Journal articles on the topic 'Symbiosis-related phenotypes'
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1
Humann, Jodi L., Hope T. Ziemkiewicz, Svetlana N. Yurgel, and Michael L. Kahn. "Regulatory and DNA Repair Genes Contribute to the Desiccation Resistance of Sinorhizobium meliloti Rm1021." Applied and Environmental Microbiology 75, no. 2 (November 21, 2008): 446–53. http://dx.doi.org/10.1128/aem.02207-08.
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ABSTRACT Sinorhizobium meliloti can form a nitrogen-fixing symbiotic relationship with alfalfa after bacteria in the soil infect emerging root hairs of the growing plant. To be successful at this, the bacteria must be able to survive in the soil between periods of active plant growth, including when conditions are dry. The ability of S. meliloti to withstand desiccation has been known for years, but genes that contribute to this phenotype have not been identified. Transposon mutagenesis was used in combination with novel screening techniques to identify four desiccation-sensitive mutants of S. meliloti Rm1021. DNA sequencing of the transposon insertion sites identified three genes with regulatory functions (relA, rpoE2, and hpr) and a DNA repair gene (uvrC). Various phenotypes of the mutants were determined, including their behavior on several indicator media and in symbiosis. All of the mutants formed an effective symbiosis with alfalfa. To test the hypothesis that UvrC-related excision repair was important in desiccation resistance, uvrA, uvrB, and uvrC deletion mutants were also constructed. These strains were sensitive to DNA damage induced by UV light and 4-NQO and were also desiccation sensitive. These data indicate that uvr gene-mediated DNA repair and the regulation of stress-induced pathways are important for desiccation resistance.
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Liu, Wei, Yan Li, Xue Bai, Haiguang Wu, Lanxing Bian, and Xiaoke Hu. "LuxR-Type Regulator AclR1 of Azorhizobium caulinodans Regulates Cyclic di-GMP and Numerous Phenotypes in Free-Living and Symbiotic States." Molecular Plant-Microbe Interactions® 33, no. 3 (March 2020): 528–38. http://dx.doi.org/10.1094/mpmi-10-19-0306-r.
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LuxR-type regulators play important roles in transcriptional regulation in bacteria and control various biological processes. A genome sequence analysis showed the existence of seven LuxR-type regulators in Azorhizobium caulinodans ORS571, an important nitrogen-fixing bacterium in both its free-living state and in symbiosis with its host, Sesbania rostrata. However, the functional mechanisms of these regulators remain unclear. In this study, we identified a LuxR-type regulator that contains a cheY-homologous receiver (REC) domain in its N terminus and designated it AclR1. Interestingly, phylogenetic analysis revealed that AclR1 exhibited relatively close evolutionary relationships with MalT/GerE/FixJ/NarL family proteins. Functional analysis of an aclR1 deletion mutant (ΔaclR1) in the free-living state showed that AclR1 positively regulated cell motility and flocculation but negatively regulated exopolysaccharide production, biofilm formation, and second messenger cyclic diguanylate (c-di-GMP)-related gene expression. In the symbiotic state, the ΔaclR1 mutant was defective in competitive colonization and nodulation on host plants. These results suggested that AclR1 could provide bacteria with the ability to compete effectively for symbiotic nodulation. Overall, our results show that the REC-LuxR-type regulator AclR1 regulates numerous phenotypes both in the free-living state and during host plant symbiosis.
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Durán, David, Luis Rey, Juan Mayo, Doris Zúñiga-Dávila, Juan Imperial, Tomás Ruiz-Argüeso, Esperanza Martínez-Romero, and Ernesto Ormeño-Orrillo. "Bradyrhizobium paxllaeri sp. nov. and Bradyrhizobium icense sp. nov., nitrogen-fixing rhizobial symbionts of Lima bean (Phaseolus lunatus L.) in Peru." International Journal of Systematic and Evolutionary Microbiology 64, Pt_6 (June 1, 2014): 2072–78. http://dx.doi.org/10.1099/ijs.0.060426-0.
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A group of strains isolated from root nodules of Phaseolus lunatus (Lima bean) in Peru were characterized by genotypic, genomic and phenotypic methods. All strains possessed identical 16S rRNA gene sequences that were 99.9 % identical to that of Bradyrhizobium lablabi CCBAU 23086T. Despite having identical 16S rRNA gene sequences, the Phaseolus lunatus strains could be divided into two clades by sequence analysis of recA, atpD, glnII, dnaK and gyrB genes. The genome sequence of a representative of each clade was obtained and compared to the genomes of closely related species of the genus Bradyrhizobium . Average nucleotide identity values below the species circumscription threshold were obtained when comparing the two clades to each other (88.6 %) and with all type strains of the genus Bradyrhizobium (≤92.9 %). Phenotypes distinguishing both clades from all described and closely related species of the genus Bradyrhizobium were found. On the basis of the results obtained, two novel species, Bradyrhizobium paxllaeri sp. nov. (type strain LMTR 21T = DSM 18454T = HAMBI 2911T) and Bradyrhizobium icense sp. nov. (type strain LMTR 13T = HAMBI 3584T = CECT 8509T = CNPSo 2583T), are proposed to accommodate the uncovered clades of Phaseolus lunatus bradyrhizobia. These species share highly related but distinct nifH and nodC symbiosis genes.
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Marie, Corinne, William J. Deakin, Tuula Ojanen-Reuhs, Ericka Diallo, Brad Reuhs, William J. Broughton, and Xavier Perret. "TtsI, a Key Regulator of Rhizobium Species NGR234 Is Required for Type III-Dependent Protein Secretion and Synthesis of Rhamnose-Rich Polysaccharides." Molecular Plant-Microbe Interactions® 17, no. 9 (September 2004): 958–66. http://dx.doi.org/10.1094/mpmi.2004.17.9.958.
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Formation of nitrogen-fixing nodules on legume roots by Rhizobium sp. NGR234 requires an array of bacterial factors, including nodulation outer proteins (Nops) secreted through a type III secretion system (TTSS). Secretion of Nops is abolished upon inactivation of ttsI (formerly y4xI), a protein with characteristics of two-component response regulators that was predicted to activate transcription of TTSS-related genes. During the symbiotic interaction, the phenotype of NGRΩttsI differs from that of a mutant with a nonfunctional secretion machine, however. This indicated that TtsI regulates the synthesis of other symbiotic factors as well. Conserved sequences, called tts boxes, proposed to act as binding sites for TtsI, were identified not only within the TTSS cluster but also in the promoter regions of i) genes predicted to encode homologs of virulence factors secreted by pathogenic bacteria, ii) loci involved in the synthesis of a rhamnose-rich component (rhamnan) of the lipopolysaccharides (LPS), and iii) open reading frames that play roles in plasmid partitioning. Transcription studies showed that TtsI and tts boxes are required for the activation of TTSS-related genes and those involved in rhamnose synthesis. Furthermore, extraction of polysaccharides revealed that inactivation of ttsI abolishes the synthesis of the rhamnan component of the LPS. The phenotypes of mutants impaired in TTSS-dependent protein secretion, rhamnan synthesis, or in both functions were compared to assess the roles of some of the TtsI-controlled factors during symbiosis.
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Robbins, Michael. "Psychoanalytic and Biological Approaches to Mental Illness: Schizophrenia." Journal of the American Psychoanalytic Association 40, no. 2 (April 1992): 425–54. http://dx.doi.org/10.1177/000306519204000206.
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Biological psychiatrists tend to look upon the phenomena of mind and meaning, which are the data of psychoanalysis, as meaningless epiphenomena, and propose reductive explanations of complex mental states, whereas psychoanalysis tend to ignore the proliferation of neurobiological data indicating the importance of constitutional factors in mental illness. Interactive models which confuse biological causes and psychological consequences, or vice-versa, are theoretically unsound. A scientific model hierarchy is proposed, along with some principles for coexistence and collaboration between neurobiology and psychoanalysis. The problem is illustrated with schizophrenia, a condition whose probable biological underpinnings are now generally considered to remove it from the realm of psychoanalysis. Schizophrenia-vulnerable phenotypes consistent with organic findings and clinical observations are hypothesized, and some ideas about their development in the context of early object relations, leading to pathological forms of symbiosis, are elaborated. A neurobiological rationale for the psychoanalytic treatment of schizophrenia is presented, and special problems related to the biological and symbiotic substrate are examined.
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Zhao, Wenlong, Huixia Zhu, Feng Wei, Donglai Zhou, Youguo Li, and Xue-Xian Zhang. "Investigating the Involvement of Cytoskeletal Proteins MreB and FtsZ in the Origin of Legume-Rhizobial Symbiosis." Molecular Plant-Microbe Interactions® 34, no. 5 (May 2021): 547–59. http://dx.doi.org/10.1094/mpmi-10-20-0299-fi.
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Rhizobia are rod-shaped bacteria that form nitrogen-fixing root nodules on leguminous plants; however, they don’t carry MreB, a key determinant of rod-like cell shape. Here, we introduced an actin-like mreB homolog from a pseudomonad into Mesorhizobium huakuii 7653R (a microsymbiont of Astragalus sinicus L.) and examined the molecular, cellular, and symbiotic phenotypes of the resultant mutant. Exogenous mreB caused an enlarged cell size and slower growth in laboratory medium. However, the mutant formed small, ineffective nodules on A. sinicus (Nod+ Fix−), and rhizobial cells in the infection zone were unable to differentiate into bacteroids. RNA sequencing analysis also revealed minor effects of mreB on global gene expression in free-living cells but larger effects for cells grown in planta. Differentially expressed nodule-specific genes include cell cycle regulators such as the tubulin-like ftsZ1 and ftsZ2. Unlike the ubiquitous FtsZ1, an FtsZ2 homolog was commonly found in Rhizobium, Sinorhizobium, and Mesorhizobium spp. but not in closely related nonsymbiotic species. Bacterial two-hybrid analysis revealed that MreB interacts with FtsZ1 and FtsZ2, which are targeted by the host-derived nodule-specific cysteine-rich peptides. Significantly, MreB mutation D283A disrupted the protein–protein interactions and restored the aforementioned phenotypic defects caused by MreB in M. huakuii. Together, our data indicate that MreB is detrimental for modern rhizobia and its interaction with FtsZ1 and FtsZ2 causes the symbiotic process to cease at the late stage of bacteroid differentiation. These findings led to a hypothesis that loss of mreB in the common ancestor of members of Rhizobiales and subsequent acquisition of ftsZ2 are critical evolutionary steps leading to legume-rhizobial symbiosis. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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Papa, M. F. Del, M. Pistorio, W. O. Draghi, M. J. Lozano, M. A. Giusti, C. Medina, P. van Dillewijn, et al. "Identification and Characterization of a nodH Ortholog from the Alfalfa-Nodulating Or191-Like Rhizobia." Molecular Plant-Microbe Interactions® 20, no. 2 (February 2007): 138–45. http://dx.doi.org/10.1094/mpmi-20-2-0138.
