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Bibliography on: Symbiosis

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 23 May 2019 at 01:46 Created: 

Symbiosis

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

Created with PubMed® Query: symbiosis NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-05-22

Beinart RA (2019)

The Significance of Microbial Symbionts in Ecosystem Processes.

mSystems, 4(3): pii:4/3/e00127-19.

It is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained. Here, I explore the idea that, in some habitats, host-associated microbes may have an outsized role in ecosystem processes relative to functionally equivalent free-living microbes due to key aspects of the physiology, ecology, and evolution of symbiotic interactions. My research quantifying symbiont metabolism has shown that microbial symbionts have the potential to make a substantial impact on carbon and sulfur cycling. It is my perspective that direct measurement of symbiont activity and comparison to free-living counterparts will expand our understanding of the significance of microbial symbioses and, more broadly, the role of microbial processes in ecosystems.

RevDate: 2019-05-22

Kleiner M (2019)

Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities.

mSystems, 4(3): pii:4/3/e00115-19.

Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the "expressed" metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.

RevDate: 2019-05-22

Vaidya A, Singh S, Limaye L, et al (2019)

Chimeric feeders of mesenchymal stromal cells and stromal cells modified with constitutively active AKT expand hematopoietic stem cells.

Regenerative medicine [Epub ahead of print].

Aim: To examine whether AKT-modified stromal cells expand human CD34+ hematopoietic stem cells (HSCs). Methods: Coculture, in vitro functional assays, immuno-fluorescence microscopy, flow cytometry. Results: M2-10B4 stromal cells (M2) modified with AKT1 (M2-AKT) expanded primitive CD34+38- HSCs, but affected their functionality. A chimeric feeder layer comprising naive human bone marrow-derived mesenchymal stromal cells and M2-AKT not only overcame the negative effects of M2-AKT, but, unexpectedly, also gave a synergistic effect on the growth and functionality of the HSCs. Conditioned medium of bone marrow stromal cells worked as effectively, but cell-cell contact between HSCs and M2-AKT cells was necessary for the synergistic effect of M2-AKT and bone marrow-derived mesenchymal stromal cells or their CM. Conclusion: Chimeric feeders expand HSCs.

RevDate: 2019-05-22

Liu YS, Geng JC, Sha XY, et al (2019)

Effect of Rhizobium Symbiosis on Low-Temperature Tolerance and Antioxidant Response in Alfalfa (Medicago sativa L.).

Frontiers in plant science, 10:538.

Low temperature-induced stress is a major environmental factor limiting the growth and development of plants. Alfalfa (Medicago sativa L.) is a legume well known for its tolerance of extreme environments. In this study, we sought to experimentally investigate the role of rhizobium symbiosis in alfalfa's performance under a low-temperature stress condition. To do this, alfalfa "Ladak+" plants carrying active nodules (AN), inactive nodules (IN), or no nodules (NN) were exposed to an imposed low temperature stress and their survivorship calculated. The antioxidant defense responses, the accumulation of osmotic regulation substances, the cell membrane damage, and the expression of low temperature stress-related genes were determined in both the roots and the shoots of alfalfa plants. We found that more plants with AN survived than those with IN or NN under the same low temperature-stress condition. Greater activity of oxidation protective enzymes was observed in the AN and IN groups, conferring higher tolerance to low temperature in these plants. In addition, rhizobia nodulation also enhanced alfalfa's ability to tolerate low temperature by altering the expression of regulatory and metabolism-associated genes, which resulted in the accumulation of soluble proteins and sugars in the nodulated plants. Taken together, the findings of this study indicate that rhizobium inoculation offers a practical way to promote the persistence and growth potential of alfalfa "Ladak+" in cold areas.

RevDate: 2019-05-22

González V, Santamaría RI, Bustos P, et al (2019)

Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters.

Frontiers in microbiology, 10:910.

The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.

RevDate: 2019-05-22

Serra L, Macchietto M, Macias-Muñoz A, et al (2019)

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-chromosome.

G3 (Bethesda, Md.) pii:g3.119.400180 [Epub ahead of print].

Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the most complete genome of the S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36 Mb. The largest scaffold, with 20.9 Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this improved genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae's chromosome X to be primarily orthologous to C. elegans' and P. pacificus' chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between adult male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for additional comparative genomic and gene expression studies within the Steinernema clade and across the Nematoda phylum.

RevDate: 2019-05-22

Ballinger MJ, SJ Perlman (2019)

The defensive Spiroplasma.

Current opinion in insect science, 32:36-41.

Defensive microbes are of great interest for their roles in arthropod health, disease transmission, and biocontrol efforts. Obligate bacterial passengers of arthropods, such as Spiroplasma, confer protection against the natural enemies of their hosts to improve their own fitness. Although known for less than a decade, Spiroplasma's defensive reach extends to diverse parasites, both microbial and multicellular. We provide an overview of known defensive phenotypes against nematodes, parasitoid wasps, and fungi, and highlight recent studies supporting the role of Spiroplasma-encoded ribosome-inactivating proteins in protection. With cellular features well-suited for life in the hemolymph, broad distribution among invertebrate hosts, and the capacity to repeatedly evolve vertical transmission, Spiroplasma may be uniquely equipped to form intimate, defensive associations to combat extracellular parasites. Along with insights into defensive mechanisms, recent significant advances have been made in male-killing - a phenotype with interesting evolutionary ties to defense. Finally, we look forward to an exciting decade using the genetic tools of Drosophila, and the rapidly-advancing tractability of Spiroplasma itself, to better understand mechanisms and evolution in defensive symbiosis.

RevDate: 2019-05-22
CmpDate: 2019-05-22

Yadav S, I Eleftherianos (2018)

The Imaginal Disc Growth Factors 2 and 3 participate in the Drosophila response to nematode infection.

Parasite immunology, 40(10):e12581.

The Drosophila imaginal disc growth factors (IDGFs) induce the proliferation of imaginal disc cells and terminate cell proliferation at the end of larval development. However, the participation of Idgf-encoding genes in other physiological processes of Drosophila including the immune response to infection is not fully understood. Here, we show the contribution of Idgf2 and Idgf3 in the Drosophila response to infection with Steinernema carpocapsae nematodes carrying or lacking their mutualistic Xenorhabdus nematophila bacteria (symbiotic or axenic nematodes, respectively). We find that Idgf2 and Idgf3 are upregulated in Drosophila larvae infected with symbiotic or axenic Steinernema and inactivation of Idgf2 confers a survival advantage to Drosophila larvae against axenic nematodes. Inactivation of Idgf2 induces the Imd and Jak/Stat pathways, whereas inactivation of Idgf3 induces the Imd, Toll and Jak/Stat pathways. We also show that inactivation of the Imd pathway receptor PGRP-LE upregulates Idgf2 against Steinernema nematode infection. Finally, we demonstrate that inactivation of Idgf3 induces the recruitment of larval haemocytes in response to Steinernema. Our results indicate that Idgf2 and Idgf3 might be involved in different yet crucial immune functions in the Drosophila antinematode immune response. Similar findings will promote the development of new targets for species-specific pest control strategies.

RevDate: 2019-05-22
CmpDate: 2019-05-22

Shi B, Leung DYM, Taylor PA, et al (2018)

Methicillin-Resistant Staphylococcus aureus Colonization Is Associated with Decreased Skin Commensal Bacteria in Atopic Dermatitis.

The Journal of investigative dermatology, 138(7):1668-1671.

RevDate: 2019-05-21

Ji J, Zhang C, Sun Z, et al (2019)

Genome Editing in Cowpea Vigna unguiculata Using CRISPR-Cas9.

International journal of molecular sciences, 20(10): pii:ijms20102471.

Cowpea (Vigna unguiculata) is widely cultivated across the world. Due to its symbiotic nitrogen fixation capability and many agronomically important traits, such as tolerance to low rainfall and low fertilization requirements, as well as its high nutrition and health benefits, cowpea is an important legume crop, especially in many semi-arid countries. However, research in Vigna unguiculata is dramatically hampered by the lack of mutant resources and efficient tools for gene inactivation in vivo. In this study, we used clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9). We applied the CRISPR/Cas9-mediated genome editing technology to efficiently disrupt the representative symbiotic nitrogen fixation (SNF) gene in Vigna unguiculata. Our customized guide RNAs (gRNAs) targeting symbiosis receptor-like kinase (SYMRK) achieved ~67% mutagenic efficiency in hairy-root-transformed plants, and nodule formation was completely blocked in the mutants with both alleles disrupted. Various types of mutations were observed near the PAM region of the respective gRNA. These results demonstrate the applicability of the CRISPR/Cas9 system in Vigna unguiculata, and therefore should significantly stimulate functional genomics analyses of many important agronomical traits in this unique crop legume.

RevDate: 2019-05-21

Saridis G, Chorianopoulou SN, Ventouris YE, et al (2019)

An Exploration of the Roles of Ferric Iron Chelation-Strategy Components in the Leaves and Roots of Maize Plants.

Plants (Basel, Switzerland), 8(5): pii:plants8050133.

Plants have developed sophisticated mechanisms for acquiring iron from the soil. In the graminaceous species, a chelation strategy is in charge, in order to take up ferric iron from the rhizosphere. The ferric iron chelation-strategy components may also be present in the aerial plant parts. The aim of this work was to search for possible roles of those components in maize leaves. To this end, the expression patterns of ferric iron chelation-strategy components were monitored in the leaves and roots of mycorrhizal and non-mycorrhizal sulfur-deprived maize plants, both before and after sulfate supply. The two levels of sulfur supply were chosen due to the strong impact of this nutrient on iron homeostasis, whilst mycorrhizal symbiosis was chosen as a treatment that forces the plant to optimize its photosynthetic efficiency, in order to feed the fungus. The results, in combination with the findings of our previous works, suggest a role for the aforementioned components in ferric chelation and/or unloading from the xylem vessels to the aerial plant parts. It is proposed that the gene expression of the DMA exporter ZmTOM1 can be used as an early indicator for the establishment of a mycorrhizal symbiotic relationship in maize.

RevDate: 2019-05-21
CmpDate: 2019-05-21

Roy M, Vasco-Palacios A, Geml J, et al (2017)

The (re)discovery of ectomycorrhizal symbioses in Neotropical ecosystems sketched in Florianópolis.

The New phytologist, 214(3):920-923.

RevDate: 2019-05-21
CmpDate: 2019-05-21

Truong C, Mujic AB, Healy R, et al (2017)

How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity.

The New phytologist, 214(3):913-919.

RevDate: 2019-05-21
CmpDate: 2019-05-21

Wurzburger N, Brookshire EN, McCormack ML, et al (2017)

Mycorrhizal fungi as drivers and modulators of terrestrial ecosystem processes.

The New phytologist, 213(3):996-999.

RevDate: 2019-05-20

Rigo R, Bazin J, Crespi M, et al (2019)

Alternative Splicing in the Regulation of Plant-Microbe Interactions.

Plant & cell physiology pii:5491834 [Epub ahead of print].

As sessile organisms, plants are continuously exposed to a wide range of biotic interactions. While some biotic interactions are beneficial or even essential for the plant (e.g. rhizobia, mycorrhiza), others such as pathogens are detrimental and require fast adaptation. Plants partially achieve this growth and developmental plasticity by modulating the repertoire of genes they express. In the past few years, high-throughput transcriptome sequencing have revealed that, in addition to transcriptional control of gene expression, post-transcriptional processes, notably alternative splicing (AS), emerged as a key mechanism for gene regulation during plant adaptation to the environment. AS can increase proteome diversity by generating multiple transcripts from a single gene but also can reduce gene expression by yielding isoforms degraded by mechanisms such as nonsense-mediated mRNA decay. In this review, we will summarize recent discoveries detailing the contribution of alternative splicing to the regulation of plant-microbe interactions, with an emphasis on the modulation of immunity receptor function and other components of the signaling pathways that deal with pathogen responses. We will also discuss emerging evidences that AS could contribute to dynamic reprogramming of the plant transcriptome during beneficial interactions, such as the legume-symbiotic interaction.

RevDate: 2019-05-20

Wright RM, Strader ME, Genuise HM, et al (2019)

Effects of thermal stress on amount, composition, and antibacterial properties of coral mucus.

PeerJ, 7:e6849 pii:6849.

The surface mucus layer of reef-building corals supports feeding, sediment clearing, and protection from pathogenic invaders. As much as half of the fixed carbon supplied by the corals' photosynthetic symbionts is incorporated into expelled mucus. It is therefore reasonable to expect that coral bleaching (disruption of the coral-algal symbiosis) would affect mucus production. Since coral mucus serves as an important nutrient source for the entire reef community, this could have substantial ecosystem-wide consequences. In this study, we examined the effects of heat stress-induced coral bleaching on the composition and antibacterial properties of coral mucus. In a controlled laboratory thermal challenge, stressed corals produced mucus with higher protein (β = 2.1, p < 0.001) and lipid content (β = 15.7, p = 0.02) and increased antibacterial activity (likelihood ratio = 100, p < 0.001) relative to clonal controls. These results are likely explained by the expelled symbionts in the mucus of bleached individuals. Our study suggests that coral bleaching could immediately impact the nutrient flux in the coral reef ecosystem via its effect on coral mucus.

