglected for a long time and now re-discovered, is the study of epibionts of ciliates. This promises a variety of interesting outcomes. Last, but not least, we stress the new technologies such as next generation sequencing and the use of genomics data which all can clarify many new aspects of relevance. For this reason, a brief overview of achievements in genomics studies on ciliate's symbionts is provided. Summing up the results of numerous scientific contributions, we systematically update current knowledge and outline the prospects as to how symbiology of Ciliophora may develop in the near future.

RevDate: 2022-01-10

Ferguson TD, Vanzant ES, KR McLeod (2021)

Endophyte Infected Tall Fescue: Plant Symbiosis to Animal Toxicosis.

Frontiers in veterinary science, 8:774287.

Endophyte-infected fescue is a major cool season forage used for livestock production in the United States and through other areas of the world. A unique aspect of this forage resource is the symbiotic relationship with an endophytic fungus (Epichloë coenophiala) that has detrimental impact on herbivores due to toxic ergot alkaloids. Research over the past 50 years has unveiled details regarding this symbiotic relationship. This review focuses on the origin of tall fescue in the United States and the consequences of its wide-spread utilization as a livestock forage, along with the discovery and toxicodynamics of ergot alkaloids produced by E. coenophiala. The majority of past ergot alkaloid research has focused on observing phenotypic changes that occur in livestock affected by ergot alkaloids, but recent investigation of the metabolome, transcriptome, and proteome have shown that fescue toxicity-related illnesses are much more complex than previous research suggests.

RevDate: 2022-01-10

R E, Jain DK, Kotecha K, et al (2021)

Hybrid Deep Neural Network for Handling Data Imbalance in Precursor MicroRNA.

Frontiers in public health, 9:821410.

Over the last decade, the field of bioinformatics has been increasing rapidly. Robust bioinformatics tools are going to play a vital role in future progress. Scientists working in the field of bioinformatics conduct a large number of researches to extract knowledge from the biological data available. Several bioinformatics issues have evolved as a result of the creation of massive amounts of unbalanced data. The classification of precursor microRNA (pre miRNA) from the imbalanced RNA genome data is one such problem. The examinations proved that pre miRNAs (precursor microRNAs) could serve as oncogene or tumor suppressors in various cancer types. This paper introduces a Hybrid Deep Neural Network framework (H-DNN) for the classification of pre miRNA in imbalanced data. The proposed H-DNN framework is an integration of Deep Artificial Neural Networks (Deep ANN) and Deep Decision Tree Classifiers. The Deep ANN in the proposed H-DNN helps to extract the meaningful features and the Deep Decision Tree Classifier helps to classify the pre miRNA accurately. Experimentation of H-DNN was done with genomes of animals, plants, humans, and Arabidopsis with an imbalance ratio up to 1:5000 and virus with a ratio of 1:400. Experimental results showed an accuracy of more than 99% in all the cases and the time complexity of the proposed H-DNN is also very less when compared with the other existing approaches.

RevDate: 2022-01-10

Zani ROA, Ferro M, M Bacci (Jr) (2021)

Three phylogenetically distinct and culturable diazotrophs are perennial symbionts of leaf-cutting ants.

Ecology and evolution, 11(24):17686-17699 pii:ECE38213.

The obligate mutualistic basidiomycete fungus, Leucocoprinus gongylophorus, mediates nutrition of leaf-cutting ants with carbons from vegetal matter. In addition, diazotrophic Enterobacteriales in the fungus garden and intestinal Rhizobiales supposedly mediate assimilation of atmospheric nitrogen, and Entomoplasmatales in the genus Mesoplasma, as well as other yet unidentified strains, supposedly mediate ant assimilation of other compounds from vegetal matter, such as citrate, fructose, and amino acids. Together, these nutritional partners would support the production of high yields of leafcutter biomass. In the present investigation, we propose that three phylogenetically distinct and culturable diazotrophs in the genera Ralstonia, Methylobacterium, and Pseudomonas integrate this symbiotic nutrition network, facilitating ant nutrition on nitrogen. Strains in these genera were often isolated and directly sequenced in 16S rRNA libraries from the ant abdomen, together with the nondiazotrophs Acinetobacter and Brachybacterium. These five isolates were underrepresented in libraries, suggesting that none of them is dominant in vivo. Libraries have been dominated by four uncultured Rhizobiales strains in the genera Liberibacter, Terasakiella, and Bartonella and, only in Acromyrmex ants, by the Entomoplasmatales in the genus Mesoplasma. Acromyrmex also presented small amounts of two other uncultured Entomoplasmatales strains, Entomoplasma and Spiroplasma. The absence of Entomoplasmatales in Atta workers implicates that the association with these bacteria is not mandatory for ant biomass production. Most of the strains that we detected in South American ants were genetically similar with strains previously described in association with leafcutters from Central and North America, indicating wide geographic dispersion, and suggesting fixed ecological services.

RevDate: 2022-01-10

Unger S, Habermann FM, Schenke K, et al (2021)

Arbuscular Mycorrhizal Fungi and Nutrition Determine the Outcome of Competition Between Lolium multiflorum and Trifolium subterraneum.

Frontiers in plant science, 12:778861.

Arbuscular mycorrhizal fungi (AMF) may affect competitive plant interactions, which are considered a prevalent force in shaping plant communities. Aiming at understanding the role of AMF in the competition between two pasture species and its dependence on soil nutritional status, a pot experiment with mycorrhizal and non-mycorrhizal Lolium multiflorum and Trifolium subterraneum was conducted, with manipulation of species composition (five levels), and nitrogen (N)- and phosphorus (P)- fertilization (three levels). In the non-mycorrhizal state, interspecific competition did not play a major role. However, in the presence of AMF, Lolium was the strongest competitor, with this species being facilitated by Trifolium. While N-fertilization did not change the competitive balance, P-fertilization gave Lolium, a competitive advantage over Trifolium. The effect of AMF on the competitive outcome may be driven by differential C-P trade benefits, with Lolium modulating carbon investment in the mycorrhizal network and the arbuscule/vesicle ratio at the cost of Trifolium.