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Nodulation of Medicago sativa (alfalfa) is known to be restricted to Sinorhizobium meliloti and a few other rhizobia that include the poorly characterized isolates related to Rhizobium sp. strain Or191. Distinctive features of the symbiosis between alfalfa and S. meliloti are the marked specificity from the plant to the bacteria and the strict requirement for the presence of sulfated lipochitooligosac-charides (Nod factors [NFs]) at its reducing end. Here, we present evidence of the presence of a functional nodH-encoded NF sulfotransferase in the Or191-like rhizobia. The nodH gene, present in single copy, maps to a high molecular weight megaplasmid. As in S. meliloti, a nodF homolog was identified immediately upstream of nodH that was transcribed in the opposite direction (local synteny). This novel nodH ortholog was cloned and shown to restore both NF sulfation and the Nif+Fix+ phenotypes when introduced into an S. meliloti nodH mutant. Unexpectedly, however, nodH disruption in the Or191-like bacteria did not abolish their ability to nodulate alfalfa, resulting instead in a severely delayed nodulation. In agreement with evidence from other authors, the nodH sequence analysis strongly supports the idea that the Or191-like rhizobia most likely represent a genetic mosaic resulting from the horizontal transfer of symbiotic genes from a sinorhizobial megaplas-mid to a not yet clearly identified ancestor.
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Liu, Bin, Ke Liu, Xiaorong Chen, Duohong Xiao, Tingjin Wang, Yang Yang, Hui Shuai, Sumei Wu, Lu Yuan, and Liping Chen. "Comparative Transcriptome Analysis Reveals the Interaction of Sugar and Hormone Metabolism Involved in the Root Hair Morphogenesis of the Endangered Fir Abies beshanzuensis." Plants 12, no. 2 (January 6, 2023): 276. http://dx.doi.org/10.3390/plants12020276.
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Abies beshanzuensis, an extremely rare and critically endangered plant with only three wild adult trees globally, is strongly mycorrhizal-dependent, leading to difficulties in protection and artificial breeding without symbiosis. Root hair morphogenesis plays an important role in the survival of mycorrhizal symbionts. Due to the lack of an effective genome and transcriptome of A. beshanzuensis, the molecular signals involved in the root hair development remain unknown, which hinders its endangered mechanism analysis and protection. Herein, transcriptomes of radicles with root hair (RH1) and without root hair (RH0) from A. beshanzuensis in vitro plantlets were primarily established. Functional annotation and differentially expressed gene (DEG) analysis showed that the two phenotypes have highly differentially expressed gene clusters. Transcriptome divergence identified hormone and sugar signaling primarily involved in root hair morphogenesis of A. beshanzuensis. Weighted correlation network analysis (WGCNA) coupled with quantitative real-time PCR (qRT-PCR) found that two hormone–sucrose–root hair modules were linked by IAA17, and SUS was positioned in the center of the regulation network, co-expressed with SRK2E in hormone transduction and key genes related to root hair morphogenesis. Our results contribute to better understanding of the molecular mechanisms of root hair development and offer new insights into deciphering the survival mechanism of A. beshanzuensis and other endangered species, utilizing root hair as a compensatory strategy instead of poor mycorrhizal growth.
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Cohen, Michael F., and Hideo Yamasaki. "Flavonoid-Induced Expression of a Symbiosis-Related Gene in the Cyanobacterium Nostoc punctiforme." Journal of Bacteriology 182, no. 16 (August 15, 2000): 4644–46. http://dx.doi.org/10.1128/jb.182.16.4644-4646.2000.
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ABSTRACT The flavonoid naringin was found to induce the expression ofhrmA, a gene with a symbiotic phenotype in the cyanobacterium Nostoc punctiforme. A comparative analysis of several flavonoids revealed the 7-O-neohesperidoside, 4′-OH, and C-2-C-3 double bond in naringin as structural determinants of its hrmA-inducing activity.
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diCenzo, George C., Maryam Zamani, Hannah N. Ludwig, and Turlough M. Finan. "Heterologous Complementation Reveals a Specialized Activity for BacA in the Medicago–Sinorhizobium meliloti Symbiosis." Molecular Plant-Microbe Interactions® 30, no. 4 (April 2017): 312–24. http://dx.doi.org/10.1094/mpmi-02-17-0030-r.
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The bacterium Sinorhizobium meliloti Rm2011 forms N2-fixing root nodules on alfalfa and other leguminous plants. The pSymB chromid contains a 110-kb region (the ETR region) showing high synteny to a chromosomally located region in Sinorhizobium fredii NGR234 and related rhizobia. We recently introduced the ETR region from S. fredii NGR234 into the S. meliloti chromosome. Here, we report that, unexpectedly, the S. fredii NGR234 ETR region did not complement deletion of the S. meliloti ETR region in symbiosis with Medicago sativa. This phenotype was due to the bacA gene of NGR234 not being functionally interchangeable with the S. meliloti bacA gene during M. sativa symbiosis. Further analysis revealed that, whereas bacA genes from S. fredii or Rhizobium leguminosarum bv. viciae 3841 failed to complement the Fix− phenotype of a S. meliloti bacA mutant with M. sativa, they allowed for further developmental progression prior to a loss of viability. In contrast, with Melilotus alba, bacA from S. fredii and R. leguminosarum supported N2 fixation by a S. meliloti bacA mutant. Additionally, the S. meliloti bacA gene can support N2 fixation of a R. leguminosarum bacA mutant during symbiosis with Pisum sativum. A phylogeny of BacA proteins illustrated that S. meliloti BacA has rapidly diverged from most rhizobia and has converged toward the sequence of pathogenic genera Brucella and Escherichia. These data suggest that the S. meliloti BacA has evolved toward a specific interaction with Medicago and highlights the limitations of using a single model system for the study of complex biological topics.
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Miozzi, Laura, Anna Maria Vaira, Federico Brilli, Valerio Casarin, Mara Berti, Alessandra Ferrandino, Luca Nerva, Gian Paolo Accotto, and Luisa Lanfranco. "Arbuscular Mycorrhizal Symbiosis Primes Tolerance to Cucumber Mosaic Virus in Tomato." Viruses 12, no. 6 (June 22, 2020): 675. http://dx.doi.org/10.3390/v12060675.
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Tomato plants can establish symbiotic interactions with arbuscular mycorrhizal fungi (AMF) able to promote plant nutrition and prime systemic plant defenses against pathogens attack; the mechanism involved is known as mycorrhiza-induced resistance (MIR). However, studies on the effect of AMF on viral infection, still limited and not conclusive, indicate that AMF colonization may have a detrimental effect on plant defenses against viruses, so that the term “mycorrhiza-induced susceptibility” (MIS) has been proposed for these cases. To expand the case studies to a not yet tested viral family, that is, Bromoviridae, we investigated the effect of the colonization by the AMF Funneliformis mosseae on cucumber mosaic virus (CMV) infection in tomato by phenotypic, physiological, biochemical, and transcriptional analyses. Our results showed that the establishment of a functional AM symbiosis is able to limit symptoms development. Physiological and transcriptomic data highlighted that AMF mitigates the drastic downregulation of photosynthesis-related genes and the reduction of photosynthetic CO2 assimilation rate caused by CMV infection. In parallel, an increase of salicylic acid level and a modulation of reactive oxygen species (ROS)-related genes, toward a limitation of ROS accumulation, was specifically observed in CMV-infected mycorrhizal plants. Overall, our data indicate that the AM symbiosis influences the development of CMV infection in tomato plants and exerts a priming effect able to enhance tolerance to viral infection.
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Chagas Junior, Aloisio Freitas, Luiz Antônio De Oliveira, Henrique Guilhon De Castro, Gabriel de Lima Cornélio, Gil Rodrigues Dos Santos, Lillian França Borges Chagas, and Jefferson da Luz Costa. "Isolation and phenotypic characterization of rhizobia that nodulate cowpea in the Cerrado in Tocantins State, Brazil." Journal of Biotechnology and Biodiversity 4, no. 3 (August 1, 2013): 249–59. http://dx.doi.org/10.20873/jbb.uft.cemaf.v4n3.chagasjunior.
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Depending on the nutritional characteristics and hardiness, the cowpea has become an important source of protein in North and Northeast regions of Brazil. The cowpea benefits from biological nitrogen fixation (BNF) and may receive part of the nitrogen needed for culture via symbiosis, which reduces production costs. Aiming to contribute to the optimization of the BNF in the culture of cowpea (Vigna unguiculata (L) Walp) in the cerrado of Tocantins, through the effectiveness of populations and diversity of rhizobia obtained in seven areas with and without crops , phenotypic isolation and characterization were performed (pH, time of growth characteristics of the colonies and mucus). We obtained 72 rhizobia and evaluated in a dendrogram showed a great diversity, with the formation of 18 groups and the five large groups with 70% similarity. The study of morphological and physiological characteristics reveals a fairly wide diversity of rhizobia and is usually related to studies at the DNA level.
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Bazghaleh, Navid, Chantal Hamel, Yantai Gan, Bunyamin Tar'an, and Joan Diane Knight. "Genotype-Specific Variation in the Structure of Root Fungal Communities Is Related to Chickpea Plant Productivity." Applied and Environmental Microbiology 81, no. 7 (January 23, 2015): 2368–77. http://dx.doi.org/10.1128/aem.03692-14.
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ABSTRACTIncreasing evidence supports the existence of variations in the association of plant roots with symbiotic fungi that can improve plant growth and inhibit pathogens. However, it is unclear whether intraspecific variations in the symbiosis exist among plant cultivars and if they can be used to improve crop productivity. In this study, we determined genotype-specific variations in the association of chickpea roots with soil fungal communities and evaluated the effect of root mycota on crop productivity. A 2-year field experiment was conducted in southwestern Saskatchewan, the central zone of the chickpea growing region of the Canadian prairie. The effects of 13 cultivars of chickpea, comprising a wide range of phenotypes and genotypes, were tested on the structure of root-associated fungal communities based on internal transcribed spacer (ITS) and 18S rRNA gene markers using 454 amplicon pyrosequencing. Chickpea cultivar significantly influenced the structure of the root fungal community. The magnitude of the effect varied with the genotypes evaluated, and effects were consistent across years. For example, the roots of CDC Corrine, CDC Cory, and CDC Anna hosted the highest fungal diversity and CDC Alma and CDC Xena the lowest.Fusariumsp. was dominant in chickpea roots but was less abundant in CDC Corrine than the other cultivars. A bioassay showed that certain of these fungal taxa, includingFusariumspecies, can reduce the productivity of chickpea, whereasTrichoderma harzianumcan increase chickpea productivity. The large variation in the profile of chickpea root mycota, which included growth-promoting and -inhibiting species, supports the possibility of improving the productivity of chickpea by improving its root mycota in chickpea genetic improvement programs using traditional breeding techniques.