RevDate: 2019-05-20

Goto Y (2019)

[REGULATION OF INTESTINAL EPITHELIAL α1, 2-FUCOSE].

Arerugi = [Allergy], 68(3):151-154.

RevDate: 2019-05-20
CmpDate: 2019-05-20

Kampfraath AA, Klasson L, Anvar SY, et al (2019)

Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model.

BMC genomics, 20(1):106 pii:10.1186/s12864-019-5492-9.

BACKGROUND: Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol genome to other Wolbachia genomes. In addition, we also search for candidate genes related to parthenogenesis induction (PI).

RESULTS: Within wFol, we found five phage WO regions representing 25.4% of the complete genome, few pseudogenized genes, and an expansion of DNA-repair genes in comparison to other Wolbachia. These signs of genome conservation were mirrored in the wFol host, the springtail F. candida, which also had an expanded DNA-repair gene family and many horizontally transferred genes. Across all Wolbachia genomes, there was a strong correlation between gene numbers of Wolbachia strains and their hosts. In order to identify genes with a potential link to PI, we assembled the genome of an additional PI strain, wLcla. Comparisons between four PI Wolbachia, including wFol and wLcla, and fourteen non-PI Wolbachia yielded a small set of potential candidate genes for further investigation.

CONCLUSIONS: The strong similarities in genome content of wFol and its host, as well as the correlation between host and Wolbachia gene numbers suggest that there may be some form of convergent evolution between endosymbiont and host genomes. If such convergent evolution would be strong enough to overcome the evolutionary forces causing genome reduction, it would enable expanded genomes within long-term obligate endosymbionts.

RevDate: 2019-05-20

Marczak M, Żebracki K, Koper P, et al (2019)

Mgl2 Is a Hypothetical Methyltransferase Involved in Exopolysaccharide Production, Biofilm Formation, and Motility in Rhizobium leguminosarum bv. trifolii.

Molecular plant-microbe interactions : MPMI [Epub ahead of print].

In this study, functional characterization of the mgl2 gene located near the Pss-I exopolysaccharide biosynthesis region in Rhizobium leguminosarum bv. trifolii TA1 is described. The hypothetical protein encoded by the mgl2 gene was found to be similar to methyltransferases (MTases). Protein homology and template-based modeling facilitated prediction of the Mgl2 structure, which greatly resembled class I MTases with a S-adenosyl-L-methionine-binding cleft. The Mgl2 protein was engaged in exopolysaccharide, but not lipopolysaccharide, synthesis. The mgl2 deletion mutant produced exopolysaccharide comprised of only low molecular weight fractions, while overexpression of mgl2 caused overproduction of exopolysaccharide with a normal low to high molecular weight ratio. The deletion of the mgl2 gene resulted in disturbances in biofilm formation and a slight increase in motility in minimal medium. Red clover (Trifolium pratense) inoculated with the mgl2 mutant formed effective nodules, and the appearance of the plants indicated active nitrogen fixation. The mgl2 gene was preceded by an active and strong promoter. Mgl2 was defined as an integral membrane protein and formed homodimers in vivo; however, it did not interact with Pss proteins encoded within the Pss-I region. The results are discussed in the context of the possible involvement of the newly described potential MTase in various metabolic traits, such as the exopolysaccharide synthesis and motility that are important for rhizobial saprophytic and symbiotic relationships.

RevDate: 2019-05-20
CmpDate: 2019-05-20

Schretter CE, Vielmetter J, Bartos I, et al (2018)

A gut microbial factor modulates locomotor behaviour in Drosophila.

Nature, 563(7731):402-406.

While research into the biology of animal behaviour has primarily focused on the central nervous system, cues from peripheral tissues and the environment have been implicated in brain development and function1. There is emerging evidence that bidirectional communication between the gut and the brain affects behaviours including anxiety, cognition, nociception and social interaction1-9. Coordinated locomotor behaviour is critical for the survival and propagation of animals, and is regulated by internal and external sensory inputs10,11. However, little is known about how the gut microbiome influences host locomotion, or the molecular and cellular mechanisms involved. Here we report that germ-free status or antibiotic treatment results in hyperactive locomotor behaviour in the fruit fly Drosophila melanogaster. Increased walking speed and daily activity in the absence of a gut microbiome are rescued by mono-colonization with specific bacteria, including the fly commensal Lactobacillus brevis. The bacterial enzyme xylose isomerase from L. brevis recapitulates the locomotor effects of microbial colonization by modulating sugar metabolism in flies. Notably, thermogenetic activation of octopaminergic neurons or exogenous administration of octopamine, the invertebrate counterpart of noradrenaline, abrogates the effects of xylose isomerase on Drosophila locomotion. These findings reveal a previously unappreciated role for the gut microbiome in modulating locomotion, and identify octopaminergic neurons as mediators of peripheral microbial cues that regulate motor behaviour in animals.

RevDate: 2019-05-20
CmpDate: 2019-05-20

Ma ZP, Song Y, Cai ZH, et al (2018)

Anti-quorum Sensing Activities of Selected Coral Symbiotic Bacterial Extracts From the South China Sea.

Frontiers in cellular and infection microbiology, 8:144.

The worldwide increase in antibiotic-resistant pathogens means that identification of alternative antibacterial drug targets and the subsequent development of new treatment strategies are urgently required. One such new target is the quorum sensing (QS) system. Coral microbial consortia harbor an enormous diversity of microbes, and are thus rich sources for isolating novel bioactive and pharmacologically valuable natural products. However, to date, the versatility of their bioactive compounds has not been broadly explored. In this study, about two hundred bacterial colonies were isolated from a coral species (Pocillopora damicornis) and screened for their ability to inhibit QS using the bioreporter strain Chromobacterium violaceum ATCC 12472. Approximately 15% (30 isolates) exhibited anti-QS activity, against the indicator strain. Among them, a typical Gram-positive bacterium, D11 (Staphylococcus hominis) was identified and its anti-QS activity was investigated. Confocal microscopy observations showed that the bacterial extract inhibited the biofilm formation of clinical isolates of wild-type P. aeruginosa PAO1 in a dose-dependent pattern. Chromatographic separation led to the isolation of a potent QS inhibitor that was identified by high-performance liquid chromatography-mass spectrometry (HPLC-MS) and nuclear magnetic resonance (NMR) spectroscopy as DL-homocysteine thiolactone. Gene expression analyses using RT-PCR showed that strain D11 led to a significant down-regulation of QS regulatory genes (lasI, lasR, rhlI, and rhlR), as well as a virulence-related gene (lasB). From the chemical structure, the target compound (DL-homocysteine thiolactone) is an analog of the acyl-homoserine lactones (AHLs), and we presume that DL-homocysteine thiolactone outcompetes AHL in occupying the receptor and thereby inhibiting QS. Whole-genome sequence analysis of S. hominis D11 revealed the presence of predicted genes involved in the biosynthesis of homocysteine thiolactone. This study indicates that coral microbes are a resource bank for developing QS inhibitors and they will facilitate the discovery of new biotechnologically relevant compounds that could be used instead of traditional antibiotics.

RevDate: 2019-05-19

Vander Linden C, C Corbet (2019)

Reconciling environment-mediated metabolic heterogeneity with the oncogene-driven cancer paradigm in precision oncology.

Seminars in cell & developmental biology pii:S1084-9521(18)30166-6 [Epub ahead of print].

Precision oncology is the practice of matching one therapy to one specific patient, based on particular genetic tumor alterations, in order to achieve the best clinical response. Despite an expanding arsenal of targeted therapies, many patients still have a poor outcome because tumor cells show a remarkable capacity to develop drug resistance, thereby leading to tumor relapse. Besides genotype-driven resistance mechanisms, tumor microenvironment (TME) peculiarities strongly contribute to generate an intratumoral phenotypic heterogeneity that affects disease progression and treatment outcome. In this Review, we describe how TME-mediated metabolic heterogeneities actively participate to therapeutic failure. We report how a lactate-based metabolic symbiosis acts as a mechanism of adaptive resistance to targeted therapies and we describe the role of mitochondrial metabolism, in particular oxidative phosphorylation (OXPHOS), to support the growth and survival of therapy-resistant tumor cells in a variety of cancers. Finally, we detail potential metabolism-interfering therapeutic strategies aiming to eradicate OXPHOS-dependent relapse-sustaining malignant cells and we discuss relevant (pre)clinical models that may help integrate TME-driven metabolic heterogeneity in precision oncology.

RevDate: 2019-05-18

Steinfeld L, Vafaei A, Rösner J, et al (2019)

Chitin Prevalence and Function in Bacteria, Fungi and Protists.

Advances in experimental medicine and biology, 1142:19-59.

Chitin is an important structural polysaccharide, which supports and organizes extracellular matrices in a variety of taxonomic groups including bacteria, fungi, protists, and animals. Additionally, chitin has been recognized as a molecule that is required for Rhizobia-legume symbiosis and involved in arbuscular mycorrhizal signaling in the symbiotic interaction between terrestrial plants and fungi. Moreover, it serves as a unique molecular pattern in the plant defense system against pathogenic fungi and parasites, and in the innate and adaptive immune response of mammals and humans. In this review, we will focus on the prevalence and structural function of chitin in bacteria, fungi, and protists, with a particular focus on the evolution of chitin synthases and the function of chitin oligosaccharides as a signaling molecule in symbiosis and immunity.

RevDate: 2019-05-18

Doni F, Mispan MS, Suhaimi NSM, et al (2019)

Roles of microbes in supporting sustainable rice production using the system of rice intensification.

Applied microbiology and biotechnology pii:10.1007/s00253-019-09879-9 [Epub ahead of print].

The system of rice intensification (SRI) is an agroecological approach to rice cultivation that seeks to create optimal conditions for healthy plant growth by minimizing inter-plant competition, transplanting widely spaced young single seedlings, and optimizing favorable soil conditions with organic amendments, increased soil aeration by weeding, and controlled water management. These practices improve rice plant growth with yields up to three times more than with conventional cultivation methods, and increase crop resilience under biotic and abiotic stresses. This review discusses the roles of beneficial microbes in improving rice plant growth, yield, and resilience when SRI practices are used, and how these modifications in plant, soil, water, and nutrient management affect the populations and diversity of soil microorganisms. Mechanisms whereby symbiotic microbes support rice plants' growth and performance are also discussed.

RevDate: 2019-05-18

Queralt M, Walker JKM, de Miguel AM, et al (2019)

The ability of a host plant to associate with different symbiotic partners affects ectomycorrhizal functioning.

FEMS microbiology ecology pii:5491332 [Epub ahead of print].

Some plants that associate with ectomycorrhizal (ECM) fungi are also able to simultaneously establish symbiosis with other types of partners. The presence of alternative partners that may provide similar benefits may affect ECM functioning. Here we compared potential leucine-aminopeptidase (LA) and acid phosphatase (AP) enzyme activity (involved in N and P cycling, respectively) in ECM fungi of three hosts planted under the same conditions but differing in the type of partners: Pinus (ECM fungi only), Eucalyptus (ECM and arbuscular mycorrhizal -AM- fungi) and Acacia (ECM, AM fungi and rhizobial bacteria). We found that the ECM community on Acacia and Eucalyptus had higher potential AP activity than the Pinus community. The ECM community in Acacia also showed increased potential LA activity compared to Pinus. Morphotypes present in more than one host showed higher potential AP and LA activity when colonizing Acacia than when colonizing another host. Our results suggest that competition with AM fungi and rhizobial bacteria could promote increased ECM activity in Eucalyptus and Acacia. Alternatively, other host-related differences such as ECM community composition could also play a role. We found evidence for ECM physiological plasticity when colonizing different hosts, which might be key for adaptation to future climate scenarios.

RevDate: 2019-05-18

Feldman D, Amedi N, Carmeli S, et al (2019)

Manipulating the expression of small secreted protein 1 (Ssp1) alters patterns of development and metabolism in the white-rot fungus Pleurotus ostreatus.

Applied and environmental microbiology pii:AEM.00761-19 [Epub ahead of print].