RevDate: 2022-01-10

Cheng S, Zou YN, Kuča K, et al (2021)

Elucidating the Mechanisms Underlying Enhanced Drought Tolerance in Plants Mediated by Arbuscular Mycorrhizal Fungi.

Frontiers in microbiology, 12:809473.

Plants are often subjected to various environmental stresses during their life cycle, among which drought stress is perhaps the most significant abiotic stress limiting plant growth and development. Arbuscular mycorrhizal (AM) fungi, a group of beneficial soil fungi, can enhance the adaptability and tolerance of their host plants to drought stress after infecting plant roots and establishing a symbiotic association with their host plant. Therefore, AM fungi represent an eco-friendly strategy in sustainable agricultural systems. There is still a need, however, to better understand the complex mechanisms underlying AM fungi-mediated enhancement of plant drought tolerance to ensure their effective use. AM fungi establish well-developed, extraradical hyphae on root surfaces, and function in water absorption and the uptake and transfer of nutrients into host cells. Thus, they participate in the physiology of host plants through the function of specific genes encoded in their genome. AM fungi also modulate morphological adaptations and various physiological processes in host plants, that help to mitigate drought-induced injury and enhance drought tolerance. Several AM-specific host genes have been identified and reported to be responsible for conferring enhanced drought tolerance. This review provides an overview of the effect of drought stress on the diversity and activity of AM fungi, the symbiotic relationship that exists between AM fungi and host plants under drought stress conditions, elucidates the morphological, physiological, and molecular mechanisms underlying AM fungi-mediated enhanced drought tolerance in plants, and provides an outlook for future research.

RevDate: 2022-01-10

Moya P, Molins A, Škaloud P, et al (2021)

Biodiversity Patterns and Ecological Preferences of the Photobionts Associated With the Lichen-Forming Genus Parmelia.

Frontiers in microbiology, 12:765310.

The worldwide, ecologically relevant lichen-forming genus Parmelia currently includes 41 accepted species, of which the Parmelia sulcata group (PSULgp) and the Parmelia saxatilis group (PSAXgp) have received considerable attention over recent decades; however, phycobiont diversity is poorly known in Parmelia s. lat. Here, we studied the diversity of Trebouxia microalgae associated with 159 thalli collected from 30 locations, including nine Parmelia spp.: P. barrenoae, P. encryptata, P. ernstiae, P. mayi, P. omphalodes, P. saxatilis, P. serrana, P. submontana, and P. sulcata. The mycobionts were studied by carrying out phylogenetic analyses of the nrITS. Microalgae genetic diversity was examined by using both nrITS and LSU rDNA markers. To evaluate putative species boundaries, three DNA species delimitation analyses were performed on Trebouxia and Parmelia. All analyses clustered the mycobionts into two main groups: PSULgp and PSAXgp. Species delimitation identified 13 fungal and 15 algal species-level lineages. To identify patterns in specificity and selectivity, the diversity and abundance of the phycobionts were identified for each Parmelia species. High specificity of each Parmelia group for a given Trebouxia clade was observed; PSULgp associated only with clade I and PSAXgp with clade S. However, the degree of specificity is different within each group, since the PSAXgp mycobionts were less specific and associated with 12 Trebouxia spp., meanwhile those of PSULgp interacted only with three Trebouxia spp. Variation-partitioning analyses were conducted to detect the relative contributions of climate, geography, and symbiotic partner to phycobiont and mycobiont distribution patterns. Both analyses explained unexpectedly high portions of variability (99 and 98%) and revealed strong correlations between the fungal and algal diversity. Network analysis discriminated seven ecological clusters. Even though climatic conditions explained the largest proportion of the variation among these clusters, they seemed to show indifference relative to climatic parameters. However, the cluster formed by P. saxatilis A/P. saxatilis B/Trebouxia sp. 2/Trebouxia sp. S02/Trebouxia sp. 3A was identified to prefer cold-temperate as well as humid summer environments.

RevDate: 2022-01-10

Gite S, Mishra A, K Kotecha (2022)

Enhanced lung image segmentation using deep learning.

Neural computing & applications pii:6719 [Epub ahead of print].

With the advances in technology, assistive medical systems are emerging with rapid growth and helping healthcare professionals. The proactive diagnosis of diseases with artificial intelligence (AI) and its aligned technologies has been an exciting research area in the last decade. Doctors usually detect tuberculosis (TB) by checking the lungs' X-rays. Classification using deep learning algorithms is successfully able to achieve accuracy almost similar to a doctor in detecting TB. It is found that the probability of detecting TB increases if classification algorithms are implemented on segmented lungs instead of the whole X-ray. The paper's novelty lies in detailed analysis and discussion of U-Net + + results and implementation of U-Net + + in lung segmentation using X-ray. A thorough comparison of U-Net + + with three other benchmark segmentation architectures and segmentation in diagnosing TB or other pulmonary lung diseases is also made in this paper. To the best of our knowledge, no prior research tried to implement U-Net + + for lung segmentation. Most of the papers did not even use segmentation before classification, which causes data leakage. Very few used segmentations before classification, but they only used U-Net, which U-Net + + can easily replace because accuracy and mean_iou of U-Net + + are greater than U-Net accuracy and mean_iou , discussed in results, which can minimize data leakage. The authors achieved more than 98% lung segmentation accuracy and mean_iou 0.95 using U-Net + + , and the efficacy of such comparative analysis is validated.

RevDate: 2022-01-10

Kumar S, Sharma D, Rao S, et al (2022)

Past, present, and future of sustainable finance: insights from big data analytics through machine learning of scholarly research.

Annals of operations research pii:4410 [Epub ahead of print].

Sustainable finance is a rich field of research. Yet, existing reviews remain limited due to the piecemeal insights offered through a sub-set rather than the entire corpus of sustainable finance. To address this gap, this study aims to conduct a large-scale review that would provide a state-of-the-art overview of the performance and intellectual structure of sustainable finance. To do so, this study engages in a review of sustainable finance research using big data analytics through machine learning of scholarly research. In doing so, this study unpacks the most influential articles and top contributing journals, authors, institutions, and countries, as well as the methodological choices and research contexts for sustainable finance research. In addition, this study reveals insights into seven major themes of sustainable finance research, namely socially responsible investing, climate financing, green financing, impact investing, carbon financing, energy financing, and governance of sustainable financing and investing. To drive the field forward, this study proposes several suggestions for future sustainable finance research, which include developing and diffusing innovative sustainable financing instruments, magnifying and managing the profitability and returns of sustainable financing, making sustainable finance more sustainable, devising and unifying policies and frameworks for sustainable finance, tackling greenwashing of corporate sustainability reporting in sustainable finance, shining behavioral finance on sustainable finance, and leveraging the power of new-age technologies such as artificial intelligence, blockchain, internet of things, and machine learning for sustainable finance.