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Tena, Wondwosen, Endalkachew Wolde-Meskel, Tulu Degefu, and Fran Walley. "Genetic and phenotypic diversity of rhizobia nodulating chickpea (Cicer arietinumL.) in soils from southern and central Ethiopia." Canadian Journal of Microbiology 63, no. 8 (August 2017): 690–707. http://dx.doi.org/10.1139/cjm-2016-0776.
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Forty-two chickpea-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations of Ethiopia and were characterized on the basis of 76 phenotypic traits. Furthermore, 18 representative strains were selected and characterized using multilocus sequence analyses of core and symbiotic gene loci. Numerical analysis of the phenotypic characteristics grouped the 42 strains into 4 distinct clusters. The analysis of the 16S rRNA gene of the 18 strains showed that they belong to the Mesorhizobium genus. On the basis of the phylogenetic tree constructed from the combined genes sequences (recA, atpD, glnII, and gyrB), the test strains were distributed into 4 genospecies (designated as genospecies I–IV). Genospecies I, II, and III could be classified with Mesorhizobium ciceri, Mesorhizobium abyssinicae, and Mesorhizobium shonense, respectively, while genospecies IV might represent an unnamed Mesorhizobium genospecies. Phylogenetic reconstruction based on the symbiosis-related (nifH and nodA) genes supported a single cluster together with a previously described symbiont of chickpea (M. ciceri and Mesorhizobium mediterraneum). Overall, our results corroborate earlier findings that Ethiopian soils harbor phylogenetically diverse Mesorhizobium species, justifying further explorative studies. The observed differences in symbiotic effectiveness indicated the potential to select effective strains for use as inoculants and to improve the productivity of chickpea in the country.
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Vandepol, Natalie, Julian Liber, Alan Yocca, Jason Matlock, Patrick Edger, and Gregory Bonito. "Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species." PLOS ONE 17, no. 4 (April 12, 2022): e0261908. http://dx.doi.org/10.1371/journal.pone.0261908.
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Harnessing the plant microbiome has the potential to improve agricultural yields and protect plants against pathogens and/or abiotic stresses, while also relieving economic and environmental costs of crop production. While previous studies have gained valuable insights into the underlying genetics facilitating plant-fungal interactions, these have largely been skewed towards certain fungal clades (e.g. arbuscular mycorrhizal fungi). Several different phyla of fungi have been shown to positively impact plant growth rates, including Mortierellaceae fungi. However, the extent of the plant growth promotion (PGP) phenotype(s), their underlying mechanism(s), and the impact of bacterial endosymbionts on fungal-plant interactions remain poorly understood for Mortierellaceae. In this study, we focused on the symbiosis between soil fungus Linnemannia elongata (Mortierellaceae) and Arabidopsis thaliana (Brassicaceae), as both organisms have high-quality reference genomes and transcriptomes available, and their lifestyles and growth requirements are conducive to research conditions. Further, L. elongata can host bacterial endosymbionts related to Mollicutes and Burkholderia. The role of these endobacteria on facilitating fungal-plant associations, including potentially further promoting plant growth, remains completely unexplored. We measured Arabidopsis aerial growth at early and late life stages, seed production, and used mRNA sequencing to characterize differentially expressed plant genes in response to fungal inoculation with and without bacterial endosymbionts. We found that L. elongata improved aerial plant growth, seed mass and altered the plant transcriptome, including the upregulation of genes involved in plant hormones and “response to oxidative stress”, “defense response to bacterium”, and “defense response to fungus”. Furthermore, the expression of genes in certain phytohormone biosynthetic pathways were found to be modified in plants treated with L. elongata. Notably, the presence of Mollicutes- or Burkholderia-related endosymbionts in Linnemannia did not impact the expression of genes in Arabidopsis or overall growth rates. Together, these results indicate that beneficial plant growth promotion and seed mass impacts of L. elongata on Arabidopsis are likely driven by plant hormone and defense transcription responses after plant-fungal contact, and that plant phenotypic and transcriptional responses are independent of whether the fungal symbiont is colonized by Mollicutes or Burkholderia-related endohyphal bacteria.
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Menéndez, Esther, Jose David Flores-Félix, Martha Helena Ramírez-Bahena, Jose M. Igual, Paula García-Fraile, Alvaro Peix, and Encarna Velázquez. "Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain." Microorganisms 8, no. 6 (June 22, 2020): 939. http://dx.doi.org/10.3390/microorganisms8060939.
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In the present work, we analyse the genomic and phenotypic characteristics of a strain named RZME27T isolated from roots of a Zea mays plant grown in Spain. The phylogenetic analyses of 16S rRNA gene and whole genome sequences showed that the strain RZME27T clustered with the type strains of Neorhizobium galegae and Pseudorhizobium pelagicum from the family Rhizobiaceae. This family encompasses several genera establishing symbiosis with legumes, but the genes involved in nodulation and nitrogen fixation are absent in its genome. Nevertheless, genes related to plant colonization, such as those involved in motility, chemotaxis, quorum sensing, exopolysaccharide biosynthesis and hydrolytic enzymes production were found. The comparative pangenomic analyses showed that 78 protein clusters present in the strain RZME27T were not found in the type strains of its closest relatives N. galegae and P. pelagicum. The calculated average nucleotide identity (ANI) values between the strain RZME27T and the type strains of N. galegae and P. pelagicum were 75.61% and 75.1%, respectively, similar or lower than those found for other genera from family Rhizobiaceae. Several phenotypic differences were also found, highlighting the absence of the fatty acid C19:0 cyclo ω8c and propionate assimilation. These results support the definition of a novel genus and species named Endobacterium cerealis gen. nov. sp. nov. whose type strain is RZME27T.
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Lagares, Antonio, Daniela F. Hozbor, Karsten Niehaus, Augusto J. L. Pich Otero, Jens Lorenzen, Walter Arnold, and Alfred Pühler. "Genetic Characterization of a Sinorhizobium meliloti Chromosomal Region Involved in Lipopolysaccharide Biosynthesis." Journal of Bacteriology 183, no. 4 (February 15, 2001): 1248–58. http://dx.doi.org/10.1128/jb.183.4.1248-1258.2001.
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ABSTRACT The genetic characterization of a 5.5-kb chromosomal region ofSinorhizobium meliloti 2011 that contains lpsB, a gene required for the normal development of symbiosis withMedicago spp., is presented. The nucleotide sequence of this DNA fragment revealed the presence of six genes: greAand lpsB, transcribed in the forward direction; andlpsE, lpsD, lpsC, and lrp, transcribed in the reverse direction. Except for lpsB, none of thelps genes were relevant for nodulation and nitrogen fixation. Analysis of the transcriptional organization oflpsB showed that greA and lpsB are part of separate transcriptional units, which is in agreement with the finding of a DNA stretch homologous to a “nonnitrogen” promoter consensus sequence between greA and lpsB. The opposite orientation of lpsB with respect to its first downstream coding sequence, lpsE, indicated that the altered LPS and the defective symbiosis of lpsB mutants are both consequences of a primary nonpolar defect in a single gene. Global sequence comparisons revealed that the greA-lpsB andlrp genes of S. meliloti have a genetic organization similar to that of their homologous loci in R. leguminosarum bv. viciae. In particular, high sequence similarity was found between the translation product of lpsB and a core-related biosynthetic mannosyltransferase of R. leguminosarum bv. viciae encoded by the lpcC gene. The functional relationship between these two genes was demonstrated in genetic complementation experiments in which the S. meliloti lpsB gene restored the wild-type LPS phenotype when introduced into lpcC mutants of R. leguminosarum. These results support the view that S. meliloti lpsB also encodes a mannosyltransferase that participates in the biosynthesis of the LPS core. Evidence is provided for the presence of otherlpsB-homologous sequences in several members of the familyRhizobiaceae.
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Garrido, José Manuel García, Rafael Jorge León Morcillo, José Ángel Martín Rodríguez, and Juan Antonio Ocampo Bote. "Variations in the Mycorrhization Characteristics in Roots of Wild-Type and ABA-Deficient Tomato Are Accompanied by Specific Transcriptomic Alterations." Molecular Plant-Microbe Interactions® 23, no. 5 (May 2010): 651–64. http://dx.doi.org/10.1094/mpmi-23-5-0651.
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Abscissic acid (ABA) determines mycorrhiza functionality and arbuscule development. In this study, we performed transcriptome analysis in response to different mycorrhization status according to the ABA content in the root to identify genes that may play a role in arbuscule functionality. Affymetrix Tomato GeneChip (approximately 10,000 probes) allowed us to detect and compare the transcriptional root profiling of tomato (Solanum lycopersicum) wild-type and ABA-deficient sitiens plants colonized by Glomus intraradices. A number of identified genes in tomato belong to a category of genes already described as “mycorrhizal core-set” in other host plants. The impairment in arbuscular mycorrhiza (AM) formation in ABA-deficient mutants was associated with upregulation of genes related to defense and cell wall modification, whereas functional mycorrhization in wild-type plants was associated with activation of genes related to isoprenoid metabolism. The oxylipin pathway was activated in tomato mycorrhizal roots at late stages of interaction, and was related to the control of fungal spread in roots, not with the establishment of the symbiosis. Induction of selected genes, representing a range of biological functions and representative of the three sets of genes specifically upregulated in the different plant phenotype, was confirmed by quantitative reverse-transcription polymerase chain reaction, and their response to phythohormone treatment was tested, showing that ethylene and jasmonic acid are key regulators of gene expression during AM development. Comparative analysis of mycorrhiza upregulated functional categories revealed significant changes in gene expression associated with the different mycorrhization status according to the ABA content in the roots.
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Wang, Chun-Mei, Martin Ekman, and Birgitta Bergman. "Expression of Cyanobacterial Genes Involved in Heterocyst Differentiation and Dinitrogen Fixation Along a Plant Symbiosis Development Profile." Molecular Plant-Microbe Interactions® 17, no. 4 (April 2004): 436–43. http://dx.doi.org/10.1094/mpmi.2004.17.4.436.