The function of small secreted proteins (SSPs) in saprotrophic fungi is, for the most part, unknown. The white-rot mushroom Pleurotus ostreatus produces considerable amounts of poSSPs at the onset of secondary metabolism, during colony development and in response to chemical compounds such as 5-hydroxymethylfurfural and aryl-alcohols. Genetic manipulation of Ssp1, by knockdown (KDssp1) or overexpression (OEssp1), indicated that they are, in fact, involved in regulation of the ligninolytic system. To elucidate their potential involvement in fungal development, quantitative secretome analyses was performed during the trophophase, idiophase and at a transition point between the two growth phases. The mutations conferred a time shift in the secretion and expression patterns; OEssp1 preceded the entrance to idiophase and secondary metabolism, while KDssp1 was delayed. This was also correlated with expression patterns of selected genes. The KDssp1 colony aged at a slower pace, accompanied by a slower decline in biomass over time. In contrast, OEssp1 exhibited severe lysis and aging of the colony at the same time point. These phenomena were accompanied by variations in yellow pigment production, characteristic of entrance of the wild-type into idiophase. The pigment was produced earlier and at a higher amount in the OEssp1 and was absent from KDssp1. Furthermore, the dikaryon harboring OEssp1 exhibited a delay in initiation of fruiting body formation as well as earlier aging. It is proposed that Ssp1 might function as a part of the fungal communication network and regulating the pattern of fungal development and metabolism in P. ostreatusImportanceSmall secreted proteins (SSPs) are common in fungal saprotrophs, but their roles remain elusive. As such, they comprise part of a gene pool which may be involved in governing fungal lifestyles not limited to symbiosis and pathogenicity, in which they are commonly referred as 'effectors'. It is proposed that Ssp1 in the white-rot fungus Pleurotus ostreatus regulates the transition from primary to secondary metabolism, development, aging and fruiting body initiation. Our observations uncover a novel regulatory role of effector-like SSPs in a saprotroph, suggesting that they may act in fungal communication as well as in response to environmental cues. The presence of Ssp1 homologues in other fungal species supports a common potential role in environmental sensing and fungal development.

RevDate: 2019-05-17

Bosch TCG, Guillemin K, M McFall-Ngai (2019)

Evolutionary "Experiments" in Symbiosis: The Study of Model Animals Provides Insights into the Mechanisms Underlying the Diversity of Host-Microbe Interactions.

BioEssays : news and reviews in molecular, cellular and developmental biology [Epub ahead of print].

Current work in experimental biology revolves around a handful of animal species. Studying only a few organisms limits science to the answers that those organisms can provide. Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host-microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of the mechanisms that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host-microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease.

RevDate: 2019-05-17

Ishii Y, Maruyama S, Takahashi H, et al (2019)

Global Shifts in Gene Expression Profiles Accompanied with Environmental Changes in Cnidarian-Dinoflagellate Endosymbiosis.

G3 (Bethesda, Md.) pii:g3.118.201012 [Epub ahead of print].

Stable endosymbiotic relationships between cnidarian animals and dinoflagellate algae are vital for sustaining coral reef ecosystems. Recent studies have shown that elevated seawater temperatures can cause the collapse of their endosymbiosis, known as 'bleaching', and result in mass mortality. However, the molecular interplay between temperature responses and symbiotic states still remains unclear. To identify candidate genes relevant to the symbiotic stability, we performed transcriptomic analyses under multiple conditions using the symbiotic and apo-symbiotic (symbiont free) Exaiptasia diaphana, an emerging model sea anemone. Gene expression patterns showed that large parts of differentially expressed genes in response to heat stress were specific to the symbiotic state, suggesting that the host sea anemone could react to environmental changes in a symbiotic state-dependent manner. Comparative analysis of expression profiles under multiple conditions highlighted candidate genes potentially important in the symbiotic state transition under heat-induced bleaching. Many of these genes were functionally associated with carbohydrate and protein metabolisms in lysosomes. Symbiont algal genes differentially expressed in hospite encode proteins related to heat shock response, calcium signaling, organellar protein transport, and sugar metabolism. Our data suggest that heat stress alters gene expression in both the hosts and symbionts. In particular, heat stress may affect the lysosome-mediated degradation and transportation of substrates such as carbohydrates through the symbiosome (phagosome-derived organelle harboring symbiont) membrane, which potentially might attenuate the stability of symbiosis and lead to bleaching-associated symbiotic state transition.

RevDate: 2019-05-17
CmpDate: 2019-05-17

Sen A, Duperron S, Hourdez S, et al (2018)

Cryptic frenulates are the dominant chemosymbiotrophic fauna at Arctic and high latitude Atlantic cold seeps.

PloS one, 13(12):e0209273 pii:PONE-D-18-18638.

We provide the first detailed identification of Barents Sea cold seep frenulate hosts and their symbionts. Mitochondrial COI sequence analysis, in combination with detailed morphological investigations through both light and electron microscopy was used for identifying frenulate hosts, and comparing them to Oligobrachia haakonmosbiensis and Oligobrachia webbi, two morphologically similar species known from the Norwegian Sea. Specimens from sites previously assumed to host O. haakonmosbiensis were included in our molecular analysis, which allowed us to provide new insight on the debate regarding species identity of these Oligobrachia worms. Our results indicate that high Arctic seeps are inhabited by a species that though closely related to Oligobrachia haakonmosbiensis, is nonetheless distinct. We refer to this group as the Oligobrachia sp. CPL-clade, based on the colloquial names of the sites they are currently known to inhabit. Since members of the Oligobrachia sp. CPL-clade cannot be distinguished from O. haakonmosbiensis or O. webbi based on morphology, we suggest that a complex of cryptic Oligobrachia species inhabit seeps in the Norwegian Sea and the Arctic. The symbionts of the Oligobrachia sp. CPL-clade were also found to be closely related to O. haakonmosbiensis symbionts, but genetically distinct. Fluorescent in situ hybridization and transmission electron micrographs revealed extremely dense populations of bacteria within the trophosome of members of the Oligobrachia sp. CPL-clade, which is unusual for frenulates. Bacterial genes for sulfur oxidation were detected and small rod shaped bacteria (round in cross section), typical of siboglinid-associated sulfur-oxidizing bacteria, were seen on electron micrographs of trophosome bacteriocytes, suggesting that sulfide constitutes the main energy source. We hypothesize that specific, local geochemical conditions, in particular, high sulfide fluxes and concentrations could account for the unusually high symbiont densities in members of the Oligrobrachia sp. CPL-clade.

RevDate: 2019-05-16

Dabo M, Jaiswal SK, FD Dakora (2019)

Phylogenetic evidence of allopatric speciation of bradyrhizobia nodulating cowpea (Vigna unguiculata L. walp) in South African and Mozambican soils.

FEMS microbiology ecology pii:5490326 [Epub ahead of print].

The legume host and soil environment play a major role to establish effective symbiosis with diverse rhizobia for growth promotion and nodule formation. Aim of this study was to access morpho-physiology, distribution and phylogenetic position of rhizobia nodulating cowpea from South Africa and Mozambique. The results showed that isolate were highly diverse in their appearance on yeast mannitol agar plates. The test isolates also showed an ability to produce IAA at concentrations ranging from 0.64 to 56.46 μg.ml-1 and to solubilise phosphorus at levels from 0 to 3.55 index. Canonical correspondence analysis (CCA) showed that soil pH and mineral nutrients could significantly influence bradyrhizobial distribution. Analysis of BOX-PCR placed the isolates in eight major clusters with 0.01 to 1.00 similarity coefficient with resulted 45 unique BOX-types. Isolates' phylogenetic analyses based on 16S rRNA, atpD, glnII, gyrB and recA gene sequences showed distinct novel evolutionary lineages within the genus Bradyrhizobium, with some of them being closely related to Bradyrhizobium kavangense, B. subterraneum and B. pachyrhizi. Furthermore, symbiotic genes' phylogenies suggested that the isolates' sym loci probably relate to isolates' geographical origin. The results indicated that geographical origin did affect the isolates' phylogenetic placement and could be the basis for allopatric speciation.

RevDate: 2019-05-16

Steidinger BS, Crowther TW, Liang J, et al (2019)

Climatic controls of decomposition drive the global biogeography of forest-tree symbioses.

Nature, 569(7756):404-408.

The identity of the dominant root-associated microbial symbionts in a forest determines the ability of trees to access limiting nutrients from atmospheric or soil pools1,2, sequester carbon3,4 and withstand the effects of climate change5,6. Characterizing the global distribution of these symbioses and identifying the factors that control this distribution are thus integral to understanding the present and future functioning of forest ecosystems. Here we generate a spatially explicit global map of the symbiotic status of forests, using a database of over 1.1 million forest inventory plots that collectively contain over 28,000 tree species. Our analyses indicate that climate variables-in particular, climatically controlled variation in the rate of decomposition-are the primary drivers of the global distribution of major symbioses. We estimate that ectomycorrhizal trees, which represent only 2% of all plant species7, constitute approximately 60% of tree stems on Earth. Ectomycorrhizal symbiosis dominates forests in which seasonally cold and dry climates inhibit decomposition, and is the predominant form of symbiosis at high latitudes and elevation. By contrast, arbuscular mycorrhizal trees dominate in aseasonal, warm tropical forests, and occur with ectomycorrhizal trees in temperate biomes in which seasonally warm-and-wet climates enhance decomposition. Continental transitions between forests dominated by ectomycorrhizal or arbuscular mycorrhizal trees occur relatively abruptly along climate-driven decomposition gradients; these transitions are probably caused by positive feedback effects between plants and microorganisms. Symbiotic nitrogen fixers-which are insensitive to climatic controls on decomposition (compared with mycorrhizal fungi)-are most abundant in arid biomes with alkaline soils and high maximum temperatures. The climatically driven global symbiosis gradient that we document provides a spatially explicit quantitative understanding of microbial symbioses at the global scale, and demonstrates the critical role of microbial mutualisms in shaping the distribution of plant species.

RevDate: 2019-05-16
CmpDate: 2019-05-16

Vissa S, Hofstetter RW, Bonifácio L, et al (2019)

Phoretic mite communities associated with bark beetles in the maritime and stone pine forests of Setúbal, Portugal.

Experimental & applied acarology, 77(2):117-131.

The phoretic mite communities of prominent bark beetle pests associated with pine stands of southern Portugal were sampled to determine whether they vary across bark beetle species and stand type. Bark beetles were sampled for mites from two primary (aggressive) bark beetle species (Ips sexdentatus and Orthotomicus erosus) and the most common secondary species (Hylurgus ligniperda) in maritime pine (Pinus pinaster) and stone pine (Pinus pinea) in the Setúbal province of Portugal. Twelve mite species, spanning diverse ecological roles, are found associated with these bark beetle systems. The relative abundances of the 12 species that make up the phoretic mite communities of maritime and stone pine varied significantly between host beetle species as well as between stand type, indicating that the phoretic host and dominant tree type are important drivers of mite community composition. The functional roles of these mites are outlined and their ecological significance in pine forest ecosystems is discussed.

RevDate: 2019-05-16
CmpDate: 2019-05-16

Xie L, Lehvävirta S, Timonen S, et al (2018)

Species-specific synergistic effects of two plant growth-promoting microbes on green roof plant biomass and photosynthetic efficiency.

PloS one, 13(12):e0209432 pii:PONE-D-18-16681.

Rhizophagus irregularis, an arbuscular mycorrhizal fungus, and Bacillus amyloliquefaciens, a bacterium, are microorganisms that promote plant growth. They associate with plant roots and facilitate nutrient absorption by their hosts, increase resistance against pathogens and pests, and regulate plant growth through phytohormones. In this study, eight local plant species in Finland (Antennaria dioica, Campanula rotundifolia, Fragaria vesca, Geranium sanguineum, Lotus corniculatus, Thymus serpyllum, Trifolium repens, and Viola tricolor) were inoculated with R. irregularis and/or B. amyloliquefaciens in autoclaved substrates to evaluate the plant growth-promoting effects of different plant/microbe combinations under controlled conditions. The eight plant species were inoculated with R. irregularis, B. amyloliquefaciens, or both microbes or were not inoculated as a control. The impact of the microbes on the plants was evaluated by measuring dry shoot weight, colonization rate by the arbuscular mycorrhizal fungus, bacterial population density, and chlorophyll fluorescence using a plant phenotyping facility. Under dual inoculation conditions, B. amyloliquefaciens acted as a "mycorrhiza helper bacterium" to facilitate arbuscular mycorrhizal fungus colonization in all tested plants. In contrast, R. irregularis did not demonstrate reciprocal facilitation of the population density of B. amyloliquefaciens. Dual inoculation with B. amyloliquefaciens and R. irregularis resulted in the greatest increase in shoot weight and photosynthetic efficiency in T. repens and F. vesca.

RevDate: 2019-05-16
CmpDate: 2019-05-16

Newton AC, Boscolo D, Ferreira PA, et al (2018)

Impacts of deforestation on plant-pollinator networks assessed using an agent based model.