RevDate: 2022-01-09

Cheng H, Yuan M, Tang L, et al (2022)

Integrated microbiology and metabolomics analysis reveal responses of soil microorganisms and metabolic functions to phosphorus fertilizer on semiarid farm.

The Science of the total environment pii:S0048-9697(21)07957-2 [Epub ahead of print].

Localized fertilization of phosphorus has potential benefits in achieving higher crop productivity and nutrient use efficiency, but the underlying biological mechanisms of interactions between soil microorganisms and related metabolic cycle remain largely to be recognized. Here, we combined microbiology with non-target metabolomics to explore how P fertilizer levels and fertilization patterns affect wheat soil microbial communities and metabolic functions on high-throughput sequencing and UPLC-MS/MS platforms. The results showed P fertilizer decreased the diversity of bacterial 16S rRNA genes and fungal ITS genes, and it did significantly change both soil bacterial and fungal overall community structures and compositions. The P levels and patterns also interfered with complexity of soil bacterial and fungal symbiosis networks. Moreover, metabolomics analysis showed that P fertilizer significantly changed soil metabolite spectrum, and the differential metabolites were significantly enriched to 7 main metabolic pathways, such as arginine and proline metabolism, biosynthesis of plant hormones, amino acids, plant secondary metabolites, and alkaloids derived from ornithine. Additionally, microbes also were closely related to the accumulation of metabolites through correlation analysis. Our results indicated that localized appropriate phosphorus fertilizer plays an important role in regulating soil microbial metabolism, and their interactions in soil providing valuable information for understanding how the changed phosphorus management practices affect the complex biological processes and the adaption capacity of plants to environments.

RevDate: 2022-01-10
CmpDate: 2022-01-10

Mesny F, Miyauchi S, Thiergart T, et al (2021)

Genetic determinants of endophytism in the Arabidopsis root mycobiome.

Nature communications, 12(1):7227.

The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.

RevDate: 2022-01-10
CmpDate: 2022-01-10

Borowiec ML, Cover SP, C Rabeling (2021)

The evolution of social parasitism in Formica ants revealed by a global phylogeny.

Proceedings of the National Academy of Sciences of the United States of America, 118(38):.

Studying the behavioral and life history transitions from a cooperative, eusocial life history to exploitative social parasitism allows for deciphering the conditions under which changes in behavior and social organization lead to diversification. The Holarctic ant genus Formica is ideally suited for studying the evolution of social parasitism because half of its 172 species are confirmed or suspected social parasites, which includes all three major classes of social parasitism known in ants. However, the life history transitions associated with the evolution of social parasitism in this genus are largely unexplored. To test competing hypotheses regarding the origins and evolution of social parasitism, we reconstructed a global phylogeny of Formica ants. The genus originated in the Old World ∼30 Ma ago and dispersed multiple times to the New World and back. Within Formica, obligate dependent colony-founding behavior arose once from a facultatively polygynous common ancestor practicing independent and facultative dependent colony foundation. Temporary social parasitism likely preceded or arose concurrently with obligate dependent colony founding, and dulotic social parasitism evolved once within the obligate dependent colony-founding clade. Permanent social parasitism evolved twice from temporary social parasitic ancestors that rarely practiced colony budding, demonstrating that obligate social parasitism can originate from a facultative parasitic background in socially polymorphic organisms. In contrast to permanently socially parasitic ants in other genera, the high parasite diversity in Formica likely originated via allopatric speciation, highlighting the diversity of convergent evolutionary trajectories resulting in nearly identical parasitic life history syndromes.

RevDate: 2022-01-10
CmpDate: 2022-01-10

Stoeva MK, Garcia-So J, Justice N, et al (2021)

Butyrate-producing human gut symbiont, Clostridium butyricum, and its role in health and disease.

Gut microbes, 13(1):1-28.

Clostridium butyricum is a butyrate-producing human gut symbiont that has been safely used as a probiotic for decades. C. butyricum strains have been investigated for potential protective or ameliorative effects in a wide range of human diseases, including gut-acquired infection, intestinal injury, irritable bowel syndrome, inflammatory bowel disease, neurodegenerative disease, metabolic disease, and colorectal cancer. In this review we summarize the studies on C. butyricum supplementation with special attention to proposed mechanisms for the associated health benefits and the supporting experimental evidence. These mechanisms center on molecular signals (especially butyrate) as well as immunological signals in the digestive system that cascade well beyond the gut to the liver, adipose tissue, brain, and more. The safety of probiotic C. butyricum strains appears well-established. We identify areas where additional human randomized controlled trials would provide valuable further data related to the strains' utility as an intervention.

RevDate: 2022-01-08

Zhukova NV, Eliseikina MG, Balakirev ES, et al (2022)

Multiple bacterial partners in symbiosis with the nudibranch mollusk Rostanga alisae.

Scientific reports, 12(1):169.

The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host's ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations. A total of 74 clones belonging to the phyla α-, β-, γ-Proteobacteria, Actinobacteria, and Cyanobacteria were identified. FISH confirmed that bacteriocytes were packed with Bradyrhizobium, Maritalea, Labrenzia, Bulkholderia, Achromobacter, and Stenotrophomonas mainly in the foot and notum epidermis, and also an abundance of Synechococcus cyanobacteria in the intestinal epithelium. An ultrastructural analysis showed several bacterial morphotypes of bacteria in epidermal cells, intestine epithelium, and in mucus layer covering the mollusk body. The high proportion of typical bacterial fatty acids in R. alisae indicated that symbiotic bacteria make a substantial contribution to its nutrition. Thus, the nudibranch harbors a high diversity of specific endo- and extracellular bacteria, which previously unknown as symbionts of marine invertebrates that provide the mollusk with essential nutrients. They can provide chemical defense against predators.