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Members of the cyanobiont genus Nostoc, forming an endosymbiosis with members of the angiosperm genus Gunnera, undergo a number of characteristic phenotypic changes during the development of the symbiosis, the genetic background of which is largely unknown. Transcription patterns of genes related to heterocyst differentiation and dinitrogen fixation and corresponding protein profiles were examined, using reverse transcription-polymerase chain reaction and Western blots, along a developmental (apex to mature parts) sequence in Gunnera magellanica and G. manicata and under mimicked symbiotic conditions in a free-living Gunnera isolate (Nostoc strain 0102). The hetR gene was highly expressed and correlated positively with an increase in heterocyst frequency and with ntcA expression, whereas nifH expression was already high close to the growing apex and glnB (PII) expression decreased along the symbiotic profile. Although gene expression appeared to be regulated to a large extent in the same fashion as in free-living cyanobacteria, significant differences were apparent, such as the overexpression of both hetR and ntcA and the contrasting down-regulation of glnB, features indicating important regulatory differences between symbiotic and free-living cyanobacteria. The significance of these findings is discussed in a symbiotic context.
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Téllez-Sosa, Juan, Nora Soberón, Alicia Vega-Segura, María E. Torres-Márquez, and Miguel A. Cevallos. "The Rhizobium etli cyaC Product: Characterization of a Novel Adenylate Cyclase Class." Journal of Bacteriology 184, no. 13 (July 1, 2002): 3560–68. http://dx.doi.org/10.1128/jb.184.13.3560-3568.2002.
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ABSTRACT Adenylate cyclases (ACs) catalyze the formation of 3′,5′-cyclic AMP (cAMP) from ATP. A novel AC-encoding gene, cyaC, was isolated from Rhizobium etli by phenotypic complementation of an Escherichia coli cya mutant. The functionality of the cyaC gene was corroborated by its ability to restore cAMP accumulation in an E. coli cya mutant. Further, overexpression of a malE::cyaC fusion protein allowed the detection of significant AC activity levels in cell extracts of an E. coli cya mutant. CyaC is unrelated to any known AC or to any other protein exhibiting a currently known function. Thus, CyaC represents the first member of a novel class of ACs (class VI). Hypothetical genes of unknown function similar to cyaC have been identified in the genomes of the related bacterial species Mesorhizobium loti, Sinorhizobium meliloti, and Agrobacterium tumefaciens. The cyaC gene is cotranscribed with a gene similar to ohr of Xanthomonas campestris and is expressed only in the presence of organic hydroperoxides. The physiological performance of an R. etli cyaC mutant was indistinguishable from that of the wild-type parent strain both under free-living conditions and during symbiosis.
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Tu, Ting-Chen, Shih-Han Lin, and Fo-Ting Shen. "Enhancing Symbiotic Nitrogen Fixation and Soybean Growth through Co-Inoculation with Bradyrhizobium and Pseudomonas Isolates." Sustainability 13, no. 20 (October 19, 2021): 11539. http://dx.doi.org/10.3390/su132011539.
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The present study was undertaken to explore acidotolerant rhizobial and non-rhizobial bacteria associated with root nodules of soybean (Glycine max L.). Genotypic and phenotypic characterization regarding nitrogen fixation, nodulation and other potentially plant growth-promotion traits were performed in several isolates. Influences of bacterial inoculation on symbiotic nitrogen fixation and soybean growth were evaluated through flask and pot experiments in a greenhouse. The highest nitrogen-fixing activity was recorded in isolate Bra6, which was closely related to Bradyrhizobium diazoefficiens based on 16S rDNA, nifH, and nodD gene sequences. All the non-rhizobial Pseudomonas isolates possessed multiple plant growth-promoting traits, with various hydrolytic patterns toward plant constituents. In sterile water agar-containing flasks, Bra6 + Pse2 treatment significantly (p < 0.05) increased the number of nodules, fresh weight, and dry weight of both root and shoot. This also led to the increment of most of the nutrients in the soybean plant compared with the uninoculated control or sole inoculation of Bra6. In non-sterile strongly acidic soil-containing pots, co-inoculation with Bra6 and various Pseudomonas isolates showed distinctively positive effects on symbiotic nitrogen fixation and soybean growth. The highest symbiotic nitrogen-fixing activity; root and shoot biomass; as well as N, P, K, Ca, Mg, S, Mn, Cu, and Zn contents of soybean plant were observed in Bra6 + Pse2 treatment. Synergistic symbiosis occurred through co-inoculation with Bradyrhizobium and Pseudomonas isolates, which further enhanced nutrients’ acquisition and growth of soybean in the strongly acidic soils.
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Pereira, André C., Beatriz Ramos, Ana C. Reis, and Mónica V. Cunha. "Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches." Microorganisms 8, no. 9 (September 9, 2020): 1380. http://dx.doi.org/10.3390/microorganisms8091380.
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Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.
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Bellés-Sancho, Paula, Martina Lardi, Yilei Liu, Leo Eberl, Nicola Zamboni, Aurélien Bailly, and Gabriella Pessi. "Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by Paraburkholderia phymatum NifA." Metabolites 11, no. 7 (July 15, 2021): 455. http://dx.doi.org/10.3390/metabo11070455.
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Paraburkholderia phymatum STM815 is a nitrogen-fixing endosymbiont that nodulate the agriculturally important Phaseolus vulgaris and several other host plants. We previously showed that the nodules induced by a STM815 mutant of the gene encoding the master regulator of nitrogen fixation NifA showed no nitrogenase activity (Fix−) and increased in number compared to P. vulgaris plants infected with the wild-type strain. To further investigate the role of NifA during symbiosis, nodules from P. phymatum wild-type and nifA mutants were collected and analyzed by metabolomics and dual RNA-Sequencing, allowing us to investigate both host and symbiont transcriptome. Using this approach, several metabolites’ changes could be assigned to bacterial or plant responses. While the amount of the C4-dicarboxylic acid succinate and of several amino acids was lower in Fix− nodules, the level of indole-acetamide (IAM) and brassinosteroids increased. Transcriptome analysis identified P. phymatum genes involved in transport of C4-dicarboxylic acids, carbon metabolism, auxin metabolism and stress response to be differentially expressed in absence of NifA. Furthermore, P. vulgaris genes involved in autoregulation of nodulation (AON) are repressed in nodules in absence of NifA potentially explaining the hypernodulation phenotype of the nifA mutant. These results and additional validation experiments suggest that P. phymatum STM815 NifA is not only important to control expression of nitrogenase and related enzymes but is also involved in regulating its own auxin production and stress response. Finally, our data indicate that P. vulgaris does sanction the nifA nodules by depleting the local carbon allocation rather than by mounting a strong systemic immune response to the Fix− rhizobia.
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Dunlap, Paul V., and Jennifer C. Ast. "Genomic and Phylogenetic Characterization of Luminous Bacteria Symbiotic with the Deep-Sea Fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae)." Applied and Environmental Microbiology 71, no. 2 (February 2005): 930–39. http://dx.doi.org/10.1128/aem.71.2.930-939.2005.
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ABSTRACT Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040T, and the type strain of Photobacterium iliopiscarium, ATCC 51760T. Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040T. These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated the kishitanii clade, that is related to but evolutionarily distinct from P. phosphoreum. Members of the kishitanii clade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes.
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Vysochanska, V. V., and G. M. Koval. "The Role of Genes and Skin Microbiome in the Development of Seborrheic Dermatitis." Ukraïnsʹkij žurnal medicini, bìologìï ta sportu 7, no. 2 (May 6, 2022): 18–26. http://dx.doi.org/10.26693/jmbs07.02.018.
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The purpose of the study was to identify specific links between genotypic and phenotypic changes in the body that can lead to inflammatory skin diseases and dysbiosis. Materials and methods. Medline / PubMed, Embase, Web of Science databases were searched and research studies related to inflammatory skin diseases: immunity, genetics, epigenetics, epidermal barrier, skin microbiome, etc. were analyzed. The results of microbiome studies based on cultivation methods were excluded from the study. Results and discussion. Inflammatory skin diseases often lead to physical or psychological disorders, but the cause of these diseases is still unclear. Pathogenesis of inflammatory skin diseases includes heredity, environmental impact, immunity changes, epidermal barrier dysfunction, mental disorders, infections, and more. A better understanding of the role of microbiome, genetic abnormalities and phenotypic changes may help to predict the occurrence of seborrheic dermatitis in humans. The human microbiome is directly involved in the formation of host immunity. In particular, skin residents maintain the stability of the skin barrier, regulate inflammation and the immune response. Mutualistic symbioses provide homeostasis of the human-host relationship and the microbiome. However, under the influence of the external environment, genetic and physiological changes, the balance of the microbial community and man is disturbed, which can negatively regulate the condition of the host and cause disease. Most symbiotic skin microbiota coexists peacefully with the host and become pathogenic only under certain conditions. The transition from symbiosis to pathogenicity is a complex process, because the skin is well resistant to aggressive factors. Potential attackers must induce gene expression to enable adhesion, invasion, and avoidance of the immune response. The skin microbiome induces inflammation and skin healing. Also it may change its qualitative and quantitative composition to adapt to existing inflammatory conditions. Conclusion. Microorganisms grown under conditions of homeostasis perfectly interact with the human-host in a healthy symbiotic relationship. Under conditions of impaired immune system response, abnormal gene expression or dysfunction of the skin barrier microbiome residents use a variety of defense mechanisms to survive, that plays an important role in the pathogenesis of inflammatory skin diseases. Understanding the species composition of the microbiome, its dynamic changes and effects on human skin makes it possible to predict the possible occurrence of seborrheic dermatitis, control inflammation and prevent exacerbations
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Corning, Peter A. "Holistic Darwinism: The new evolutionary paradigm and some implications for political science." Politics and the Life Sciences 27, no. 1 (March 2008): 22–54. http://dx.doi.org/10.2990/27_1_22.