PloS one, 13(12):e0209406 pii:PONE-D-18-20677.

Plant-pollinator networks have been widely used to understand the ecology of mutualistic interactions between plants and animals. While a number of general patterns have been identified, the mechanisms underlying the structure of plant-pollinator networks are poorly understood. Here we present an agent based model (ABM) that simulates the movement of bees over heterogeneous landscapes and captures pollination events, enabling the influence of landscape pattern on pollination networks to be explored. Using the model, we conducted a series of experiments using virtual landscapes representing a gradient of forest loss and fragmentation. The ABM was able to produce expected trends in network structure, from simulations of interactions between individual plants and pollinators. For example, results indicated an increase in the index of complementary specialization (H2') and a decline in network connectance with increasing forest cover. Furthermore, network nestedness was not associated with the degree of forest cover, but was positively related to forest patch size, further supporting results obtained in the field. This illustrates the potential value of ABMs for exploring the structure and dynamics of plant-pollinator networks, and for understanding the mechanisms that underlie them. We attribute the results obtained primarily to a shift from specialist to generalist pollinators with increasing forest loss, a trend that has been observed in some field situations.

RevDate: 2019-05-16
CmpDate: 2019-05-16

Lee FJ, Miller KI, McKinlay JB, et al (2018)

Differential carbohydrate utilization and organic acid production by honey bee symbionts.

FEMS microbiology ecology, 94(8):.

The honey bee worker gut hosts a community of bacteria that comprises 8-10 core bacterial species, along with a set of more transient environmental microbes. Collectively, these microbes break down and ferment saccharides present in the host's diet, based on analyses of metagenomes, and metatranscriptomes from this environment. As part of this metabolism, the bacteria produce short-chain fatty acids that may serve as a food source for the host bee, stimulating biological processes that may contribute to host weight gain. To identify metabolic contributions of symbionts within the honey bee gut, we utilized a combination of molecular and biochemical approaches. We show significant variation in the metabolic capabilities of honey bee-associated taxa, highlighting the fact that honey bee gut microbiota members of the same clade are highly variable in their ability to use specific carbohydrates and produce organic acids. Finally, we confirm that the honey bee core microbes are active in vivo, expressing key enzymatic genes critical for utilizing plant-derived molecules and producing organic acids (i.e. acetate and lactate). These results suggest that core taxa may contribute significantly to weight gain in the honey bee, specifically through the production of organic acids.

RevDate: 2019-05-16
CmpDate: 2019-05-16

Marie A (2018)

"Self-sacrifice" as an accidental outcome of extreme within-group mutualism.

The Behavioral and brain sciences, 41:e210.

Whitehouse makes no room for evolutionary approaches to extreme behaviors based on partner choice and mutualism, which have been convincingly invoked to make sense of ordinary morality. Extended to intergroup warfare, these evolutionary mechanisms may play a pivotal role in explaining the existence of extreme - though not functionally sacrificial - behaviors, benefiting non-kin fellow fighters, together with the distinctive phenomenology those behaviors display.

RevDate: 2019-05-16
CmpDate: 2019-05-16

Lavy A, Keren R, Yu K, et al (2018)

A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.

Environmental microbiology, 20(2):800-814.

Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus.

RevDate: 2019-05-15

Ramakrishna C, Kujawski M, Chu H, et al (2019)

Bacteroides fragilis polysaccharide A induces IL-10 secreting B and T cells that prevent viral encephalitis.

Nature communications, 10(1):2153 pii:10.1038/s41467-019-09884-6.

The gut commensal Bacteroides fragilis or its capsular polysaccharide A (PSA) can prevent various peripheral and CNS sterile inflammatory disorders. Fatal herpes simplex encephalitis (HSE) results from immune pathology caused by uncontrolled invasion of the brainstem by inflammatory monocytes and neutrophils. Here we assess the immunomodulatory potential of PSA in HSE by infecting PSA or PBS treated 129S6 mice with HSV1, followed by delayed Acyclovir (ACV) treatment as often occurs in the clinical setting. Only PSA-treated mice survived, with dramatically reduced brainstem inflammation and altered cytokine and chemokine profiles. Importantly, PSA binding by B cells is essential for induction of regulatory CD4+ and CD8+ T cells secreting IL-10 to control innate inflammatory responses, consistent with the lack of PSA mediated protection in Rag-/-, B cell- and IL-10-deficient mice. Our data reveal the translational potential of PSA as an immunomodulatory symbiosis factor to orchestrate robust protective anti-inflammatory responses during viral infections.

RevDate: 2019-05-15

Schorn MA, Jordan PA, Podell S, et al (2019)

Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges.

mBio, 10(3): pii:mBio.00821-19.

Marine sponges are recognized as valuable sources of bioactive metabolites and renowned as petri dishes of the sea, providing specialized niches for many symbiotic microorganisms. Sponges of the family Dysideidae are well documented to be chemically talented, often containing high levels of polyhalogenated compounds, terpenoids, peptides, and other classes of bioactive small molecules. This group of tropical sponges hosts a high abundance of an uncultured filamentous cyanobacterium, Hormoscilla spongeliae Here, we report the comparative genomic analyses of two phylogenetically distinct Hormoscilla populations, which reveal shared deficiencies in essential pathways, hinting at possible reasons for their uncultivable status, as well as differing biosynthetic machinery for the production of specialized metabolites. One symbiont population contains clustered genes for expanded polybrominated diphenylether (PBDE) biosynthesis, while the other instead harbors a unique gene cluster for the biosynthesis of the dysinosin nonribosomal peptides. The hybrid sequencing and assembly approach utilized here allows, for the first time, a comprehensive look into the genomes of these elusive sponge symbionts.IMPORTANCE Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their genetic blueprint. A cell enrichment procedure, combined with a hybrid sequencing and assembly approach, enabled detailed genomic analysis of uncultivated cyanobacterial symbiont populations in two chemically rich tropical marine sponges. These population genomes reveal a wealth of secondary metabolism potential as well as possible reasons for historical difficulties in their cultivation.

RevDate: 2019-05-15

Bell-Roberts L, Douglas AE, GDA Werner (2019)

Match and mismatch between dietary switches and microbial partners in plant sap-feeding insects.

Proceedings. Biological sciences, 286(1902):20190065.

Some animal groups associate with the same vertically transmitted microbial symbionts over extended periods of evolutionary time, punctuated by occasional symbiont switches to different microbial taxa. Here we test the oft-repeated suggestion that symbiont switches are linked with host diet changes, focusing on hemipteran insects of the suborder Auchenorrhyncha. These insects include the only animals that feed on plant xylem sap through the life cycle, as well as taxa that feed on phloem sap and plant parenchyma cells. Ancestral state reconstruction provides strong statistical support for a xylem feeding auchenorrhynchan ancestor bearing the dual symbiosis with the primary symbiont Sulcia (Bacteroidetes) and companion symbiont 'β-Sym' (β-proteobacteria). We identified seven dietary transitions from xylem feeding (six to phloem feeding, one to parenchyma feeding), but no reversions to xylem feeding; five evolutionary losses of Sulcia, including replacements by yeast symbionts, exclusively in phloem/parenchyma-feeding lineages; and 14-15 losses of β-Sym, including nine transitions to a different bacterial companion symbiont. Our analysis indicates that, although companion symbiont switching is not associated with shifts in host diet, Sulcia is probably required for xylem-feeding. Furthermore, the ancestral auchenorrhynchan bearing Sulcia and β-Sym probably represents the sole evolutionary origin of xylem feeding in the animal kingdom.

RevDate: 2019-05-15

Zhou Y, Ge S, Jin L, et al (2019)

A novel CO2 -responsive systemic signaling pathway controlling plant mycorrhizal symbiosis.

The New phytologist [Epub ahead of print].

Rising atmospheric carbon dioxide concentrations (eCO2) promote symbiosis between roots and arbuscular mycorrhizal fungi (AMF), modifying plant nutrient acquisition and cycling of carbon, nitrogen and phosphate. However, the biological mechanisms by which plants transmit aerial eCO2 cues to roots, to alter the symbiotic associations remain unknown. We used a range of interdisciplinary approaches, including gene silencing, grafting, transmission electron microscopy, LC-MS/MS, biochemical methodologies and gene transcript analysis to explore the complexities of environmental signal transmission from the point of perception in the leaves at the apex to the roots. Here we show that eCO2 triggers apoplastic H2 O2 -dependent auxin production in tomato shoots followed by systemic signaling that results in strigolactone biosynthesis in the roots. This redox-auxin-strigolactone systemic signaling cascade facilitates eCO2 -induced AMF symbiosis and phosphate utilization. Our results challenge the current paradigm of eCO2 effects on AMF and provide new insights into potential targets for manipulation of AMF symbiosis for high nutrient utilization under future climate change scenarios. This article is protected by copyright. All rights reserved.

RevDate: 2019-05-15

Burgsdorf I, Handley KM, Bar-Shalom R, et al (2019)

Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont.

mSystems, 4(4): pii:mSystems00057-19.

"Candidatus Synechococcus feldmannii" is a facultative intracellular symbiont of the Atlanto-Mediterranean sponge Petrosia ficiformis. Genomic information of sponge-associated cyanobacteria derives thus far from the obligate and extracellular symbiont "Candidatus Synechococcus spongiarum." Here we utilized a differential methylation-based approach for bacterial DNA enrichment combined with metagenomics to obtain the first draft genomes of "Ca. Synechococcus feldmannii." By comparative genomics, we revealed that some genomic features (e.g., iron transport mediated by siderophores, eukaryotic-like proteins, and defense mechanisms, like CRISPR-Cas [clustered regularly interspaced short palindromic repeats-associated proteins]) are unique to both symbiont types and absent or rare in the genomes of taxonomically related free-living cyanobacteria. These genomic features likely enable life under the conditions found inside the sponge host. Interestingly, there are many genomic features that are shared by "Ca. Synechococcus feldmannii" and free-living cyanobacteria, while they are absent in the obligate symbiont "Ca. Synechococcus spongiarum." These include genes related to cell surface structures, genetic regulation, and responses to environmental stress, as well as the composition of photosynthetic genes and DNA metabolism. We speculate that the presence of these genes confers on "Ca. Synechococcus feldmannii" its facultative nature (i.e., the ability to respond to a less stable environment when free-living). Our comparative analysis revealed that distinct genomic features depend on the nature of the symbiotic interaction: facultative and intracellular versus obligate and extracellular. IMPORTANCE Given the evolutionary position of sponges as one of the earliest phyla to depart from the metazoan stem lineage, studies on their distinct and exceptionally diverse microbial communities should yield a better understanding of the origin of animal-bacterium interactions. While genomes of several extracellular sponge symbionts have been published, the intracellular symbionts have, so far, been elusive. Here we compare the genomes of two unicellular cyanobacterial sponge symbionts that share an ancestor but followed different evolutionary paths-one became intracellular and the other extracellular. Counterintuitively, the intracellular cyanobacteria are facultative, while the extracellular ones are obligate. By sequencing the genomes of the intracellular cyanobacteria and comparing them to the genomes of the extracellular symbionts and related free-living cyanobacteria, we show how three different cyanobacterial lifestyles are reflected by adaptive genomic features.

RevDate: 2019-05-15

González-Pech RA, Bhattacharya D, Ragan MA, et al (2019)

Genome Evolution of Coral Reef Symbionts as Intracellular Residents.

Trends in ecology & evolution pii:S0169-5347(19)30132-6 [Epub ahead of print].

Coral reefs are sustained by symbioses between corals and symbiodiniacean dinoflagellates. These symbioses vary in the extent of their permanence in and specificity to the host. Although dinoflagellates are primarily free-living, Symbiodiniaceae diversified mainly as symbiotic lineages. Their genomes reveal conserved symbiosis-related gene functions and high sequence divergence. However, the evolutionary mechanisms that underpin the transition from the free-living lifestyle to symbiosis remain poorly understood. Here, we discuss the genome evolution of Symbiodiniaceae in diverse ecological niches across the broad spectrum of symbiotic associations, from free-living to putative obligate symbionts. We pose key questions regarding genome evolution vis-à-vis the transition of dinoflagellates from free-living to symbiotic and propose strategies for future research to better understand coral-dinoflagellate and other eukaryote-eukaryote symbioses.

RevDate: 2019-05-15

Ortiz-Castro R, J López-Bucio (2019)

Review: Phytostimulation and root architectural responses to quorum-sensing signals and related molecules from rhizobacteria.

Plant science : an international journal of experimental plant biology, 284:135-142.