RevDate: 2022-01-07

Guha S, Molla F, Sarkar M, et al (2022)

Nod factor-independent 'crack-entry' symbiosis in dalbergoid legume Arachis hypogaea.

Environmental microbiology [Epub ahead of print].

Dalbergoids are typified by crack-entry symbiosis which is evidenced to be Nod Factor (NF)- independent in several Aeschynomene legumes. Natural symbionts of the dalbergoid legume Arachis hypogaea are always NF-producing, prompting us to check whether symbiosis in this legume could also be NF-independent. For this, we followed the symbiosis with two NF containing bradyrhizobial strains- SEMIA6144, a natural symbiont of Arachis and ORS285, a versatile nodulator of Aeschynomene legumes, along with their corresponding nodulation (nod) mutants. Additionally, we investigated NF-deficient bradyrhizobia like BTAi1, a natural symbiont of Aeschynomene indica and the WBOS strains that were natural endophytes of Oryza sativa, collected from an Arachis-Oryza intercropped field. While SEMIA6144ΔnodC was non-nodulating, both ORS285 and ORS285ΔnodB could induce functional nodulation, although with lower efficiency than SEMIA6144. On the other hand, all the NF-deficient strains- BTAi1, WBOS2 and WBOS4 showed comparable nodulation with ORS285 indicating Arachis to harbour a NF-independent mechanism of symbiosis. Intriguingly, symbiosis in Arachis, irrespective of whether it was NF-dependent or independent, was always associated with the curling or branching of the rosette root hairs at the lateral root bases. Thus, despite being predominantly described as NF-dependent legume, Arachis does retain a vestigial, less-efficient form of NF-independent symbiosis. This article is protected by copyright. All rights reserved.

RevDate: 2022-01-07

Banerji R, Iyer P, SD Saroj (2022)

Spermidine enhances the survival of Streptococcus pyogenes M3 under oxidative stress.

Molecular oral microbiology [Epub ahead of print].

Streptococcus pyogenes, a host-restricted gram-positive pathogen during infection, initially adheres to the epithelia of the nasopharynx and respiratory tract of the human host; followed by disseminating to other organs and evading the host immune system. Upon phagocytosis, S. pyogenes encounters oxidative stress inside the macrophages. The role of polyamines in regulating various physiological functions, including stress resistance in bacteria have been reported widely. Since S. pyogenes lacks the machinery for the biosynthesis of polyamines, the study aimed to understand the role of extracellular polyamines in the survival of S. pyogenes under oxidative stress environments. S. pyogenes being a catalase-negative organism, we report that its survival within the macrophages and H2 O2 is enhanced by the presence of spermidine. The increased survival can be attributed to the upregulation of oxidative stress response genes like sodM, npx, and mtsABC. In addition, spermidine influences the upregulation of virulence factors such as sagA, slo, and hasA. Also, spermidine leads to a decrease in hydrophobicity of the cell membrane and an increase in hyaluronic acid. This report suggests a role for extracellular spermidine in the survival of S. pyogenes under oxidative stress environments. Recognizing the factors that modulate S. pyogenes survival and virulence under stress will assist in understanding its interactions with the host. This article is protected by copyright. All rights reserved.

RevDate: 2022-01-07

Lee JG, Lee S, Jeon J, et al (2022)

Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism.

Microbiome, 10(1):3.

BACKGROUND: Host tp53 mutations are frequently found during the early stages of colitis-associated colorectal cancer (CAC), but whether such mutations induce gut microbiota dysbiosis and chronic intestinal inflammation that contributes to the development of CAC, remains unknown.

RESULTS: We found that zebrafish tp53 mutant larvae exhibited elevated intestinal inflammation, by monitoring the NFκB activity in the mid-distal intestines of zebrafish larvae using an NFκB:EGFP transgenic reporter line in vivo as well as neutrophil infiltration into the intestine. This inflammation was due to dysbiotic gut microbiota with reduced diversity, revealed using both 16S rRNA amplicon sequencing and a germfree larva model. In this dysbiosis, Aeromonas spp. were aberrantly enriched as major pathobionts and exhibited the capacity for aggressive colonization in tp53 mutants. Importantly, the ex-germfree experiments supported the causality of the host tp53 mutation for inducing the inflammation. Transcriptome and high-performance liquid chromatography analyses of the host gastrointestinal tracts identified dysregulated sialic acid (SA) metabolism concomitant with increased host Neu5Gc levels as the key determinant of aberrant inflammation, which was reversed by the sialidase inhibitors oseltamivir and Philippin A.

CONCLUSIONS: These results demonstrate a crucial role for host tp53 in maintaining symbiosis and immune homeostasis via SA metabolism. Disturbed SA metabolism via a tp53 mutation may be exploited by specific elements of the gut microbiome, eliciting both dysbiosis and inflammation. Manipulating sialometabolism may therefore provide an efficacious therapeutic strategy for tp53 mutation-induced dysbiosis, inflammation, and ultimately, related cancers. Video Abstract.

RevDate: 2022-01-07

Pereira AM, de Lurdes Nunes Enes Dapkevicius M, AES Borba (2022)

Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission?.

Animal microbiome, 4(1):5.

Agriculture is responsible for a great share of the anthropogenic sources of greenhouse gases that, by warming the earth, threaten its biodiversity. Among greenhouse gas emissions, enteric CH4 from livestock is an important target to slow down climate changes. The CH4 is originated from rumen fermentation and its concentration is affected by several factors, including genetics and nutrition. Ruminants have an extraordinary symbiosis with microorganisms (bacteria, fungi, and protozoa) that ferment otherwise indigestible carbohydrates, from which they obtain energy to grow and continue actively producing, among other products, volatile fatty acids, CO2 and H2. Detrimental ruminal accumulation of H2 is avoided by methanogenesis carried out by Archaea methanogens. Importantly, methanogenesis is not the only H2 sink pathway. In fact, other bacteria can reduce substrates using metabolic hydrogen formed during carbohydrate fermentation, namely propionate production and reductive acetogenesis, thus lowering the CH4 produced. Although the complexity of rumen poses challenges to mitigate CH4 production, the emergence of sequencing techniques that allow the study of microbial communities, gene expression, and metabolome are largely contributing to unravel pathways and key players in the rumen. Indeed, it is now recognized that in vivo emissions of CH4 are correlated to microbial communities, and particularly with the abundance of methanogens, several bacterial groups, and their genes. The goal of CH4 mitigation is to work in favor of the natural processes, without compromising rumen function, animal health, and productivity. Notwithstanding, the major challenge continues to be the feasibility and affordability of the proposed solutions.