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Holistic Darwinism is a candidate name for a major paradigm shift that is currently underway in evolutionary biology and related disciplines. Important developments include (1) a growing appreciation for the fact that evolution is a multilevel process, from genes to ecosystems, and that interdependent coevolution is a ubiquitous phenomenon in nature; (2) a revitalization of group selection theory, which was banned (prematurely) from evolutionary biology over 30 years ago (groups may in fact be important evolutionary units); (3) a growing respect for the fact that the genome is not a “bean bag” (in biologist Ernst Mayr's caricature), much less a gladiatorial arena for competing selfish genes, but a complex, interdependent, cooperating system; (4) an increased recognition that symbiosis is an important phenomenon in nature and that symbiogenesis is a major source of innovation in evolution; (5) an array of new, more advanced game theory models, which support the growing evidence that cooperation is commonplace in nature and not a rare exception; (6) new research and theoretical work that stresses the role of nurture in evolution, including developmental processes, phenotypic plasticity, social information transfer (culture), and especially the role of behavioral innovations as pacemakers of evolutionary change (e.g., niche construction theory, which is concerned with the active role of organisms in shaping the evolutionary process, and gene-culture coevolution theory, which relates especially to the dynamics of human evolution); (7) and, not least, a broad effort to account for the evolution of biological complexity — from major transition theory to the “Synergism Hypothesis.” Here I will briefly review these developments and will present a case for the proposition that this paradigm shift has profound implications for the social sciences, including specifically political theory, economic theory, and political science as a discipline. Interdependent superorganisms, it turns out, have played a major role in evolution — from eukaryotes to complex human societies.
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Masoero, Giorgio, Pier Giorgio Peiretti, Alberto Cugnetto, and Giusto Giovannetti. "Raw pH fall-out as a sign of a mycorrhizal modifier of Sorghum sudanensis." Journal of Agronomy Research 1, no. 2 (August 15, 2018): 1–11. http://dx.doi.org/10.14302/issn.2639-3166.jar-18-2264.
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The management of symbiotic Microbial Biota (MB) in the soil as agents that promote the yield and health of crops, is aimed at inducing modifications of the phenotype of plants, both over and under the ground. It is here shown, in Sorghumsudanensis plants, that: i) a simple response to MB inoculation is the result of the fall out of the raw pH; ii) the simple NIR scans of leaves can be considered to rapidly classify the outcomes; iii) the raw pH can be considered a key-variable of leaf modifications. An experiment was carried out on Sorghumsudanensis. The plants were seeded in pots and grown for 66 d, and then a control non-inoculated group (C) was compared with thirteen Arbuscular Mycorrhizae (AM) Glomus inoculated groups and with two commercial MB products. A total of 374 raw pH measurements conducted on the leaves showed that the 5.18 pH units in the C group were scaled by -1.9% (P<0.0336) in the MB group and by -3.4% in the AM group (P<0.0001), with a relevant diversity between groups. Direct discrimination of these three groups, by means of smart NIR-SCIO, showed a % reclassification of the C, MB and AM groups of 74%, 59% and 96% in the fresh leaves and of 65%, 51% and 94% in the dried ground leaves, respectively. The composition of the dried leaves, based on a set of 14 variables predicted via NIRS models, plus the total foliar dry weight and percentage, showed a typical increase in protein, ash and hemicellulose, and a typical decrease in the cellulose, dry matter, crude fiber and crop maturity index. These variables were related to the foliar pH, as a key-variable, by means of a PLS standard model (R2 0.81) in which a low pH steadily favored the dry mass weight and, to a lesser extent, the hemicellulose and the digestible NDF contents; on the other hand, a high pH increased the dry matter percentage and the cellulose content of the leaves. As expected, the leaves of the inoculated plants showed a more juvenile ontogenic status. The epigean botanical modifications can be considered harmonic expressions of a luxuriant symbiosis, as testified by the homologous NIR categorization. The outlook for a symbiotic agriculture, with mycorrhizal plants, should consider the raw pH as a multifaceted variable.
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Bamba, Masaru, Seishiro Aoki, Tadashi Kajita, Hiroaki Setoguchi, Yasuyuki Watano, Shusei Sato, and Takashi Tsuchimatsu. "Massive rhizobial genomic variation associated with partner quality in Lotus–Mesorhizobium symbiosis." FEMS Microbiology Ecology 96, no. 12 (October 5, 2020). http://dx.doi.org/10.1093/femsec/fiaa202.
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ABSTRACT Variation in partner quality is commonly observed in diverse cooperative relationships, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variation. Here, we investigated how genetic variation in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variation in the core genome and the similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using 9 sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variation represented by plant growth phenotypes, including genotype-by-genotype interactions. Variation in quality was not associated with the presence/absence variation in known symbiosis-related genes in the symbiosis island; rather, it showed significant correlation with the core genome variation. Given the recurrent HGT of the symbiosis islands into diverse Mesorhizobium strains, local Mesorhizobium communities could serve as a major source of variation for core genomes, which might prevent variation in partner quality from fixing, even in the presence of selection favoring high-quality partners. These findings highlight the novel role of HGT of symbiosis islands in maintaining partner quality variation in the legume–rhizobia symbiosis.
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Ratu, Safirah Tasa Nerves, Atsushi Hirata, Christian Oliver Kalaw, Michiko Yasuda, Mitsuaki Tabuchi, and Shin Okazaki. "Multiple Domains in the Rhizobial Type III Effector Bel2-5 Determine Symbiotic Efficiency With Soybean." Frontiers in Plant Science 12 (June 7, 2021). http://dx.doi.org/10.3389/fpls.2021.689064.
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Bradyrhizobium elkanii utilizes the type III effector Bel2-5 for nodulation in host plants in the absence of Nod factors (NFs). In soybean plants carrying the Rj4 allele, however, Bel2-5 causes restriction of nodulation by triggering immune responses. Bel2-5 shows similarity with XopD of the phytopathogen Xanthomonas campestris pv. vesicatoria and possesses two internal repeat sequences, two ethylene (ET)-responsive element-binding factor-associated amphiphilic repression (EAR) motifs, a nuclear localization signal (NLS), and a ubiquitin-like protease (ULP) domain, which are all conserved in XopD except for the repeat domains. By mutational analysis, we revealed that most of the putative domains/motifs in Bel2-5 were essential for both NF-independent nodulation and nodulation restriction in Rj4 soybean. The expression of soybean symbiosis- and defense-related genes was also significantly altered by inoculation with the bel2-5 domain/motif mutants compared with the expression upon inoculation with wild-type B. elkanii, which was mostly consistent with the phenotypic changes of nodulation in host plants. Notably, the functionality of Bel2-5 was mostly correlated with the growth inhibition effect of Bel2-5 expressed in yeast cells. The nodulation phenotypes of the domain-swapped mutants of Bel2-5 and XopD indicated that both the C-terminal ULP domain and upstream region are required for the Bel2-5-dependent nodulation phenotypes. These results suggest that Bel2-5 interacts with and modifies host targets via these multiple domains to execute both NF-independent symbiosis and nodulation restriction in Rj4 soybean.
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Zou, Qian, Yanlin Zhou, Guojun Cheng, Yang Peng, Sha Luo, Hetao Wu, Chuanlan Yan, Xiaohua Li, and Donglan He. "Antioxidant ability of glutaredoxins and their role in symbiotic nitrogen fixation in Rhizobium leguminosarum bv. viciae 3841." Applied and Environmental Microbiology, December 4, 2020. http://dx.doi.org/10.1128/aem.01956-20.
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Glutaredoxins (Grx) are redoxin family proteins that reduce disulfides and mixed disulfides between glutathione and proteins. Rhizobium leguminosarum bv. Viciae 3841 contains three genes coding for glutaredoxins: RL4289 (grxA) codes for a dithiolic glutaredoxin, RL2615 (grxB) codes for a monothiol glutaredoxin, while RL4261 (grxC) codes for a glutaredoxin-like NrdH protein. We generated mutants interrupted in one, two, or three glutaredoxin genes. These mutants had no obvious differences in growth phenotypes from the wild type RL3841. However, while a mutant of grxC did not affect the antioxidant or symbiotic capacities of R. leguminosarum, grxA-derived or grxB mutants decreased antioxidant and nitrogen fixation capacities. Furthermore, grxA mutants were severely impaired in rhizosphere colonization, and formed smaller nodules with defects of bacteroid differentiation, whereas nodules induced by grxB mutants contained abnormally thick cortices and prematurely senescent bacteroids. The grx triple mutant had the greatest defect in antioxidant and symbiotic capacities of R. leguminosarum and quantitative proteomics revealed it had 56 up-regulated and 81 down-regulated proteins relative to wildtype. Of these proteins, twenty-eight are involved in transporter activity, twenty are related to stress response and virulence, and sixteen are involved in amino acid metabolism. Overall, R. leguminosarum glutaredoxins behave as antioxidant proteins mediating root nodule symbiosis. IMPORTANCE Glutaredoxin catalyzes glutathionylation/deglutathionylation reactions, protects SH-groups from oxidation and restores functionally active thiols. Three glutaredoxins exist in R. leguminosarum and their properties were investigated in free-living bacteria and during nitrogen-fixing symbiosis. All the glutaredoxins were necessary for oxidative stress defense. Dithiol GrxA affects nodulation and nitrogen fixation of bacteroids by altering deglutathionylation reactions, monothiol GrxB is involved in symbiotic nitrogen fixation by regulating Fe-S cluster biogenesis, and GrxC may participate in symbiosis by an unknown mechanism. Proteome analysis provides clues to explain the differences between the grx triple mutant and wild-type nodules.
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Newton, Irene L. G., and Barton E. Slatko. "Symbiosis Comes of Age at the 10th Biennial Meeting of Wolbachia Researchers." Applied and Environmental Microbiology 85, no. 8 (February 22, 2019). http://dx.doi.org/10.1128/aem.03071-18.
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ABSTRACT Wolbachia pipientis is an alphaproteobacterial obligate intracellular microbe and arguably the most successful infection on our planet, colonizing 40% to 60% of insect species. Wolbachia spp. are also present in most, but not all, filarial nematodes, where they are obligate mutualists and are the targets for antifilarial drug discovery. Although Wolbachia spp. are related to important human pathogens, they do not infect mammals but instead are well known for their reproductive manipulations of insect populations, inducing the following phenotypes: male killing, feminization, parthenogenesis induction, and cytoplasmic incompatibility (CI). The most common of these, CI, results in a sperm-egg incompatibility and increases the relative fecundity of infected females in a population. In the last decade, Wolbachia spp. have also been shown to provide a benefit to insects, where the infection can inhibit RNA virus replication within the host. Wolbachia spp. cannot be cultivated outside host cells, and no genetic tools are available in the symbiont, limiting approaches available for their study. This means that many questions fundamental to our understanding of Wolbachia basic biology remained unknown for decades. The 10th biennial international Wolbachia conference, Wolbachia Evolution, Ecology, Genomics and Cell Biology: A Chronicle of the Most Ubiquitous Symbiont, was held on 17 to 22 June 2018 in Salem, MA. In this review, we highlight the new science presented at the meeting, link it to prior efforts to answer these questions across the Wolbachia genus, and present the importance of these findings to the field of symbiosis. The topics covered in this review are based on the presentations at the conference.