Bacteria rely on chemical communication to sense the environment and to retrieve information on their population densities. Accordingly, a vast repertoire of molecules is released, which synchronizes expression of genes, coordinates behavior through a process termed quorum-sensing (QS), and determines the relationships with eukaryotic species. Already identified QS molecules from Gram negative bacteria can be grouped into two main classes, N-acyl-L-homoserine lactones (AHLs) and cyclodipeptides (CDPs), with roles in biofilm formation, bacterial virulence or symbiotic interactions. Noteworthy, plants detect each of these molecules, change their own gene expression programs, re-configurate root architecture, and activate defense responses, improving in this manner their adaptation to natural and agricultural ecosystems. AHLs may act as alarm signals, pathogen and/or microbe-associated molecular patterns, whereas CDPs function as hormonal mimics for plants via their putative interactions with the auxin receptor Transport Inhibitor Response1 (TIR1). A major challenge is to identify the molecular pathways of QS-mediated crosstalk and the plant receptors and interacting proteins for AHLs, CDPs and related signals.

RevDate: 2019-05-14
CmpDate: 2019-05-14

Bennek E, Mandić AD, Verdier J, et al (2019)

Subcellular antigen localization in commensal E. coli is critical for T cell activation and induction of specific tolerance.

Mucosal immunology, 12(1):97-107.

Oral tolerance to soluble antigens is critically important for the maintenance of immunological homeostasis in the gut. The mechanisms of tolerance induction to antigens of the gut microbiota are still less well understood. Here, we investigate whether the subcellular localization of antigens within non-pathogenic E. coli has a role for its ability to induce antigen-specific tolerance. E. coli that express an ovalbumin (OVA) peptide in the cytoplasm, at the outer membrane or as secreted protein were generated. Intestinal colonization of mice with non-pathogenic E. coli expressing OVA at the membrane induced the expansion of antigen-specific Foxp3+ Tregs and mediated systemic immune tolerance. In contrast, cytoplasmic OVA was ignored by antigen-specific CD4+ T cells and failed to induce tolerance. In vitro experiments revealed that surface-displayed OVA of viable E. coli was about two times of magnitude more efficient to activate antigen-specific CD4+ T cells than soluble antigens, surface-displayed antigens of heat-killed E. coli or cytoplasmic antigen of viable or heat-killed E. coli. This effect was independent of the antigen uptake efficiency in dendritic cells. In summary, our results show that subcellular antigen localization in viable E. coli strongly influences antigen-specific CD4+ cell expansion and tolerance induction upon intestinal colonization.

RevDate: 2019-05-13

Elizalde-Díaz JP, Hernández-Lucas I, Medina-Aparicio L, et al (2019)

Rhizobium tropici CIAT 899 copA gene plays a fundamental role in copper tolerance in both free life and symbiosis with Phaseolus vulgaris.

Microbiology (Reading, England) [Epub ahead of print].

Rhizobium tropici CIAT 899 is a facultative symbiotic diazotroph able to deal with stressful concentrations of metals. Nevertheless the molecular mechanisms involved in metal tolerance have not been elucidated. Copper (Cu2+) is a metal component essential for the heme-copper respiratory oxidases and enzymes that catalyse redox reactions, however, it is highly toxic when intracellular trace concentrations are surpassed. In this study, we report that R. tropici CIAT 899 is more tolerant to Cu2+ than other Rhizobium and Sinorhizobium species. Through Tn5 random mutagenesis we identify a R. tropici mutant strain with a severe reduction in Cu2+ tolerance. The Tn5 insertion disrupted the gene RTCIAT899_CH17575, encoding a putative heavy metal efflux P1B-1-type ATPase designated as copA. Phaseolus vulgaris plants inoculated with the copA::Tn5 mutant in the presence of toxic Cu2+ concentrations showed a drastic reduction in plant and nodule dry weight, as well as nitrogenase activity. Nodules induced by the copA::Tn5 mutant present an increase in H2O2 concentration, lipoperoxidation and accumulate 40-fold more Cu2+ than nodules formed by the wild-type strain. The copA::Tn5 mutant complemented with the copA gene recovered the wild-type symbiotic phenotypes. Therefore, the copA gene is essential for R. tropici CIAT 899 to survive in copper-rich environments in both free life and symbiosis with P. vulgaris plants.

RevDate: 2019-05-13

Parekh VS, MA Jacobs (2019)

Deep learning and radiomics in precision medicine.

Expert review of precision medicine and drug development, 4(2):59-72.

Introduction: The radiological reading room is undergoing a paradigm shift to a symbiosis of computer science and radiology using artificial intelligence integrated with machine and deep learning with radiomics to better define tissue characteristics. The goal is to use integrated deep learning and radiomics with radiological parameters to produce a personalized diagnosis for a patient.

Areas covered: This review provides an overview of historical and current deep learning and radiomics methods in the context of precision medicine in radiology. A literature search for 'Deep Learning', 'Radiomics', 'Machine learning', 'Artificial Intelligence', 'Convolutional Neural Network', 'Generative Adversarial Network', 'Autoencoders', Deep Belief Networks", Reinforcement Learning", and 'Multiparametric MRI' was performed in PubMed, ArXiv, Scopus, CVPR, SPIE, IEEE Xplore, and NIPS to identify articles of interest.

Expert opinion: In conclusion, both deep learning and radiomics are two rapidly advancing technologies that will unite in the future to produce a single unified framework for clinical decision support with a potential to completely revolutionize the field of precision medicine.

RevDate: 2019-05-13

Schlöffel MA, Käsbauer C, AA Gust (2019)

Interplay of plant glycan hydrolases and LysM proteins in plant-Bacteria interactions.

International journal of medical microbiology : IJMM pii:S1438-4221(18)30647-7 [Epub ahead of print].

Plants are always found together with bacteria and other microbes. Although plants can be attacked by phytopathogenic bacteria, they are more often engaged in neutral or mutualistic bacterial interactions. In the soil, plants associate with rhizobia or other plant growth promoting rhizosphere bacteria; above ground, bacteria colonise plants as epi- and endophytes. For mounting appropriate responses, such as permitting colonisation by beneficial symbionts while at the same time fending off pathogenic invaders, plants need to distinguish between the "good" and the "bad". Plants make use of proteins containing the lysin motif (LysM) for perception of N-acetylglucosamine containing carbohydrate structures, such as chitooligosaccharides functioning as symbiotic nodulation factors or bacterial peptidoglycan. Moreover, plant hydrolytic enzymes of the chitinase family, which are able to cleave bacterial peptidoglycan or chitooligosaccharides, are essential for cellular signalling induced by rhizobial nodulation factors during symbiosis as well as bacterial peptidoglycan during pathogenesis. Hence, LysM receptors seem to work in concert with hydrolytic enzymes that fine-tune ligand availability to either allow symbiotic interactions or trigger plant immunity.

RevDate: 2019-05-13
CmpDate: 2019-05-13

Odeniran PO, Macleod ET, Ademola IO, et al (2019)

Endosymbionts interaction with trypanosomes in Palpalis group of Glossina captured in southwest Nigeria.

Parasitology international, 70:64-69.

Glossina species epidemiological studies were conducted in "fly-belt" endemic zone of southwest Nigeria. Two major study areas were identified and four Nzi traps were set in each site for tsetse collection. This study was conducted to determine the prevalence of endosymbionts (Wigglesworthia glossinidia, Sodalis glossinidius and Wolbachia) in natural field-trapped populations of G. p. palpalis and G. tachinoides and investigate the corresponding interactions with African trypanosomes. A total of 64 tsetse flies were collected, these included G. p. palpalis (n = 28) and G. tachinoides (n = 36). Trypanosome infection and endosymbionts of these flies were determined using polymerase chain reaction (PCR) amplification. The infection rates of W. glossinidia was 100.0% in both species, no flies were positive for Wolbachia. Sodalis glossinidius prevalence was similar between the two-tsetse species, with G. p. palpalis and G. tachinoides showing prevalence of 35.7% (95%CI: 20.7-54.2) and 27.8% (95%CI: 15.9-44.0) respectively. No relationship was found between the endosymbionts and trypanosomes in trapped tsetse flies. More studies are needed to enhance the potential control interventions mediated by endosymbionts to reduce parasitic infections.

RevDate: 2019-05-13
CmpDate: 2019-05-13

Kumar U, Nayak AK, Panneerselvam P, et al (2019)

Cyanobiont diversity in six Azolla spp. and relation to Azolla-nutrient profiling.

Planta, 249(5):1435-1447.

MAIN CONCLUSION: Illumina-Miseq®-based cyanobiont diversity and biomass were analyzed in six Azolla spp. Results revealed that 93-98% of total operational taxonomic units (OTUs) belong to Nostacaceae followed by Cylindrospermopsis with about 1-6% OTUs. The taxonomy of Azolla-cyanobiont is a long-term debate within the scientific community. Morphological and biochemical-based reports indicated the presence of Anabaena, Nostoc and/or Trichormus azollae as abundant Azolla-cyanobionts, however, molecular data did not support the abundance of Anabaena and/or Nostoc. To understand furthermore, the cyanobiont diversity in six species of Azolla (A. microphylla, A. mexicana, A. filiculoides, A. caroliniana, A. pinnata and A. rubra) was analyzed based on 16S rRNA Illumina-MiSeq sequencing. Additionally, biomass and nutrient profiling of Azolla spp. were analyzed and correlated with cyanobiont diversity. Illumina-MiSeq data revealed that 99.6-99.9% of total operational taxonomic units (OTUs) belonged to Nostocophycideae (class), Nostocales (order) and Nostacaceae (family). At genus level, the unassigned affiliation (93.4-97.9%) under Nostacaceae family was abundant followed by Cylindrospermopsis OTUs (1.1-6.0%). Interestingly, A. pinnata harboured maximum Cylindrospermopsis OTUs and also recorded higher biomass (40.67 g m-2 day-1), whereas crude protein (25.9%) and antioxidants (76.9%) were recorded to be higher in A. microphylla. Biplot analysis revealed that A. pinnata and its cyanobiont abundance were positively correlated with neutral and acid detergent fibers. Overall, the present findings deepened the understanding about cyanobiont in Azolla and its relations with Azolla nutrient profiling.

RevDate: 2019-05-13
CmpDate: 2019-05-13

Angers A, Ouimet P, Tsyvian-Dzyabko A, et al (2019)

[The underestimated coding potential of mitochondrial DNA].

Medecine sciences : M/S, 35(1):46-54.

Mitochondria are ancient organelles that emerged from the endosymbiosis of free-living proto-bacteria. They still retain a semi-autonomous genetic system with a small genome. Mitochondrial DNA (mtDNA) codes for 13 essential proteins for the production of ATP, the sequences of which are relatively conserved across Metazoans. The discovery of additional mitochondria-derived peptides (MDPs) indicates an underestimated coding potential. Humanin, an anti-apoptotic peptide, is likely independently transcribed from within the 16S rRNA gene, as are recently described SHLPs. MOTS-c, discovered in silico, has been demonstrated to be involved in metabolism and insulin sensitivity. Gau, is a positionally conserved open reading frame (ORF) sequence found in the antisense strand of the COX1 gene and its corresponding peptide is strictly colocalized with mitochondrial markers. In bivalves with doubly uniparental inheritance of mtDNA, male and female mtDNAs each carry a separate additional gene possibly involved in sex determination. Other MDPs likely exist and their investigation will shed light on the underestimated functional repertoire of mitochondria.

RevDate: 2019-05-13
CmpDate: 2019-05-13

Enebe MC, OO Babalola (2019)

The impact of microbes in the orchestration of plants' resistance to biotic stress: a disease management approach.

Applied microbiology and biotechnology, 103(1):9-25.

The struggle for survival is a natural and a continuous process. Microbes are struggling to survive by depending on plants for their nutrition while plants on the other hand are resisting the attack of microbes in order to survive. This interaction is a tug of war and the knowledge of microbe-plant relationship will enable farmers/agriculturists improve crop health, yield, sustain regular food supply, and minimize the use of agrochemicals such as fungicides and pesticides in the fight against plant pathogens. Although, these chemicals are capable of inhibiting pathogens, they also constitute an environmental hazard. However, certain microbes known as plant growth-promoting microbes (PGPM) aid in the sensitization and priming of the plant immune defense arsenal for it to conquer invading pathogens. PGPM perform this function by the production of elicitors such as volatile organic compounds, antimicrobials, and/or through competition. These elicitors are capable of inducing the expression of pathogenesis-related genes in plants through induced systemic resistance or acquired systemic resistance channels. This review discusses the current findings on the influence and participation of microbes in plants' resistance to biotic stress and to suggest integrative approach as a better practice in disease management and control for the achievement of sustainable environment, agriculture, and increasing food production.

RevDate: 2019-05-13
CmpDate: 2019-05-13

Ferlian O, Biere A, Bonfante P, et al (2018)

Growing Research Networks on Mycorrhizae for Mutual Benefits.

Trends in plant science, 23(11):975-984.