RevDate: 2022-01-07

Donner SD, Skirving WJ, Little CM, et al (2005)

Global assessment of coral bleaching and required rates of adaptation under climate change.

Global change biology, 11(12):2251-2265.

Elevated ocean temperatures can cause coral bleaching, the loss of colour from reef-building corals because of a breakdown of the symbiosis with the dinoflagellate Symbiodinium. Recent studies have warned that global climate change could increase the frequency of coral bleaching and threaten the long-term viability of coral reefs. These assertions are based on projecting the coarse output from atmosphere-ocean general circulation models (GCMs) to the local conditions around representative coral reefs. Here, we conduct the first comprehensive global assessment of coral bleaching under climate change by adapting the NOAA Coral Reef Watch bleaching prediction method to the output of a low- and high-climate sensitivity GCM. First, we develop and test algorithms for predicting mass coral bleaching with GCM-resolution sea surface temperatures for thousands of coral reefs, using a global coral reef map and 1985-2002 bleaching prediction data. We then use the algorithms to determine the frequency of coral bleaching and required thermal adaptation by corals and their endosymbionts under two different emissions scenarios. The results indicate that bleaching could become an annual or biannual event for the vast majority of the world's coral reefs in the next 30-50 years without an increase in thermal tolerance of 0.2-1.0°C per decade. The geographic variability in required thermal adaptation found in each model and emissions scenario suggests that coral reefs in some regions, like Micronesia and western Polynesia, may be particularly vulnerable to climate change. Advances in modelling and monitoring will refine the forecast for individual reefs, but this assessment concludes that the global prognosis is unlikely to change without an accelerated effort to stabilize atmospheric greenhouse gas concentrations.

RevDate: 2022-01-07
CmpDate: 2022-01-07

Cao L, Jansen PA, Wang B, et al (2022)

Mutual cheating strengthens a tropical seed dispersal mutualism.

Ecology, 103(1):e03574.

While cheating can cause the degradation or collapse of mutualisms, mutualisms may theoretically stabilize or strengthen if the cheating is mutual. Here, we present an asymmetric two-player game model to explore the evolutionary dynamics of mutual cheating in a mutualistic interaction. We found that the interaction evolved toward mutual cheating if cheating can help both partners obtain higher benefits or if counter-cheating yields more benefits to victims than simply tolerating exploitation by partners. Then, we present empirical evidence for such mutual cheating strengthening a seed dispersal mutualism in which rodents disperse seeds by scatter hoarding, rodents sabotage seed germination by pruning radicles, and seeds escape rodents by resprouting. By tracking >8,000 Pittosporopsis kerrii seeds throughout the dispersal process in a tropical forest in southwest China, we found that rodents provided better dispersal to seeds that they pruned, i.e., pruned seeds were dispersed farther and were more likely to establish seedlings than unpruned seeds. Compared with unpruned seeds, pruned seeds retained more of their nutrients, i.e., dry mass of pruned seeds was greater than that of unpruned seeds, and were stored for longer by rodents. These findings indicate that mutual cheating benefited both partners. Payoffs estimated from the field experiments indicated that mutual cheating was indeed favored in rodents and plants P. kerrii, and that neither partner was enslaved by the other under mutual cheating. Rather, the mutualism remained stable because the partners were able to exploit each other, and each partner attempted to gain the maximum benefits from the interaction. Our findings indicate that mutual cheating between two mutualists can enhance and stabilize mutualisms.

RevDate: 2022-01-07
CmpDate: 2022-01-07

Maffo CGT, Sandeu MM, Fadel AN, et al (2021)

Molecular detection and maternal transmission of a bacterial symbiont Asaia species in field-caught Anopheles mosquitoes from Cameroon.

Parasites & vectors, 14(1):539.

BACKGROUND: Malaria control relies mainlyon insecticide-based tools. However, the effectiveness of these tools is threatened by widespread insecticide resistance in malaria vectors, highlighting the need for alternative control approaches. The endosymbiont Asaia has emerged as a promising candidate for paratransgenic control of malaria, but its biology and genetics still need to be further analyzed across Africa. Here, we investigated the prevalence of Asaia and its maternal transmission in the natural population of Anopheles mosquitoes in Cameroon.

METHODS: Indoor-resting adult mosquitoes belonging to four species (An. coluzzii, An. arabiensis, An. funestus and An. gambiae) were collected from eight localities across Cameroon from July 2016 to February 2020. PCR was performed on the Asaia-specific 16S ribosomal RNA gene, and samples positive by PCR for Asaia were confirmed by Sanger sequencing and phylogenetic analysis. The vertical transmission of Asaia was investigated by screening F1 mosquitoes belonging to F0 Asaia-positive females.

RESULTS: A total of 895 mosquitoes were screened. We found 43% (384) Asaia infection prevalence in four mosquito species. Phylogenetic analysis revealed that Asaia from Cameroon clustered together with the strains of Asaia isolated from other parts of the world. In addition, seven nucleotide sequence variants were found with low genetic diversity (π = 0.00241) and nucleotide sequence variant diversity (Hd = 0.481). Asaia was vertically transmitted with high frequency (range from 42.5 to 100%).

CONCLUSIONS: This study provides field-based evidence of the presence of Asaia in Anopheles mosquitoes in Cameroon for exploitation as a symbiont in the control of malaria in sub-Saharan Africa.

RevDate: 2022-01-07

Simon C, Cooley JR, Karban R, et al (2022)

Advances in the Evolution and Ecology of 13- and 17-Year Periodical Cicadas.

Annual review of entomology, 67:457-482.