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Gonçalves, Camila Silva, Carolina Moura Costa Catta-Preta, Bruno Repolês, Jeremy C. Mottram, Wanderley De Souza, Carlos Renato Machado, and Maria Cristina M. Motta. "Importance of Angomonas deanei KAP4 for kDNA arrangement, cell division and maintenance of the host-bacterium relationship." Scientific Reports 11, no. 1 (April 28, 2021). http://dx.doi.org/10.1038/s41598-021-88685-8.
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AbstractAngomonas deanei coevolves in a mutualistic relationship with a symbiotic bacterium that divides in synchronicity with other host cell structures. Trypanosomatid mitochondrial DNA is contained in the kinetoplast and is composed of thousands of interlocked DNA circles (kDNA). The arrangement of kDNA is related to the presence of histone-like proteins, known as KAPs (kinetoplast-associated proteins), that neutralize the negatively charged kDNA, thereby affecting the activity of mitochondrial enzymes involved in replication, transcription and repair. In this study, CRISPR-Cas9 was used to delete both alleles of the A. deanei KAP4 gene. Gene-deficient mutants exhibited high compaction of the kDNA network and displayed atypical phenotypes, such as the appearance of a filamentous symbionts, cells containing two nuclei and one kinetoplast, and division blocks. Treatment with cisplatin and UV showed that Δkap4 null mutants were not more sensitive to DNA damage and repair than wild-type cells. Notably, lesions caused by these genotoxic agents in the mitochondrial DNA could be repaired, suggesting that the kDNA in the kinetoplast of trypanosomatids has unique repair mechanisms. Taken together, our data indicate that although KAP4 is not an essential protein, it plays important roles in kDNA arrangement and replication, as well as in the maintenance of symbiosis.
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Nadal-Jimenez, Pol, Steven R. Parratt, Stefanos Siozios, and Gregory D. D. Hurst. "Isolation, culture and characterization of Arsenophonus symbionts from two insect species reveal loss of infectious transmission and extended host range." Frontiers in Microbiology 14 (February 1, 2023). http://dx.doi.org/10.3389/fmicb.2023.1089143.
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Vertically transmitted “Heritable” microbial symbionts represent an important component of the biology and ecology of invertebrates. These symbioses evolved originally from ones where infection/acquisition processes occurred within the environment (horizontal transmission). However, the pattern of evolution that follows transition from horizontal to vertical transmission is commonly obscured by the distant relationship between microbes with differing transmission modes. In contrast, the genus Arsenophonus provides an opportunity to investigate these processes with clarity, as it includes members that are obligate vertically transmitted symbionts, facultative vertically transmitted symbionts, strains with mixed modes of transmission and ones that are purely horizontally transmitted. Significantly, some of the strains are culturable and amenable to genetic analysis. We first report the isolation of Arsenophonus nasoniae strain aPv into culture from the ectoparasitic wasp Pachycrepoideus vindemmiae and characterize the symbiosis. We demonstrate maternal vertical transmission and find no evidence for paternal inheritance, horizontal transmission or reproductive parasitism phenotypes. This leads us to conclude this strain, in contrast to related strains, is a facultative heritable symbiont which is likely to be beneficial. We then report the serendipitous discovery and onward culture of a strain of Arsenophonus (strain aPb) from the blue butterfly, Polyommatus bellargus. This association extends the range of host species carrying Arsenophonus nasoniae/Arsenophonus apicola symbionts beyond the Hymenoptera for the first time. We perform basic metabolic analysis of the isolated strains using Biolog plates. This analysis indicates all strains utilize a restricted range of carbon sources, but these restrictions are particularly pronounced in the A. nasoniae aPv strain that is solely vertically transmitted. Finally, we demonstrate the Arsenophonus sp. strain aPb from the blue butterfly can infect Galleria waxworms, providing a model system for investigating the functional genetics of Arsenophonus-insect interactions. These results are consistent with a model of reduced metabolic competence in strains evolving under vertical transmission only. The data also broadens the range of host species infected with nasoniae/apicola clade strains beyond the Hymenoptera, and indicate the potential utility of the Galleria model for investigation of symbiosis mechanism.
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Völkner, Carsten, Lorenz Josef Holzner, Philip M. Day, Amra Dhabalia Ashok, Jan de Vries, Bettina Bölter, and Hans-Henning Kunz. "Two plastid POLLUX ion channel-like proteins are required for stress-triggered stromal Ca2+ release." Plant Physiology, September 7, 2021. http://dx.doi.org/10.1093/plphys/kiab424.
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Abstract Two decades ago, large cation currents were discovered in the envelope membranes of Pisum sativum L. (pea) chloroplasts. The deduced K+-permeable channel was coined fast-activating chloroplast cation (FACC) channel but its molecular identity remained elusive. To reveal candidates, we mined proteomic datasets of isolated pea envelopes. Our search uncovered distant members of the nuclear POLLUX ion channel family. Since pea is not amenable to molecular genetics, we used Arabidopsis thaliana to characterize the two gene homologs. Using several independent approaches, we show that both candidates localize to the chloroplast envelope membrane. The proteins, designated PLASTID ENVELOPE ION CHANNELS (PEC1/2), form oligomers with regulator of K+ conductance (RCK) domains protruding into the intermembrane space. Heterologous expression of PEC1/2 rescues yeast mutants deficient in K+ uptake. Nuclear POLLUX ion channels cofunction with Ca2+ channels to generate Ca2+ signals, critical for establishing mycorrhizal symbiosis and root development. Chloroplasts also exhibit Ca2+ transients in the stroma, probably to relay abiotic and biotic cues between plastids and the nucleus via the cytosol. Our results show that pec1pec2 loss-of-function double mutants fail to trigger the characteristic stromal Ca2+ release observed in wild-type plants exposed to external stress stimuli. Besides this molecular abnormality, pec1pec2 double mutants do not show obvious phenotypes. Future studies of PEC proteins will help to decipher the plant’s stress-related Ca2+ signaling network and the role of plastids. More importantly, the discovery of PECs in the envelope membrane is another critical step towards completing the chloroplast ion transport protein inventory.
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Jou, Eric, Noe Rodriguez-Rodriguez, and Andrew N. J. McKenzie. "Emerging roles for IL-25 and IL-33 in colorectal cancer tumorigenesis." Frontiers in Immunology 13 (October 3, 2022). http://dx.doi.org/10.3389/fimmu.2022.981479.
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Colorectal cancer (CRC) is the second leading cause of cancer-related death worldwide, and is largely refractory to current immunotherapeutic interventions. The lack of efficacy of existing cancer immunotherapies in CRC reflects the complex nature of the unique intestinal immune environment, which serves to maintain barrier integrity against pathogens and harmful environmental stimuli while sustaining host-microbe symbiosis during homeostasis. With their expression by barrier epithelial cells, the cytokines interleukin-25 (IL-25) and IL-33 play key roles in intestinal immune responses, and have been associated with inappropriate allergic reactions, autoimmune diseases and cancer pathology. Studies in the past decade have begun to uncover the important roles of IL-25 and IL-33 in shaping the CRC tumour immune microenvironment, where they may promote or inhibit tumorigenesis depending on the specific CRC subtype. Notably, both IL-25 and IL-33 have been shown to act on group 2 innate lymphoid cells (ILC2s), but can also stimulate an array of other innate and adaptive immune cell types. Though sometimes their functions can overlap they can also produce distinct phenotypes dependent on the differential distribution of their receptor expression. Furthermore, both IL-25 and IL-33 modulate pathways previously known to contribute to CRC tumorigenesis, including angiogenesis, tumour stemness, invasion and metastasis. Here, we review our current understanding of IL-25 and IL-33 in CRC tumorigenesis, with specific focus on dissecting their individual function in the context of distinct subtypes of CRC, and the potential prospects for targeting these pathways in CRC immunotherapy.
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Barros-Carvalho, Gesiele Almeida, Mariangela Hungria, Fabrício Martins Lopes, and Marie-Anne Van Sluys. "Brazilian-adapted soybean Bradyrhizobium strains uncover IS elements with potential impact on biological nitrogen fixation." FEMS Microbiology Letters 366, no. 11 (March 12, 2019). http://dx.doi.org/10.1093/femsle/fnz046.
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ABSTRACTBradyrhizobium diazoefficiens CPAC 7 and Bradyrhizobium japonicum CPAC 15 are broadly used in commercial inoculants in Brazil, contributing to most of the nitrogen required by the soybean crop. These strains differ in their symbiotic properties: CPAC 7 is more efficient in fixing nitrogen, whereas CPAC 15 is more competitive. Comparative genomics revealed many transposases close to genes associated with symbiosis in the symbiotic island of these strains. Given the importance that insertion sequences (IS) elements have to bacterial genomes, we focused on identifying the local impact of these elements in the genomes of these and other related Bradyrhizobium strains to further understand their phenotypic differences. Analyses were performed using bioinformatics approaches. We found IS elements disrupting and inserted at regulatory regions of genes involved in symbiosis. Further comparative analyses with 21 Bradyrhizobium genomes revealed insertional polymorphism with distinguishing patterns between B. diazoefficiens and B. japonicum lineages. Finally, 13 of these potentially impacted genes are differentially expressed under symbiotic conditions in B. diazoefficiens USDA 110. Thus, IS elements are associated with the diversity of Bradyrhizobium, possibly by providing mechanisms for natural variation of symbiotic effectiveness.
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Wang, Erlong, Ya Zhou, Yue Liang, Fei Ling, Xiaoshu Xue, Xianlin He, Xuliang Zhai, et al. "Rice flowering improves the muscle nutrient, intestinal microbiota diversity, and liver metabolism profiles of tilapia (Oreochromis niloticus) in rice-fish symbiosis." Microbiome 10, no. 1 (December 16, 2022). http://dx.doi.org/10.1186/s40168-022-01433-6.