Research on mycorrhizal interactions has traditionally developed into separate disciplines addressing different organizational levels. This separation has led to an incomplete understanding of mycorrhizal functioning. Integration of mycorrhiza research at different scales is needed to understand the mechanisms underlying the context dependency of mycorrhizal associations, and to use mycorrhizae for solving environmental issues. Here, we provide a road map for the integration of mycorrhiza research into a unique framework that spans genes to ecosystems. Using two key topics, we identify parallels in mycorrhiza research at different organizational levels. Based on two current projects, we show how scientific integration creates synergies, and discuss future directions. Only by overcoming disciplinary boundaries, we will achieve a more comprehensive understanding of the functioning of mycorrhizal associations.

RevDate: 2019-05-13
CmpDate: 2019-05-13

Banks JA (2018)

Fern genomes finally here.

Nature plants, 4(7):404-405.

RevDate: 2019-05-13
CmpDate: 2019-05-13

Kust A, Mareš J, Jokela J, et al (2018)

Discovery of a Pederin Family Compound in a Nonsymbiotic Bloom-Forming Cyanobacterium.

ACS chemical biology, 13(5):1123-1129.

The pederin family includes a number of bioactive compounds isolated from symbiotic organisms of diverse evolutionary origin. Pederin is linked to beetle-induced dermatitis in humans, and pederin family members possess potent antitumor activity caused by selective inhibition of the eukaryotic ribosome. Their biosynthesis is accomplished by a polyketide/nonribosomal peptide synthetase machinery employing an unusual trans-acyltransferase mechanism. Here, we report a novel pederin type compound, cusperin, from the free-living cyanobacterium Cuspidothrix issatschenkoi (earlier Aphanizomenon). The chemical structure of cusperin is similar to that of nosperin recently isolated from the lichen cyanobiont Nostoc sharing the tehrahydropyran moiety and major part of the linear backbone. However, the cusperin molecule is extended by a glycine residue and lacks one hydroxyl substituent. Pederins were previously thought to be exclusive to symbiotic relationships. However, C. issatschenkoi is a nonsymbiotic planktonic organism and a frequent component of toxic water blooms. Cusperin is devoid of the cytotoxic activity reported for other pederin family members. Hence, our findings raise questions about the role of pederin analogues in cyanobacteria and broaden the knowledge of ecological distribution of this group of polyketides.

RevDate: 2019-05-13
CmpDate: 2019-05-13

Tatu AL, LC Nwabudike (2018)

Reply to: Kubiak K et al. Endosymbiosis and its significance in dermatology.

Journal of the European Academy of Dermatology and Venereology : JEADV, 32(9):e346-e347.

RevDate: 2019-05-12

Wiles TJ, K Guillemin (2019)

The Other Side of the Coin: What Beneficial Microbes Can Teach us about Pathogenic Potential.

Journal of molecular biology pii:S0022-2836(19)30255-4 [Epub ahead of print].

Koch's postulates and molecular Koch's postulates have made an indelible mark on how we study and classify microbes, particularly pathogens. However, rigid adherence to these historic postulates constrains our view of not only microbial pathogenesis, but host-microbe relationships in general. Collectively the postulates imply that a 'microbial pathogen' is a clearly identifiable organism with the exclusive capacity to elicit disease through an arsenal of pathogen-specific 'virulence factors'. This narrow definition has been repeatedly contradicted. Advances in DNA sequencing technologies and new experimental systems have revealed that the outcomes of host-microbe interactions are highly contextual and dynamic, especially those involving resident microbiota and variable aspects of host biology. Clarifying what differentiates pathogenic from non-pathogenic microbes, including their paradoxical ability to masquerade as one another, is critical to developing targeted diagnostics and treatments for infectious disease. Such endeavors will also inform the design of therapeutic strategies based on microbiome engineering by providing insights into how manipulating entire host-microbe systems may directly or indirectly alter the pathogenic potential of microbial communities. With these goals in mind, we discuss the need to develop experimental models that better capture the contexts that determine the nature of host-microbe relationships. To demonstrate the potential of one such model-the zebrafish and its resident microbiota-we describe recent work that has revealed the thin line between pathogenic and mutualistic relationships, how the intestine physically shapes bacterial populations and inflammation, and the ability of microbial transmission to override the host's innate immune system.

RevDate: 2019-05-12

Verdonk CJ, Sullivan JT, Williman KM, et al (2019)

Delineation of the integrase-attachment and origin-of-transfer regions of the symbiosis island ICEMlSymR7A.

Plasmid pii:S0147-619X(18)30152-5 [Epub ahead of print].

Integrative and conjugative elements (ICEs) are chromosomally-integrated mobile genetic elements that excise from their host chromosome and transfer to other bacteria via conjugation. ICEMlSymR7A is the prototypical member of a large family of "symbiosis ICEs" which confer upon their hosts the ability to form a nitrogen-fixing symbiosis with a variety of legume species. Mesorhizobial symbiosis ICEs carry a common core of mobilisation genes required for integration, excision and conjugative transfer. IntS of ICEMlSymR7A enables recombination between the ICEMlSymR7A attachment site attP and the 3' end of the phe-tRNA gene. Here we identified putative IntS attP arm (P) sites within the attP region and demonstrated that the outermost P1 and P5 sites demarcated the minimal region for efficient IntS-mediated integration. We also identified the ICEMlSymR7A origin-of-transfer (oriT) site directly upstream of the relaxase-gene rlxS. The ICEMlSymR7A conjugation system mobilised a plasmid carrying the cloned oriT to Escherichia coli in an rlxS-dependent manner. Surprisingly, an in-frame, markerless deletion mutation in the ICEMlSymR7A recombination directionality factor (excisionase) gene rdfS, but not a mutation in intS, abolished mobilisation, suggesting the rdfS deletion tentatively has downstream effects on conjugation or its regulation. In summary, this work defines two critical cis-acting regions required for excision and transfer of ICEMlSymR7A and related ICEs.

RevDate: 2019-05-11

Songwattana P, Tittabutr P, Wongdee J, et al (2019)

Symbiotic properties of a chimeric Nod-independent photosynthetic Bradyrhizobium strain obtained by conjugative transfer of a symbiotic plasmid.

Environmental microbiology [Epub ahead of print].

The lateral transfer of symbiotic genes converting a predisposed soil bacteria into a legume symbiont has occurred repeatedly and independently during the evolution of rhizobia. We experimented the transfer of a symbiotic plasmid between Bradyrhizobium strains. The originality of the DOA9 donor is that it harbors a symbiotic mega-plasmid (pDOA9) containing nod, nif and T3SS genes while the ORS278 recipient has the unique property of inducing nodules on some Aeschynomene species in the absence of Nod factors (NFs). We observed that the chimeric strain ORS278-pDOA9* lost its ability to develop a functional symbiosis with A. indica and A. evenia. The mutation of rhcN and nodB led to partial restoration of nodule efficiency, indicating that T3SS effectors and NFs block the establishment of the NF-independent symbiosis. Conversely, ORS278-pDOA9* strain acquired the ability to form nodules on Crotalaria juncea and Macroptillium artropurpureum but not on NF-dependent Aeschynomene (A. afraspera and A. americana), suggesting that the ORS278 strain also harbors incompatible factors that block the interaction with these species. These data indicate that the symbiotic properties of a chimeric rhizobia cannot be anticipated due to new combination of symbiotic and non-symbiotic determinants that may interfere during the interaction with the host plant. This article is protected by copyright. All rights reserved.

RevDate: 2019-05-11

Shiratake K, Notaguchi M, Makino H, et al (2019)

Petunia PLEIOTROPIC DRUG RESISTANCE 1 is a Strigolactone Short-distance Transporter with Long-distance Outcomes.

Plant & cell physiology pii:5488007 [Epub ahead of print].

Phytohormones of the strigolactone (SL) family have been characterized as negative regulators of lateral bud outgrowth and triggers of symbioses between plants and mycorrhizal fungi. Strigolactones and their precursors are synthesized in root tips as well as along shoot and root vasculature; they either move shoot-wards and regulate plant architecture or are exuded from roots into the soil to establish mycorrhizal symbiosis. Owing to the difficulty in quantification of SL in shoot tissues because of low abundance, it is not yet clear how SL distribution in plants is regulated at short- and long-distances from SL biosynthetic and target tissues. To address this question, we grafted wildtype scions and rootstocks from different petunia mutants for SL biosynthesis/transport and investigated SL activity by quantifying lateral bud outgrowth in the main shoot. Based on these results, we show that i) the previously reported petunia SL transporter PLEIOTROPIC DRUG RESISTANCE 1 (PDR1) directly accounts for short-distance SL transport and ii) long distance transport of SLs seems to be partially and not-directly dependent on PDR1. These data suggest that the root-to-shoot transport of SLs occurs either via the vasculature bundle through transporters other than PDR1 or involves SL precursors that are not substrates of PDR1.

RevDate: 2019-05-11

Brunk CF, WF Martin (2019)

Archaeal Histone Contributions to the Origin of Eukaryotes.

Trends in microbiology pii:S0966-842X(19)30095-2 [Epub ahead of print].

The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.

RevDate: 2019-05-10

Chaudhary S, Gupta P, Srivastava S, et al (2019)

Understanding dynamics of Rhizophagus irregularis ontogenesis in axenically developed co-culture through basic and advanced microscopic techniques.

Journal of basic microbiology [Epub ahead of print].

Detailed information on structural changes that occur during ontogenesis of Rhizophagus irregularis in axenically developed co-cultures is limited. Our study aims to investigate the series of events that occur during mycorrhizal ontogenesis under axenic condition through basic and advanced microscopic techniques followed by comparison amongst these to identify the suitable technique for rapid and detailed analysis of mycorrhizal structures. Three stages were identified in mycorrhizal ontogenesis from initiation (pre-infection stage of hyphae; its branching, infection and appressoria formation; epidermal opening; hyphal entry), progression (arbuscular development; hyphal coils and vesicles) to maturity (extra-radical spores). Scanning electron microscopy was found to be an efficient tool for studying spatial three-dimensional progression. Adding to the advantages of advanced microscopy, the potential of autofluorescence to explore the stages of symbiosis non-destructively was established. We also report imaging of ultrathin sections by bright field microscopy to provide finer details at subcellular interface. Owing to the merits of non-destructive sampling, ease of sample preparation, autofluorescence (no dye required), no use of toxic chemicals, rapid analysis and in depth characterization confocal laser scanning microscopy was identified as the most preferred technique. The method thus developed can be used for detailed structural inquisition of mycorrhizal symbiosis both in in planta and in an in vitro system. This article is protected by copyright. All rights reserved.

RevDate: 2019-05-10

Gao M, Benge A, Wu TJ, et al (2019)

Use of Plasmid pVMG to Make Transcriptional ß-Glucuronidase Reporter Gene Fusions in the Rhizobium Genome for Monitoring the Expression of Rhizobial Genes In Vivo.

Biological procedures online, 21:8 pii:96.

Background: The soil bacterium Sinorhizobium meliloti and its allies are important nitrogen-fixing bacterial symbionts that cause N2-fixing nodules on the roots of legumes. Chromosomal ß-glucuronidase gene (uidA) transcriptional fusions are frequently used to monitor the expression of bacterial genes during the symbiosis. However, the construction of the fusions is laborious.

Results: The narrow-host-range, fusion selective plasmid pVMG was constructed and used as a vector for the construction of chromosomal uidA transcriptional fusions in the S. meliloti genome. Translation termination codons were added in all three reading frames upstream of the promoterless uidA in this vector to ensure transcriptional fusions. pVMG replicated to high copy number in Escherichia coli, offering advantages for the isolation of fusion-containing plasmids and the restriction analysis. Genomic locations of uidA fusions were verified in a simple PCR experiment. All these helps reduce the sample processing time and efforts. As a demonstration of its usefulness, the N-acyl homoserine lactone (AHL) signal synthase gene promoter was fused to uidA and shown to be expressed by S. meliloti in the senescence zone of the nodule on the host plant, M. truncatula. This indicates the presence of AHL signals at the late stages of symbiosis.

Conclusions: A simple, pVMG-based method for construction of chromosomal uidA transcriptional fusions has been successfully used in the model rhizobium S. meliloti. It is also applicable for other rhizobial strains.

RevDate: 2019-05-10

Chamberlain NB, Mehari YT, Hayes BJ, et al (2019)

Infection and nuclear interaction in mammalian cells by 'Candidatus Berkiella cookevillensis', a novel bacterium isolated from amoebae.

BMC microbiology, 19(1):91 pii:10.1186/s12866-019-1457-z.