Apart from model organisms, 13- and 17-year periodical cicadas (Hemiptera: Cicadidae: Magicicada) are among the most studied insects in evolution and ecology. They are attractive subjects because they predictably emerge in large numbers; have a complex biogeography shaped by both spatial and temporal isolation; and include three largely sympatric, parallel species groups that are, in a sense, evolutionary replicates. Magicicada are also relatively easy to capture and manipulate, and their spectacular, synchronized mass emergences facilitate outreach and citizen science opportunities. Since the last major review, studies of Magicicada have revealed insights into reproductive character displacement and the nature of species boundaries, provided additional examples of allochronic speciation, found evidence for repeated and parallel (but noncontemporaneous) evolution of 13- and 17-year life cycles, quantified the amount and direction of gene flow through time, revealed phylogeographic patterning resulting from paleoclimate change, examined the timing of juvenile development, and created hypotheses for the evolution of life-cycle control and the future effects of climate changeon Magicicada life cycles. New ecological studies have supported and questioned the role of prime numbers in Magicicada ecology and evolution, found bidirectional shifts in population size over generations, quantified the contribution of Magicicada to nutrient flow in forest ecosystems, and examined behavioral and biochemical interactions between Magicicada and their fungal parasites and bacterial endosymbionts.

RevDate: 2022-01-07
CmpDate: 2022-01-07

Vitali A, Sasal Y, Vázquez DP, et al (2022)

The disruption of a keystone interaction erodes pollination and seed dispersal networks.

Ecology, 103(1):e03547.

Understanding the impacts of global change on ecological communities is a major challenge in modern ecology. The gain or loss of particular species and the disruption of key interactions are both consequences and drivers of global change that can lead to the disassembly of ecological networks. We examined whether the disruption of a hummingbird-mistletoe-marsupial mutualism by the invasion of non-native species can have cascading effects on both pollination and seed dispersal networks in the temperate forest of Patagonia, Argentina. We focused on network motifs, subnetworks composed of a small number of species exhibiting particular patterns of interaction, to examine the structure and diversity of mutualistic networks. We found that the hummingbird-mistletoe-marsupial mutualism plays a critical role in the community by increasing the complexity of pollination and seed dispersal networks through supporting a high diversity of interactions. Moreover, we found that the disruption of this tripartite mutualism by non-native ungulates resulted in diverse indirect effects that led to less complex pollination and seed dispersal networks. Our results demonstrate that the gains and losses of particular species and the alteration of key interactions can lead to cascading effects in the community through the disassembly of mutualistic networks.

RevDate: 2022-01-07

Vorburger C (2022)

Defensive Symbionts and the Evolution of Parasitoid Host Specialization.

Annual review of entomology, 67:329-346.

Insect host-parasitoid interactions abound in nature and are characterized by a high degree of host specialization. In addition to their behavioral and immune defenses, many host species rely on heritable bacterial endosymbionts for defense against parasitoids. Studies on aphids and flies show that resistance conferred by symbionts can be very strong and highly specific, possibly as a result of variation in symbiont-produced toxins. I argue that defensive symbionts are therefore an important source of diversifying selection, promoting the evolution of host specialization by parasitoids. This is likely to affect the structure of host-parasitoid food webs. I consider potential changes in terms of food web complexity, although the nature of these effects will also be influenced by whether maternally transmitted symbionts have some capacity for lateral transfer. This is discussed in the light of available evidence for horizontal transmission routes. Finally, I propose that defensive mutualisms other than microbial endosymbionts may also exert diversifying selection on insect parasitoids.

RevDate: 2022-01-07
CmpDate: 2022-01-07

Pellon A, Barriales D, Peña-Cearra A, et al (2021)

The commensal bacterium Lactiplantibacillus plantarum imprints innate memory-like responses in mononuclear phagocytes.

Gut microbes, 13(1):1939598.

Gut microbiota is a constant source of antigens and stimuli to which the resident immune system has developed tolerance. However, the mechanisms by which mononuclear phagocytes, specifically monocytes/macrophages, cope with these usually pro-inflammatory signals are poorly understood. Here, we show that innate immune memory promotes anti-inflammatory homeostasis, using as model strains of the commensal bacterium Lactiplantibacillus plantarum. Priming of monocytes/macrophages with bacteria, especially in its live form, enhances bacterial intracellular survival and decreases the release of pro-inflammatory signals to the environment, with lower production of TNF and higher levels of IL-10. Analysis of the transcriptomic landscape of these cells shows downregulation of pathways associated with the production of reactive oxygen species (ROS) and the release of cytokines, chemokines and antimicrobial peptides. Indeed, the induction of ROS prevents memory-induced bacterial survival. In addition, there is a dysregulation in gene expression of several metabolic pathways leading to decreased glycolytic and respiratory rates in memory cells. These data support commensal microbe-specific metabolic changes in innate immune memory cells that might contribute to homeostasis in the gut.

RevDate: 2022-01-06

Chuzho N, Kumar N, Mishra N, et al (2021)

Differential HLA Association of GAD65 and IA2 Autoantibodies in North Indian Type 1 Diabetes Patients.

Journal of diabetes research, 2021:4012893.

The human leucocyte antigen (HLA) association with type 1 diabetes (T1D) is well known but there are limited studies investigating the association between β-cell autoantibodies and HLA genes. We evaluated the prevalence of GAD65 and IA-2 autoantibodies (GADA and IA2A) in 252 T1D patients from North India and investigated the genetic association of GADA and IA2A with HLA class I and class II genes/haplotypes. GADA and IA2A were detected in 50.79% and 15.87% of T1D patients, respectively, while only 8.73% had both GADA and IA2A. HLA-DRB1∗03 was observed to be significantly higher in GADA+ T1D patients as compared to GADA- (91.41% vs. 66.13%, Bonferroni-corrected P (P c) = 1.11 × 10-5; OR = 5.45; 95% CI: 2.67-11.08). Similarly, HLA-DQB1∗02 was found to be significantly increased in GADA+ patients (94.53%, P c = 2.19 × 10-5; OR = 6.27; 95% CI: 2.7-14.49) as compared to GADA- (73.39%). The frequencies of HLA-DRB1∗04 and DQB1∗03 were increased in IA2A+ patients (45.0% and 52.5%, respectively) as compared to that in IA2A- (25.94% and 33.96%, respectively). Further, the frequency of DRB1∗03-DQB1∗02 haplotype was found to be significantly increased in GADA+ T1D patients as compared to GADA- (60.55% vs. 41.94%, P = 3.94 × 10-5; OR = 2.13; 95%CI = 1.49-3.03). Similarly, HLA-DRB1∗04-DQB1∗03 haplotype was found to be significantly increased in IA2A+ T1D patients compared to IA2A- patients (22.5% vs. 12.97%; P = 0.041; OR = 1.95; 95%CI = 1.08-3.52). None of the HLA class I genes (HLA-A, B, and Cw) was found to be associated with GADA or IA2A in people with T1D. Our findings suggest that HLA-DRB1∗03/DQB1∗02 and HLA-DRB1∗04/DQB1∗03 might play an important role in the development of GADA and IA2A, respectively.