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Abstract Background Rice-fish symbiosis, as an ecological and green aquaculture model, is an effective measure to relieve the environmental stress from intensive aquaculture. Compared with traditional aquaculture, the altered rearing pattern and environment will make differences in muscle nutrient and quality, intestinal microbiota, body metabolism, and even disease resistance in fish. Results To investigate this, we explored the differences between rice-tilapia (aRT and bRT) and tank-tilapia (aTT and bTT) models at the periods before and after rice flowering using 16S rRNA sequencing and untargeted metabolomics. The results showed that compared with tilapia reared in the tank model, the fish body length and weight, the muscle total umami amino acid, and monounsaturated fatty acid content were obviously higher in the rice-fish model, especially after rice flowering. Compared with other groups, the intestinal microbiota diversity of fish in the bRT group was significantly higher; the dominant microbiota was Bacteroidetes and Firmicutes at the phylum level, Bacteroides and Turicibacter at the genus level, and the relative abundances of Gram-negative, potentially pathogenic, and stress-tolerant bacteria were the highest, lowest, and highest, respectively. Besides, the differential metabolite analysis indicated that rice-fish symbiosis improved the metabolic profiles and modulated the metabolic pathways in tilapia. Moreover, the correlation analysis of 16S sequencing and metabolomics showed that Bacteroides showed a positive correlation with many metabolites related to amino acid, fatty acid, and lipid metabolism. Conclusions In summary, rice flowering improves the tilapia muscle nutrient, intestinal microbiota diversity, and disease resistance and modulates the host metabolism to acclimatize the comprehensive environment in rice-fish symbiosis. Specifically, rice flowering alters the microbiota abundance involved in amino acid, fatty acid, and lipid metabolism, resulting in improving the muscle nutrient and quality through the crosstalk of gut microbial and host metabolism. Our study will provide not only new insight into the gut microbiota-metabolism-phenotype axis, but also strong support for the promotion and application of rice-fish symbiosis in aquaculture.
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Fan, Xiaorui, Bin Liu, Junyi Zhou, Xinru Gu, Yanyan Zhou, Yifei Yang, Feifei Guo, et al. "High-Fat Diet Alleviates Neuroinflammation and Metabolic Disorders of APP/PS1 Mice and the Intervention With Chinese Medicine." Frontiers in Aging Neuroscience 13 (June 8, 2021). http://dx.doi.org/10.3389/fnagi.2021.658376.
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Alzheimer's disease (AD) is a progressive neurodegenerative disease caused by the complex interaction of multiple mechanisms. Recent studies examining the effect of high-fat diet (HFD) on the AD phenotype have demonstrated a significant influence on both inflammation and cognition. However, different studies on the effect of high-fat diet on AD pathology have reported conflicting conclusions. To explore the involvement of HFD in AD, we investigated phenotypic and metabolic changes in an AD mouse model in response to HFD. The results indicated there was no significant effect on Aβ levels or contextual memory due to HFD treatment. Of note, HFD did moderate neuroinflammation, despite spurring inflammation and increasing cholesterol levels in the periphery. In addition, diet affected gut microbiota symbiosis, altering the production of bacterial metabolites. HFD created a favorable microenvironment for bile acid alteration and arachidonic acid metabolism in APP/PS1 mice, which may be related to the observed improvement in LXR/PPAR expression. Our previous research demonstrated that Huanglian Jiedu decoction (HLJDD) significantly ameliorated impaired learning and memory. Furthermore, HLJDD may globally suppress inflammation and lipid accumulation to relieve cognitive impairment after HFD intervention. It was difficult to define the effect of HFD on AD progression because the results were influenced by confounding factors and biases. Although there was still obvious damage in AD mice treated with HFD, there was no deterioration and there was even a slight remission of neuroinflammation. Moreover, HLJDD represents a potential AD drug based on its anti-inflammatory and lipid-lowering effects.
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Griffin, Joanne S., Michael Gerth, and Gregory D. D. Hurst. "Rapid divergence in independent aspects of the compatibility phenotype in a Spiroplasma–Drosophila interaction." Microbiology 168, no. 12 (December 13, 2022). http://dx.doi.org/10.1099/mic.0.001281.
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Heritable symbionts represent important components of the biology, ecology and evolution of their arthropod hosts. Particular microbial taxa have become common across arthropods as a consequence of their ability to establish in new host species. For a host shift to occur, the symbiont must be exposed to a novel host and then be compatible: it must not cause excess pathology, must have good vertical transmission and must possess a drive phenotype that enables spread. Here we investigate the lability of compatibility to symbiosis with Spiroplasma . We used transinfection to establish the protective Spiroplasma symbiont from Drosophila hydei in two closely related novel hosts, Drosophila simulans and Drosophila melanogaster. The Spiroplasma had contrasting compatibility in the two species, exhibiting pathology and low vertical transmission but delivering protection from wasp attack in D. melanogaster but being asymptomatic and transmitted with high efficiency but with lower protection in D. simulans. Further work indicated that pathological interactions occurred in two other members of the melanogaster species group, such that D. simulans was unusual in being able to carry the symbiont without damage. The differing compatibility of the symbiont with these closely related host species emphasizes the rapidity with which host–symbiont compatibility evolves, despite compatibility itself not being subject to direct selection. Further, the requirement to fit three independent components of compatibility (pathology, transmission, protection) is probably to be a major feature limiting the rate of host shifts that will likely impact on the utility of Spiroplasma in pest and vector control. Moving forward, the variation between sibling species pairs provides an opportunity to identify the mechanisms behind variable compatibility, which will drive hypotheses as to the evolutionary drivers of compatibility variation.
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Kruasuwan, Worarat, Karan Lohmaneeratana, John T. Munnoch, Wanwipa Vongsangnak, Chatchawan Jantrasuriyarat, Paul A. Hoskisson, and Arinthip Thamchaipenet. "Transcriptome Landscapes of Salt-Susceptible Rice Cultivar IR29 Associated with a Plant Growth Promoting Endophytic Streptomyces." Rice 16, no. 1 (February 4, 2023). http://dx.doi.org/10.1186/s12284-023-00622-7.
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AbstractPlant growth-promoting endophytic (PGPE) actinomycetes have been known to enhance plant growth and mitigate plant from abiotic stresses via their PGP-traits. In this study, PGPE Streptomyces sp. GKU 895 promoted growth and alleviated salt tolerance of salt-susceptible rice cultivar IR29 by augmentation of plant weight and declined ROS after irrigation with 150 mM NaCl in a pot experiment. Transcriptome analysis of IR29 exposed to the combination of strain GKU 895 and salinity demonstrated up and downregulated differentially expressed genes (DEGs) classified by gene ontology and plant reactome. Streptomyces sp. GKU 895 induced changes in expression of rice genes including transcription factors under salt treatment which involved in growth and development, photosynthesis, plant hormones, ROS scavenging, ion transport and homeostasis, and plant–microbe interactions regarding pathogenesis- and symbiosis-related proteins. Taken together, these data demonstrate that PGPE Streptomyces sp. GKU 895 colonized and enhanced growth of rice IR29 and triggered salt tolerance phenotype. Our findings suggest that utilisation of beneficial endophytes in the saline fields could allow for the use of such marginal soils for growing rice and possibly other crops.
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García-Soto, Ivette, Raphael Boussageon, Yareni Marlene Cruz-Farfán, Jesus Daniel Castro-Chilpa, Liz Xochiquetzal Hernández-Cerezo, Victor Bustos-Zagal, Alfonso Leija-Salas, et al. "The Lotus japonicus ROP3 Is Involved in the Establishment of the Nitrogen-Fixing Symbiosis but Not of the Arbuscular Mycorrhizal Symbiosis." Frontiers in Plant Science 12 (November 12, 2021). http://dx.doi.org/10.3389/fpls.2021.696450.
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Legumes form root mutualistic symbioses with some soil microbes promoting their growth, rhizobia, and arbuscular mycorrhizal fungi (AMF). A conserved set of plant proteins rules the transduction of symbiotic signals from rhizobia and AMF in a so-called common symbiotic signaling pathway (CSSP). Despite considerable efforts and advances over the past 20 years, there are still key elements to be discovered about the establishment of these root symbioses. Rhizobia and AMF root colonization are possible after a deep cell reorganization. In the interaction between the model legume Lotus japonicus and Mesorhizobium loti, this reorganization has been shown to be dependent on a SCAR/Wave-like signaling module, including Rho-GTPase (ROP in plants). Here, we studied the potential role of ROP3 in the nitrogen-fixing symbiosis (NFS) as well as in the arbuscular mycorrhizal symbiosis (AMS). We performed a detailed phenotypic study on the effects of the loss of a single ROP on the establishment of both root symbioses. Moreover, we evaluated the expression of key genes related to CSSP and to the rhizobial-specific pathway. Under our experimental conditions, rop3 mutant showed less nodule formation at 7- and 21-days post inoculation as well as less microcolonies and a higher frequency of epidermal infection threads. However, AMF root colonization was not affected. These results suggest a role of ROP3 as a positive regulator of infection thread formation and nodulation in L. japonicus. In addition, CSSP gene expression was neither affected in NFS nor in AMS condition in rop3 mutant. whereas the expression level of some genes belonging to the rhizobial-specific pathway, like RACK1, decreased in the NFS. In conclusion, ROP3 appears to be involved in the NFS, but is neither required for intra-radical growth of AMF nor arbuscule formation.
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Mohamad, Roba, Geraldine Maynaud, Antoine Le Quéré, Céline Vidal, Agnieszka Klonowska, Erika Yashiro, Jean-Claude Cleyet-Marel, and Brigitte Brunel. "Ancient Heavy Metal Contamination in Soils as a Driver of Tolerant Anthyllis vulneraria Rhizobial Communities." Applied and Environmental Microbiology 83, no. 2 (October 28, 2016). http://dx.doi.org/10.1128/aem.01735-16.