BACKGROUND: 'Candidatus Berkiella cookevillensis' and 'Ca. Berkiella aquae' have previously been described as intranuclear bacteria of amoebae. Both bacteria were isolated from amoebae and were described as appearing within the nuclei of Acanthamoeba polyphaga and ultimately lysing their host cells within 4 days. Both bacteria are Gammaproteobacteria in the order Legionellales with the greatest similarity to Coxiella burnetii. Neither bacterium grows axenically in artificial culture media. In this study, we further characterized 'Ca. B. cookevillensis' by demonstrating association with nuclei of human phagocytic and nonphagocytic cell lines.

RESULTS: Transmission electron microscopy (TEM) and confocal microscopy were used to confirm nuclear co-localization of 'Ca. B. cookevillensis' in the amoeba host A. polyphaga with 100% of cells having bacteria co-localized with host nuclei by 48 h. TEM and confocal microscopy demonstrated that the bacterium was also observed to be closely associated with nuclei of human U937 and THP-1 differentiated macrophage cell lines and nonphagocytic HeLa human epithelial-like cells. Immunofluorescent staining revealed that the bacteria-containing vacuole invaginates the nuclear membranes and appears to cross from the cytoplasm into the nucleus as an intact vacuole.

CONCLUSION: Results of this study indicate that a novel coccoid bacterium isolated from amoebae can infect human cell lines by associating with the host cell nuclei, either by crossing the nuclear membranes or by deeply invaginating the nuclear membranes. When associated with the nuclei, the bacteria appear to be bound within a vacuole and replicate to high numbers by 48 h. We believe this is the first report of such a process involving bacteria and human cell lines.

RevDate: 2019-05-10
CmpDate: 2019-05-10

Saadani O, Jebara SH, Fatnassi IC, et al (2019)

Effect of Vicia faba L. var. minor and Sulla coronaria (L.) Medik associated with plant growth-promoting bacteria on lettuce cropping system and heavy metal phytoremediation under field conditions.

Environmental science and pollution research international, 26(8):8125-8135.

Researches involving the use of association between legumes and PGPBs (plant growth-promoting bacteria) in heavy metal phytoremediation process were mainly performed for soils highly contaminated. However, even in agriculture soils, with moderate or low contamination levels, plants can accumulate high rates of heavy metals. So, food chain contamination by these metals presents a real threat to animal and human health. This work aimed to evaluate the use of two legumes/PGPB symbioses; Vicia faba var. minor and Sulla coronaria have been inoculated with specific heavy metal-resistant inocula in a crop rotation system with Lactuca sativa as a following crop, in order to assess their effects on soil fertility, lettuce yield, and heavy metal content. Our results showed that legume inoculation significantly enhanced their biomass production, nitrogen and phosphorus content. The use of our symbioses as green manure before lettuce cultivation, as a rotation cropping system, affected positively soil fertility. In fact, we recorded a higher organic matter content, with rapid decomposition in the soil of inoculated plots. Besides, results demonstrated a greater nitrogen and phosphorus content in this soil, especially in the plot cultivated with inoculated V. faba var. minor. The improvement of soil fertility enhanced lettuce yield and its nitrogen and phosphorus content. Moreover, inoculated legumes extracted and accumulated more heavy metals than non-inoculated legumes. Our symbioses play the role of organic trap for heavy metals, making them unavailable for following crops. These facts were supported by lettuce heavy metal content, showing a significant decrease in metal accumulation, mainly zinc and cadmium, in edible parts. Results showed the usefulness of the studied symbioses, as a main part of a rotation system with lettuce. Our symbioses can be suggested for agriculture soil phytoremediation, aiming to enhance non-legume crop yield and limit heavy metal translocation to food chain.

RevDate: 2019-05-10
CmpDate: 2019-05-10

Foyer CH, Nguyen HT, HM Lam (2018)

A seed change in our understanding of legume biology from genomics to the efficient cooperation between nodulation and arbuscular mycorrhizal fungi.

Plant, cell & environment, 41(9):1949-1954.

Grain legumes play a significant role in global food security. They have an advantage over cereals in that they can form symbiotic associations with nitrogen-fixing bacteria, making them self-sufficient in terms of nitrogen acquisition. In addition to this superior agronomic trait, grain legumes have excellent nutritional properties and are thus widely used as animal feed as well as in human nutrition. Current global trends towards increased legume consumption and availability of value-added products, as well as legume production in developing countries require the provision of improved cultivars with better productivity and adaptability. Intensive efforts are thus underway to elaborate genomic resources and gain an improved knowledge base in a number of legume crops. There is also an emerging understanding of the beneficial interactions between legume-associated organisms, particularly rhizobia and arbuscular mycorrhizal fungi, which result in improved nodulation and nutrient acquisition. The emerging focus on legume breeding for high sustainable yields as well as improved biotic and abiotic stress tolerance traits will serve to close the current gap between grain legume production and demand. With the support from policymakers, this increase in knowledge can be readily translated into increased crop production to meet the demands of an increasing global population.

RevDate: 2019-05-09

Rahnama M, Maclean P, Fleetwood DJ, et al (2019)

The LaeA orthologue in Epichloë festucae is required for symbiotic interaction with Lolium perenne.

Fungal genetics and biology : FG & B pii:S1087-1845(18)30261-5 [Epub ahead of print].

LaeA is a conserved global regulator of secondary metabolism and development in fungi. It is often required for successful pathogenic interactions. In this study, the laeA homologue in the fungal grass endophyte E. festucae was deleted and functionally characterised in vitro and its role in the mutualistic E. festucae interaction with Lolium perenne (perennial ryegrass) was determined. We showed that laeA in E. festucae is required for normal hyphal morphology, resistance to oxidative stress, and conidiation under nutrient-limited in vitro conditions. In planta studies revealed that laeA is expressed in a tissue-specific manner and is required to form a compatible plant interaction, with the majority of seedlings inoculated with a laeA deletion mutant either dying or being uninfected. In mature infected plants no difference was observed in the number or morphology of endophytic hyphae. However, the number of epiphyllous hyphae were greatly increased. Comparative transcriptomics analyses suggested roles for plant cell wall degradation, fungal cell wall composition, secondary metabolism and small-secreted proteins in Epichloë foliar symbiosis.

RevDate: 2019-05-09

Brown EM, Ke X, Hitchcock D, et al (2019)

Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.

Cell host & microbe, 25(5):668-680.e7.

Sphingolipids are structural membrane components and important eukaryotic signaling molecules. Sphingolipids regulate inflammation and immunity and were recently identified as the most differentially abundant metabolite in stool from inflammatory bowel disease (IBD) patients. Commensal bacteria from the Bacteroidetes phylum also produce sphingolipids, but the impact of these metabolites on host pathways is largely uncharacterized. To determine whether bacterial sphingolipids modulate intestinal health, we colonized germ-free mice with a sphingolipid-deficient Bacteroides thetaiotaomicron strain. A lack of Bacteroides-derived sphingolipids resulted in intestinal inflammation and altered host ceramide pools in mice. Using lipidomic analysis, we described a sphingolipid biosynthesis pathway and revealed a variety of Bacteroides-derived sphingolipids including ceramide phosphoinositol and deoxy-sphingolipids. Annotating Bacteroides sphingolipids in an IBD metabolomic dataset revealed lower abundances in IBD and negative correlations with inflammation and host sphingolipid production. These data highlight the role of bacterial sphingolipids in maintaining homeostasis and symbiosis in the gut.

RevDate: 2019-05-09

Lindsay PL, Williams BN, MacLean AM, et al (2019)

A phosphate-dependent requirement for the transcription factors IPD3 and IPD3L during AM symbiosis in Medicago truncatula.

Molecular plant-microbe interactions : MPMI [Epub ahead of print].

During arbuscular mycorrhizal (AM) symbiosis, activation of a symbiosis signaling pathway induces gene expression necessary for accommodation of AM fungi. Here we focus on pathway components Medicago truncatula INTERACTING PROTEIN OF DOES NOT MAKE INFECTIONS 3 (IPD3) and IPD3 LIKE (IPD3L), which are potential orthologs of Lotus japonicus CYCLOPS, a transcriptional regulator essential for AM symbiosis. In ipd3 ipd3l, hyphal entry through the epidermis and overall colonization levels are reduced relative to wild type but fully developed arbuscules are present in the cortex. In comparison with wild type, colonization of ipd3 ipd3l is acutely sensitive to higher phosphate levels in the growth medium, with a disproportionate decrease in epidermal penetration, overall colonization, and symbiotic gene expression. When constitutively expressed in ipd3 ipd3l, an autoactive DOES NOT MAKE INFECTIONS 3 (DMI3) induces the expression of transcriptional regulators REDUCED ARBUSCULAR MYCORRHIZA 1 (RAM1) and REQUIRED for ARBUSCULE DEVELOPMENT 1 (RAD1), providing a possible avenue for arbuscule development even in the absence of IPD3 and IPD3L. An increased sensitivity of ipd3 ipd3l to GA3 suggests an involvement of DELLA. The data reveal partial redundancy in the symbiosis signaling pathway which may ensure robust signaling in low-P environments, while IPD3 and IPD3L maintain signaling in higher-P environments. The latter may buffer the pathway from short-term variation in P levels encountered by roots during growth in heterogeneous soil environments.

RevDate: 2019-05-09

Vaz Martins T, VN Livina (2019)

What Drives Symbiotic Calcium Signalling in Legumes? Insights and Challenges of Imaging.

International journal of molecular sciences, 20(9): pii:ijms20092245.

We review the contribution of bioimaging in building a coherent understanding of Ca 2 + signalling during legume-bacteria symbiosis. Currently, two different calcium signals are believed to control key steps of the symbiosis: a Ca 2 + gradient at the tip of the legume root hair is involved in the development of an infection thread, while nuclear Ca 2 + oscillations, the hallmark signal of this symbiosis, control the formation of the root nodule, where bacteria fix nitrogen. Additionally, different Ca 2 + spiking signatures have been associated with specific infection stages. Bioimaging is intrinsically a cross-disciplinary area that requires integration of image recording, processing and analysis. We used experimental examples to critically evaluate previously-established conclusions and draw attention to challenges caused by the varying nature of the signal-to-noise ratio in live imaging. We hypothesise that nuclear Ca 2 + spiking is a wide-range signal involving the entire root hair and that the Ca 2 + signature may be related to cytoplasmic streaming.

RevDate: 2019-05-09
CmpDate: 2019-05-09

Murat C, Payen T, Noel B, et al (2018)

Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle.

Nature ecology & evolution, 2(12):1956-1965.

Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.

RevDate: 2019-05-09
CmpDate: 2019-05-09

Certner RH, SV Vollmer (2018)

Inhibiting bacterial quorum sensing arrests coral disease development and disease-associated microbes.

Environmental microbiology, 20(2):645-657.

Among the greatest threats to coral reefs are coral epizootics, which are increasing in frequency and severity across many reef ecosystems. In particular, white band disease (WBD) has devastated Caribbean acroporid populations since its initial outbreak in 1979. However, despite its widespread and damaging effects, the aetiology of WBD remains largely unresolved. Here, we examine the role of quorum sensing within bacterial communities associated with WBD-infected Acropora cervicornis. Microbial communities isolated from WBD-infected corals were exposed to quorum sensing inhibitor (QSI) - a N-acyl homoserine lactone autoinducer antagonist - and then dosed onto healthy test corals. WBD-associated bacteria supplemented with QSI lost the ability to establish disease, while healthy corals exposed to uninhibited WBD bacterial communities became infected within two days. Microbial 16S rRNA metagenomic sequencing analyses were then used to identify shifts in bacterial communities due to QSI exposure on WBD-associated bacterial communities. Our results demonstrated that Vibrionaceae and Flavobacteriaceae abundances were strongly inhibited by the addition of QSI to WBD-infected corals, whereas putative coral symbiont Endozoicomonas and Halomonadaceae abundances decrease dramatically in diseased corals.

RevDate: 2019-05-09
CmpDate: 2019-05-09

Astudillo-García C, Slaby BM, Waite DW, et al (2018)

Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges.

Environmental microbiology, 20(2):561-576.

Many marine sponges contain dense and diverse communities of associated microorganisms. Members of the 'sponge-associated unclassified lineage' (SAUL) are frequently recorded from sponges, yet little is known about these bacteria. Here we investigated the distribution and phylogenetic status of SAUL. A meta-analysis of the available literature revealed the widespread distribution of this clade and its association with taxonomically varied sponge hosts. Phylogenetic analyses, conducted using both 16S rRNA gene-based phylogeny and concatenated marker protein sequences, revealed that SAUL is a sister clade of the candidate phylum 'Latescibacteria'. Furthermore, we conducted a comprehensive analysis of two draft genomes assembled from sponge metagenomes, revealing novel insights into the physiology of this symbiont. Metabolic reconstruction suggested that SAUL members are aerobic bacteria with facultative anaerobic metabolism, with the capacity to degrade multiple sponge- and algae-derived carbohydrates. We described for the first time in a sponge symbiont the putative genomic capacity to transport phosphate into the cell and to produce and store polyphosphate granules, presumably constituting a phosphate reservoir for the sponge host in deprivation periods. Our findings suggest that the lifestyle of SAUL is symbiotic with the host sponge, and identify symbiont factors which may facilitate the establishment and maintenance of this relationship.