RevDate: 2022-01-06

Medeiros ID, Mazur E, Miadlikowska J, et al (2021)

Turnover of Lecanoroid Mycobionts and Their Trebouxia Photobionts Along an Elevation Gradient in Bolivia Highlights the Role of Environment in Structuring the Lichen Symbiosis.

Frontiers in microbiology, 12:774839.

Shifts in climate along elevation gradients structure mycobiont-photobiont associations in lichens. We obtained mycobiont (lecanoroid Lecanoraceae) and photobiont (Trebouxia alga) DNA sequences from 89 lichen thalli collected in Bolivia from a ca. 4,700 m elevation gradient encompassing diverse natural communities and environmental conditions. The molecular dataset included six mycobiont loci (ITS, nrLSU, mtSSU, RPB1, RPB2, and MCM7) and two photobiont loci (ITS, rbcL); we designed new primers to amplify Lecanoraceae RPB1 and RPB2 with a nested PCR approach. Mycobionts belonged to Lecanora, Bryonora, Myriolecis, Protoparmeliopsis, the "Lecanora" polytropa group, and the "L." saligna group. All of these clades except for Lecanora occurred only at high elevation. No single species of Lecanoraceae was present along the entire elevation gradient, and individual clades were restricted to a subset of the gradient. Most Lecanoraceae samples represent species which have not previously been sequenced. Trebouxia clade C, which has not previously been recorded in association with species of Lecanoraceae, predominates at low- to mid-elevation sites. Photobionts from Trebouxia clade I occur at the upper extent of mid-elevation forest and at some open, high-elevation sites, while Trebouxia clades A and S dominate open habitats at high elevation. We did not find Trebouxia clade D. Several putative new species were found in Trebouxia clades A, C, and I. These included one putative species in clade A associated with Myriolecis species growing on limestone at high elevation and a novel lineage sister to the rest of clade C associated with Lecanora on bark in low-elevation grassland. Three different kinds of photobiont switching were observed, with certain mycobiont species associating with Trebouxia from different major clades, species within a major clade, or haplotypes within a species. Lecanoraceae mycobionts and Trebouxia photobionts exhibit species turnover along the elevation gradient, but with each partner having a different elevation threshold at which the community shifts completely. A phylogenetically defined sampling of a single diverse family of lichen-forming fungi may be sufficient to document regional patterns of Trebouxia diversity and distribution.

RevDate: 2022-01-06
CmpDate: 2022-01-06

Jana SK, Islam MM, S Mandal (2022)

Endophytic Microbiota of Rice and Their Collective Impact on Host Fitness.

Current microbiology, 79(2):37.

Endophytic microbiota mainly includes positive modulator of plant growth, productivity, stress tolerance and ability to control the phytopathogens. Rice endophytes colonize in different parts like roots, shoots, leaves, seeds, flowers, ovules, etc. The diversity and colonization of endophytes depend on several factors like host specificity, environment specificity, chemotaxis, motility, etc. A mutualistic relationship between rice plant and their endophytes improves the host health. Several crucial activities of rice plants are influenced by the presence of endophytes as they endorse plant growth by producing different phytohormones, solubilized minerals, or mitigating various environmental adverse conditions. Endophytes also protect rice plants from various phytopathogen by the production of secondary metabolites, lytic enzymes, antibiotics and induced systemic acquired resistance. Furthermore, the endophytes from rice and major crops are recently been shown useful in environmental waste management and also for the synthesis of green nanoparticles. This study highlights the beneficial interaction between rice plants and their endophytic microbiota with special emphasis on highlighting their application for sustainable agricultural and environmental practices in order to enhance the agro-economy in an eco-friendly manner.

RevDate: 2022-01-06
CmpDate: 2022-01-06

Skowronek M, Sajnaga E, Kazimierczak W, et al (2021)

Screening and Molecular Identification of Bacteria from the Midgut of Amphimallon solstitiale Larvae Exhibiting Antagonistic Activity against Bacterial Symbionts of Entomopathogenic Nematodes.

International journal of molecular sciences, 22(21):.

Entomopathogenic nematodes (Rhabditida: Steinernematidae and Heterorhabditidae) are a group of organisms capable of infecting larvae of insects living in soil, including representatives of the family Scarabaeidae. Their insecticidal activity is related to the presence of symbiotic bacteria Xenorhabdus spp. or Photorhabdus spp. in the alimentary tract, which are released into the insect body, leading to its death caused by bacterial toxins and septicemia. Although the antibacterial activities of symbionts of entomopathogenic nematodes have been well described, there is insufficient knowledge of the interactions between these bacteria and microorganisms that naturally inhabit the alimentary tract of insects infested by nematodes. In this study, 900 bacterial strains isolated from midgut samples of Amphimallon solstitiale larvae were tested for their antagonistic activity against the selected five Xenorhabdus and Photorhabdus species. Cross-streak tests showed significant antibacterial activity of 20 isolates. These bacteria were identified as Bacillus [Brevibacterium] frigoritolerans, Bacillus toyonensis, Bacillus wiedmannii, Chryseobacterium lathyri, Chryseobacterium sp., Citrobacter murliniae, Enterococcus malodoratus, Paenibacillus sp., Serratia marcescens and Serratia sp. Since some representatives of the intestinal microbiota of A. solstitiale are able to inhibit the growth of Xenorhabdus and Photorhrhabdus bacteria in vitro, it can be assumed that this type of bacterial interaction may occur at certain stages of insect infection by Steinernema or Heterorhabditis nematodes.