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ABSTRACT Anthyllis vulneraria is a legume associated with nitrogen-fixing rhizobia that together offer an adapted biological material for mine-soil phytostabilization by limiting metal pollution. To find rhizobia associated with Anthyllis at a given site, we evaluated the genetic and phenotypic properties of a collection of 137 rhizobia recovered from soils presenting contrasting metal levels. Zn-Pb mine soils largely contained metal-tolerant rhizobia belonging to Mesorhizobium metallidurans or to another sister metal-tolerant species. All of the metal-tolerant isolates harbored the cadA marker gene (encoding a metal-efflux PIB-type ATPase transporter). In contrast, metal-sensitive strains were taxonomically distinct from metal-tolerant populations and consisted of new Mesorhizobium genospecies. Based on the symbiotic nodA marker, the populations comprise two symbiovar assemblages (potentially related to Anthyllis or Lotus host preferences) according to soil geographic locations but independently of metal content. Multivariate analysis showed that soil Pb and Cd concentrations differentially impacted the rhizobial communities and that a rhizobial community found in one geographically distant site was highly divergent from the others. In conclusion, heavy metal levels in soils drive the taxonomic composition of Anthyllis-associated rhizobial populations according to their metal-tolerance phenotype but not their symbiotic nodA diversity. In addition to heavy metals, local soil physicochemical and topoclimatic conditions also impact the rhizobial beta diversity. Mesorhizobium communities were locally adapted and site specific, and their use is recommended for the success of phytostabilization strategies based on Mesorhizobium-legume vegetation. IMPORTANCE Phytostabilization of toxic mine spoils limits heavy metal dispersion and environmental pollution by establishing a sustainable plant cover. This eco-friendly method is facilitated by the use of selected and adapted cover crop legumes living in symbiosis with rhizobia that can stimulate plant growth naturally through biological nitrogen fixation. We studied microsymbiont partners of a metal-tolerant legume, Anthyllis vulneraria, which is tolerant to very highly metal-polluted soils in mining and nonmining sites. Site-specific rhizobial communities were linked to taxonomic composition and metal tolerance capacity. The rhizobial species Mesorhizobium metallidurans was dominant in all Zn-Pb mines but one. It was not detected in unpolluted sites where other distinct Mesorhizobium species occur. Given the different soil conditions at the respective mining sites, including their heavy-metal contamination, revegetation strategies based on rhizobia adapting to local conditions are more likely to succeed over the long term compared to strategies based on introducing less-well-adapted strains.
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DeWerff, Samantha J., Maria A. Bautista, Matthew Pauly, Changyi Zhang, and Rachel J. Whitaker. "Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in Emergent Virus-Host Mutualism." mBio 11, no. 2 (April 28, 2020). http://dx.doi.org/10.1128/mbio.00404-20.
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ABSTRACT Theory, simulation, and experimental evolution demonstrate that diversified CRISPR-Cas immunity to lytic viruses can lead to stochastic virus extinction due to a limited number of susceptible hosts available to each potential new protospacer escape mutation. Under such conditions, theory predicts that to evade extinction, viruses evolve toward decreased virulence and promote vertical transmission and persistence in infected hosts. To better understand the evolution of host-virus interactions in microbial populations with active CRISPR-Cas immunity, we studied the interaction between CRISPR-immune Sulfolobus islandicus cells and immune-deficient strains that are infected by the chronic virus SSV9. We demonstrate that Sulfolobus islandicus cells infected with SSV9, and with other related SSVs, kill uninfected, immune strains through an antagonistic mechanism that is a protein and is independent of infectious virus. Cells that are infected with SSV9 are protected from killing and persist in the population. We hypothesize that this infection acts as a form of mutualism between the host and the virus by removing competitors in the population and ensuring continued vertical transmission of the virus within populations with diversified CRISPR-Cas immunity. IMPORTANCE Multiple studies, especially those focusing on the role of lytic viruses in key model systems, have shown the importance of viruses in shaping microbial populations. However, it has become increasingly clear that viruses with a long host-virus interaction, such as those with a chronic lifestyle, can be important drivers of evolution and have large impacts on host ecology. In this work, we describe one such interaction with the acidic crenarchaeon Sulfolobus islandicus and its chronic virus Sulfolobus spindle-shaped virus 9. Our work expands the view in which this symbiosis between host and virus evolved, describing a killing phenotype which we hypothesize has evolved in part due to the high prevalence and diversity of CRISPR-Cas immunity seen in natural populations. We explore the implications of this phenotype in population dynamics and host ecology, as well as the implications of mutualism between this virus-host pair.
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de Oliveira, André Luiz, Jessica Mitchell, Peter Girguis, and Monika Bright. "Novel Insights on Obligate Symbiont Lifestyle and Adaptation to Chemosynthetic Environment as Revealed by the Giant Tubeworm Genome." Molecular Biology and Evolution 39, no. 1 (December 6, 2021). http://dx.doi.org/10.1093/molbev/msab347.
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Abstract The mutualism between the giant tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole-genome information has impeded the full comprehension of the genotype/phenotype interface in Riftia. Here, we described the high-quality draft genome of Riftia, its complete mitogenome, and tissue-specific transcriptomic data. The Riftia genome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulfur metabolism, detoxification, antioxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establish that the trophosome is a multifunctional organ marked by intracellular digestion of endosymbionts, storage of excretory products, and hematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbor highly expressed genes involved with cell cycle, programed cell death, and immunity indicating a high cell turnover and defense mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research in Riftia, whereas it simultaneously provides new insights into the development, whole organism functions, and evolution in the giant tubeworm.
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Kozhakhmetov, Samat, Indira Tynybayeva, Dinara Baikhanova, Saule Saduakhasova, Gulnar Shakhabayeva, Almagul Kushugulova, Talgat Nurgozhin, and Zhaxybay Zhumadilov. "Metagenomic Analysis of Koumiss in Kazakhstan." Central Asian Journal of Global Health 3 (December 12, 2014). http://dx.doi.org/10.5195/cajgh.2014.163.
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Introduction. Koumiss is a low-alcohol product made from fermented mare's milk, which is popular in Kazakhstan, Russia, and other countries of Central Asia, China, and Mongolia. Natural mare's milk is fermented in symbiosis of two types of microorganisms (lactobacteria and yeast). Koumiss’s microbial composition varies depending on the geographical, climatic, and cultural conditions. Based on a phenotypic characteristic from samples, Wu, R. and colleagues identified the following bacteria isolated in inner Mongolia, an autonomous region of China: L.casei, L.helveticus, L.plantarum, L.coryniformis subsp. coryniformis, L.paracasei, L.kefiranofaciens, L.curvatus, L.fermentum, and W.kandleri. Studies of the yeast composition in koumiss also showed significant variations. Thus, there were Saccharomyces unisporus related 48.3% of isolates, to Kluyveromyces marxianus (27.6%), Pichia membranaefaciens (15.0%), and Saccharomyces cerevisiae (9.2%) from 87 isolated yeast cultures. The purpose of this study was to examine the bacterial composition in koumiss.Methods. To extract DNA, 1.8 ml of fermented milk was centrifuged to generate a pellet, which was suspended in 450 µl of lysis buffer P1 from the Powerfood Microbial DNA Isolation kit (MoBio Laboratories Inc, USA). Amplification of the microflora was used to determine the composition of a fragment of the gene 16S rRNA and ITS1. Plasmid library with target insertion was obtained on the basis of height copy plasmid vectors producing high pGem-T. The definition of direct nucleotide sequencing was performed by the method of Sanger using a set of "BigDye Terminanor v 3.1 Cycle sequencing Kit with automatic genetic analyzer ABI 3730xl (Applied Biosystems, USA). Informax Vector NTI Suite 9, Sequence Scanner v 1.0 software package used for the analysis.Results. Our studies showed that in the most samples of koumiss isolated from Akmola region (Central Kazakhstan) prevailed the following bacteria species: Lactobacillus diolivorans, Lactobacillus acidophilus, L. casei, L. curvatus yeast genus Torula (62.4%) and Saccharomyces cerevisiae (37.6%).Conclusion. Thus, the first metagenomic research of koumiss, which was conducted in Kazakhstan, showed significant variations in microbial composition.
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Mann, Evelyne, Corinne M. Stouthamer, Suzanne E. Kelly, Monika Dzieciol, Martha S. Hunter, and Stephan Schmitz-Esser. "Transcriptome Sequencing Reveals Novel Candidate Genes for Cardinium hertigii-Caused Cytoplasmic Incompatibility and Host-Cell Interaction." mSystems 2, no. 6 (November 21, 2017). http://dx.doi.org/10.1128/msystems.00141-17.
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ABSTRACT The majority of insects carry maternally inherited intracellular bacteria that are important in their hosts’ biology, ecology, and evolution. Some of these bacterial symbionts cause a reproductive failure known as cytoplasmic incompatibility (CI). In CI, the mating of symbiont-infected males and uninfected females produces few or no daughters. The CI symbiont then spreads and can have a significant impact on the insect host population. Cardinium, a bacterial endosymbiont of the parasitoid wasp Encarsia in the Bacteroidetes, is the only bacterial lineage known to cause CI outside the Alphaproteobacteria, where Wolbachia and another recently discovered CI symbiont reside. Here, we sought insight into the gene expression of a CI-inducing Cardinium strain in its natural host, Encarsia suzannae. Our study provides the first insights into the Cardinium transcriptome and provides support for the hypothesis that Wolbachia and Cardinium target similar host pathways with distinct and largely unrelated sets of genes. Cytoplasmic incompatibility (CI) is an intriguing, widespread, symbiont-induced reproductive failure that decreases offspring production of arthropods through crossing incompatibility of infected males with uninfected females or with females infected with a distinct symbiont genotype. For years, the molecular mechanism of CI remained unknown. Recent genomic, proteomic, biochemical, and cell biological studies have contributed to understanding of CI in the alphaproteobacterium Wolbachia and implicate genes associated with the WO prophage. Besides a recently discovered additional lineage of alphaproteobacterial symbionts only moderately related to Wolbachia, Cardinium (Bacteroidetes) is the only other symbiont known to cause CI, and genomic evidence suggests that it has very little homology with Wolbachia and evolved this phenotype independently. Here, we present the first transcriptomic study of the CI Cardinium strain cEper1, in its natural host, Encarsia suzannae, to detect important CI candidates and genes involved in the insect-Cardinium symbiosis. Highly expressed transcripts included genes involved in manipulating ubiquitination, apoptosis, and host DNA. Female-biased genes encoding ribosomal proteins suggest an increase in general translational activity of Cardinium in female wasps. The results confirm previous genomic analyses that indicated that Wolbachia and Cardinium utilize different genes to induce CI, and transcriptome patterns further highlight expression of some common pathways that these bacteria use to interact with the host and potentially cause this enigmatic and fundamental manipulation of host reproduction. IMPORTANCE The majority of insects carry maternally inherited intracellular bacteria that are important in their hosts’ biology, ecology, and evolution. Some of these bacterial symbionts cause a reproductive failure known as cytoplasmic incompatibility (CI). In CI, the mating of symbiont-infected males and uninfected females produces few or no daughters. The CI symbiont then spreads and can have a significant impact on the insect host population. Cardinium, a bacterial endosymbiont of the parasitoid wasp Encarsia in the Bacteroidetes, is the only bacterial lineage known to cause CI outside the Alphaproteobacteria, where Wolbachia and another recently discovered CI symbiont reside. Here, we sought insight into the gene expression of a CI-inducing Cardinium strain in its natural host, Encarsia suzannae. Our study provides the first insights into the Cardinium transcriptome and provides support for the hypothesis that Wolbachia and Cardinium target similar host pathways with distinct and largely unrelated sets of genes.