RevDate: 2022-01-06
CmpDate: 2022-01-06

Koo H, CD Morrow (2021)

Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy.

BMC microbiology, 21(1):251.

BACKGROUND: To understand inter-individual variability of fecal microbe transplantation (FMT) to enhance anti-PD-1 immunotherapy (IT) for melanoma, we analyzed the data sets from two recent publications with a microbial strain-tracking tool to determine if donor strains were dominant in the recipient feces following FMT.

RESULTS: Analysis of the Baruch et al. data set found that the presence of commensal donor microbes in recipient feces post-FMT did not correlate with the patient response to IT. From the Davar et al., data set, we found 4 patients that responded to IT had donor's related strain post-FMT, while 2 patients that did not respond to the IT also had donor's strain post-FMT. Importantly, we identified no donor microbes in the feces in one recipient post-FMT that responded to IT. Furthermore, in depth analysis from two patients who responded to IT revealed both donor and recipient strains at different times post-FMT. Colonization of the gastrointestinal tract niches is important for the interaction with the host immune system. Using a separate data set, we show that mucosa from the cecum, transverse colon, and sigmoid colon share strains, providing a large reservoir of niches containing recipient microbes.

CONCLUSIONS: We demonstrated using strain-tracking analysis individual variation with the respect to the presence of fecal dominant donor microbes in the recipient following FMT that did not correlate with the response to anti-PD-1 immunotherapy. The inter-individual differences of FMT to enhance IT might be explained by the variability of the donor microbes to occupy and outcompete recipient microbes for the gastrointestinal niches. The result from our study supports the use of new approaches to clear the niches in the gastrointestinal tract to promote donor colonization to reduce inter-individual variability of IT for melanoma and potentially other cancers.

RevDate: 2022-01-06
CmpDate: 2022-01-06

Li X, Shang L, Brandt BW, et al (2021)

Saliva-derived microcosm biofilms grown on different oral surfaces in vitro.

NPJ biofilms and microbiomes, 7(1):74.

The microbial composition of a specific oral niche could be influenced by initial bacterial adherence, nutrient and physiological property of the local surface. To investigate the influence of nutrient and surface properties on microbial composition, saliva-derived biofilms were grown in agar on three substrata: Reconstructed Human Gingiva (RHG), a hydroxyapatite (HAP) surface, and a titanium (TI) surface. Agar was mixed with either Brain Heart Infusion (BHI) or Thompson (TP) medium. After 1, 3, or 5 days, biofilm viability (by colony forming units) and microbiome profiles (by 16 S rDNA amplicon sequencing) were determined. On RHG, biofilm viability and composition were similar between BHI and TP. However, on the abiotic substrata, biofilm properties greatly depended on the type of medium and substratum. In BHI, the viability of HAP-biofilm first decreased and then increased, whereas that of TI-biofilm decreased in time until a 6-log reduction. In TP, either no or a 2-log reduction in viability was observed for HAP- or TI-biofilms respectively. Furthermore, different bacterial genera (or higher level) were differentially abundant in the biofilms on 3 substrata: Haemophilus and Porphyromonas for RHG; Bacilli for HAP and Prevotella for TI. In conclusion, RHG, the biotic substratum, is able to support a highly viable and diverse microbiome. In contrast, the viability and diversity of the biofilms on the abiotic substrata were influenced by the substrata type, pH of the environment and the richness of the growth media. These results suggest that the host (oral mucosa) plays a vital role in the oral ecology.

RevDate: 2022-01-06
CmpDate: 2022-01-06

He X, Zhang Q, Li B, et al (2021)

Network mapping of root-microbe interactions in Arabidopsis thaliana.

NPJ biofilms and microbiomes, 7(1):72.

Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are often focused on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic bases of microbial interactions that are thought to be important for microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions of Arabidopsis thaliana and find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surrounding A. thaliana root systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs, of which 91 are identified as hub QTLs. Results from gene annotation analysis suggest that most of the hub QTLs detected are in proximity to candidate genes, executing a variety of biological functions in plant growth and development, resilience against pathogens, root development, and abiotic stress resistance. This study provides a new gateway to understand how genetic variation in host plants influences microbial communities and our results could help improve crops by harnessing soil microbes.

RevDate: 2022-01-06
CmpDate: 2022-01-06

Evangelisti E, Turner C, McDowell A, et al (2021)

Deep learning-based quantification of arbuscular mycorrhizal fungi in plant roots.

The New phytologist, 232(5):2207-2219.

Soil fungi establish mutualistic interactions with the roots of most vascular land plants. Arbuscular mycorrhizal (AM) fungi are among the most extensively characterised mycobionts to date. Current approaches to quantifying the extent of root colonisation and the abundance of hyphal structures in mutant roots rely on staining and human scoring involving simple yet repetitive tasks which are prone to variation between experimenters. We developed Automatic Mycorrhiza Finder (AMFinder) which allows for automatic computer vision-based identification and quantification of AM fungal colonisation and intraradical hyphal structures on ink-stained root images using convolutional neural networks. AMFinder delivered high-confidence predictions on image datasets of roots of multiple plant hosts (Nicotiana benthamiana, Medicago truncatula, Lotus japonicus, Oryza sativa) and captured the altered colonisation in ram1-1, str, and smax1 mutants. A streamlined protocol for sample preparation and imaging allowed us to quantify mycobionts from the genera Rhizophagus, Claroideoglomus, Rhizoglomus and Funneliformis via flatbed scanning or digital microscopy, including dynamic increases in colonisation in whole root systems over time. AMFinder adapts to a wide array of experimental conditions. It enables accurate, reproducible analyses of plant root systems and will support better documentation of AM fungal colonisation analyses. AMFinder can be accessed at

RevDate: 2022-01-06
CmpDate: 2022-01-06

Nagpal J, JF Cryan (2021)

Host genetics, the microbiome & behaviour-a 'Holobiont' perspective.

Cell research, 31(8):832-833.


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.

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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 )