RevDate: 2019-05-08

Muletz-Wolz CR, Fleischer RC, KR Lips (2019)

Fungal disease and temperature alter skin microbiome structure in an experimental salamander system.

Molecular ecology [Epub ahead of print].

Pathogens compete with host microbiomes for space and resources. Their shared environment impacts pathogen-microbiome-host interactions, which can lead to variation in disease outcome. The skin microbiome of red-backed salamanders (Plethodon cinereus) can reduce infection by the pathogen Batrachochytrium dendrobatidis (Bd) at moderate infection loads, with high species richness and high abundance of competitors as putative mechanisms. However, it is unclear if the skin microbiome can reduce epizootic Bd loads across temperatures. We conducted a laboratory experiment to quantify skin microbiome and host responses (P. cinereus: n = 87) to Bd at mimicked epizootic loads across temperatures (13, 17, 21 °C). We quantified skin microbiomes using 16S rRNA gene metabarcoding and identified OTUs taxonomically similar to culturable bacteria known to kill Bd (anti-Bd OTUs). Prior to pathogen exposure, temperature changed the microbiome (OTU richness decreased by 12% and abundance of anti-Bd OTUs increased by 18% per degree increase in temperature), but these changes were not predictive of disease outcome. Post exposure, Bd changed the microbiome (OTU richness decreased by 0.1% and the abundance of anti-Bd OTUs increased by 0.2% per 1% increase in Bd load) and caused high host mortality across temperatures (35/45: 78%). Temperature indirectly impacted microbiome change and mortality through its direct effect on pathogen load. We did not find support for the microbiome impacting Bd load or host survival. Our research unravels complex host, pathogen, microbiome and environmental interactions to demonstrate that during epizootic events the microbiome will be unlikely to reduce pathogen invasion, even for putatively Bd-resistant species. This article is protected by copyright. All rights reserved.

RevDate: 2019-05-08

Martinez-Medina A, Pescador L, Fernandez I, et al (2019)

Nitric oxide and phytoglobin PHYTOGB1 are regulatory elements in the Solanum lycopersicum-Rhizophagus irregularis mycorrhizal symbiosis.

The New phytologist [Epub ahead of print].

The regulatory role of nitric oxide (NO) and phytoglobins in plant response to pathogenic and mutualistic microbes has been evidenced. However, little is known about their function in the arbuscular mycorrhizal (AM) symbiosis. We investigated whether NO and phytoglobin PHYTOGB1 are regulatory components in the AM symbiosis. Rhizophagus irregularis in vitro-grown cultures and tomato plants were used to monitor AM-associated NO-related root responses as compared to responses triggered by the pathogen Fusarium oxysporum. A genetic approach was conducted to understand the role of PHYTOGB1 on NO signaling during both interactions. After a common early peak on NO levels in response to both fungi, a specific NO accumulation pattern was triggered in tomato roots during the onset of the AM interaction. PHYTOGB1 was upregulated by the AM interaction. By contrast, the pathogen triggered a continuous NO accumulation and a strong downregulation of PHYTOGB1. Manipulation of PHYTOGB1 levels in overexpressing and silenced roots led to a deregulation of NO levels and altered mycorrhization and pathogen infection. We demonstrate that the onset of the AM symbiosis is associated with a specific NO-related signature in the host root. We propose that NO regulation by PHYTOGB1 is a regulatory component of the AM symbiosis. This article is protected by copyright. All rights reserved.

RevDate: 2019-05-08

Irisarri P, Cardozo G, Tartaglia C, et al (2019)

Selection of Competitive and Efficient Rhizobia Strains for White Clover.

Frontiers in microbiology, 10:768.

The practice of inoculating forage legumes with rhizobia strains is widespread. It is assumed that the inoculated strain determines the performance of the symbiosis and nitrogen fixation rates. However, native-naturalized strains can be competitive, and actual nodule occupancy is often scarcely investigated. In consequence, failures in establishment, and low productivity attributed to poor performance of the inoculant may merely reflect the absence of the inoculated strain in the nodules. This study lays out a strategy followed for selecting a Rhizobium leguminosarum sv. trifolii strain for white clover (Trifolium repens) with competitive nodule occupancy. First, the competitiveness of native-naturalized rhizobia strains selected for their efficiency to fix N2 in clover and tagged with gusA was evaluated in controlled conditions with different soils. Second, three of these experimental strains with superior nodule occupancy plus the currently recommended commercial inoculant, an introduced strain, were tested in the field in 2 years and at two sites. Plant establishment, herbage productivity, fixation of atmospheric N2 (15N natural abundance), and nodule occupancy (ERIC-PCR genomic fingerprinting) were measured. In both years and sites, nodule occupancy of the native-naturalized experimental strains was either higher or similar to that of the commercial inoculant in both primary and secondary roots. The difference was even greater in stolon roots nodules, where nodule occupancy of the native-naturalized experimental strains was at least five times greater. The amount of N fixed per unit plant mass was consistently higher with native-naturalized experimental strains, although the proportion of N derived from atmospheric fixation was similar for all strains. Plant establishment and herbage production, as well as clover contribution in oversown native grasslands, were either similar or higher in white clover inoculated with the native-naturalized experimental strains. These results support the use of our implemented strategy for developing a competitive inoculant from native-naturalized strains.

RevDate: 2019-05-08
CmpDate: 2019-05-08

Molina-Santiago C, Pearson JR, Navarro Y, et al (2019)

The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization.

Nature communications, 10(1):1919 pii:10.1038/s41467-019-09944-x.

Bacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these plant-beneficial bacteria are understudied. Here, we explore the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We show that the extracellular matrix protects B. subtilis colonies from infiltration by P. chlororaphis. The absence of extracellular matrix results in increased fluidity and loss of structure of the B. subtilis colony. The P. chlororaphis type VI secretion system (T6SS) is activated upon contact with B. subtilis cells, and stimulates B. subtilis sporulation. Furthermore, we find that B. subtilis sporulation observed prior to direct contact with P. chlororaphis is mediated by histidine kinases KinA and KinB. Finally, we demonstrate the importance of the extracellular matrix and the T6SS in modulating the coexistence of the two species on melon plant leaves and seeds.

RevDate: 2019-05-08
CmpDate: 2019-05-08

Landmann F (2019)

The Wolbachia Endosymbionts.

Microbiology spectrum, 7(2):.

The Wolbachia endosymbionts encompass a large group of intracellular bacteria of biomedical and veterinary relevance, closely related to Anaplasma, Ehrlichia, and Rickettsia. This genus of Gram-negative members of the Alphaproteobacteria does not infect vertebrates but is instead restricted to ecdysozoan species, including terrestrial arthropods and a family of parasitic filarial nematodes, the Onchocercidae. The Wolbachia profoundly impact not only the ecology and evolution but also the reproductive biology of their hosts, through a wide range of symbiotic interactions. Because they are essential to the survival and reproduction of their filarial nematode hosts, they represent an attractive target to fight filariasis. Their abilities to spread through insect populations and to affect vector competence through pathogen protection have made Wolbachia a staple for controlling vector-borne diseases. Estimated to be present in up to 66% of insect species, the Wolbachia are probably the most abundant endosymbionts on earth. Their success resides in their unique capacity to infect and manipulate the host germ line to favor their vertical transmission through the maternal lineage. Because the Wolbachia resist genetic manipulation and growth in axenic culture, our understanding of their biology is still in its infancy. Despite these limitations, the "-omics" revolution combined with the use of well-established and emerging experimental host models is accelerating our comprehension of the host phenotypes caused by Wolbachia, and the identification of Wolbachia effectors is ongoing.

RevDate: 2019-05-07

Joshi RK, SM Mehendale (2019)

Determinants of consistently high HIV prevalence in Indian Districts: A multi-level analysis.

PloS one, 14(5):e0216321 pii:PONE-D-16-49095.

INTRODUCTION: Factors associated with persistently high Human Immunodeficiency Virus (HIV) prevalence levels in several districts of India are not well understood. This study was undertaken to determine the association of socio-demographic characteristics, economic factors, awareness about HIV and Sexually Transmitted Infections (STIs), and condom use with consistently high HIV prevalence in the Indian districts and to ascertain whether these associations differed across various regions of India.

METHODS: This study was carried out including all 640 districts of India. Secondary analysis of data obtained from the Census of India-2011, HIV Sentinel Surveillance in India and District Level Household Survey-III was done. Population profile, socio-economic characteristics, levels of HIV/STI/condom awareness and condom use, were compared between the districts with and without consistently high HIV prevalence. Due to the presence of collinearity among predictor variables, we used principal component analysis and the principal component scores were included as covariates for further analysis. Considering the districts at level 1 and the regions at level 2, multi-level analysis was done by generalised linear mixed models. Variance partition coefficient and median odds ratio were also calculated.

RESULTS: Sixty-three districts with consistently high HIV prevalence were found clustered in the South and the North-east regions of India. Population size, density and urbanisation were found to be positively associated with consistently high HIV prevalence in these districts. Higher levels of literacy, better socio-economic status, higher proportion of population in reproductive age group and late marriages were positively associated with consistently high HIV prevalence in all regions of India except in the Southern region. Higher levels of knowledge about the role of condoms in HIV prevention and condom use were associated with low HIV prevalence at the district level.

CONCLUSIONS: Considerable heterogeneity among factors associated with consistently high HIV prevalence at the district level in different regions of India necessitates special region-specific strategies for HIV control. Increasing awareness about HIV alone is not sufficient for controlling the HIV epidemic and there is a need to raise knowledge levels about preventive measures against HIV and promote the use of condoms amongst population.

RevDate: 2019-05-07

Becerra-Rivera VA, MF Dunn (2019)

Polyamine biosynthesis and biological roles in rhizobia.

FEMS microbiology letters, 366(7):.

Polyamines are ubiquitous molecules containing two or more amino groups that fulfill varied and often essential physiological and regulatory roles in all organisms. In the symbiotic nitrogen-fixing bacteria known as rhizobia, putrescine and homospermidine are invariably produced while spermidine and norspermidine synthesis appears to be restricted to the alfalfa microsymbiont Sinorhizobium meliloti. Studies with rhizobial mutants deficient in the synthesis of one or more polyamines have shown that these compounds are important for growth, stress resistance, motility, exopolysaccharide production and biofilm formation. In this review, we describe these studies and examine how polyamines are synthesized and regulated in rhizobia.

RevDate: 2019-05-07

Dhanjal NI, Sharma S, Skalny AV, et al (2019)

Selenium-rich maize modulates the expression of prostaglandin genes in lipopolysaccharide-stimulated RAW264.7 macrophages.

Food & function [Epub ahead of print].

Cell signaling is necessary for the organs to co-ordinate with the whole body and it includes response to external stimuli, inflammation, hormonal secretions and other various metabolic functions. In the present study, we have focused on the inflammatory signals modulated by the reactive oxygen and nitrogen species (RONS). Under homeostatic conditions, these species turn on the COX-1-dependent arachidonic acid (AA) pathway towards the release of anti-inflammatory enzymes. However, the excess release of these ions induces negative effects in the form of inflammation by turning on the COX-2-dependent AA pathway to release pro-inflammatory enzymes. In the present study, we observed the shunting of the COX-2-dependent AA pathway towards the release of anti-inflammatory enzymes with the supplementation of organic dietary selenium in the form of seleniferous maize extracts. We observed that 500 nM selenium concentration in Se-maize extracts downregulated the COX-2 and mPGES-1 expressions by 3.8- and 3.2-fold and upregulated the GPx-1 and H-PGDS expressions by 5.0- and 5.4-fold, respectively. To facilitate more availability of Se from the dietary matrices, Se-maize extracts were incubated with rMETase. It was observed that the enzyme-treated cells increased the downregulation of COX-2 and mPGES-1 expressions by 24.8- and 21.0-fold and the upregulation of GPx-1 and H-PGDS expressions by 13.2- and 16.5-fold, respectively.

RevDate: 2019-05-07

Pislariu CI, Sinharoy S, Torres-Jerez I, et al (2019)

The nodule-specific PLAT-domain protein NPD1 is required for nitrogen-fixing symbiosis.

Plant physiology pii:pp.18.01613 [Epub ahead of print].

Symbiotic nitrogen fixation by rhizobia in legume root nodules is a key source of nitrogen for sustainable agriculture. Genetic approaches have revealed important roles for only a few of the thousands of plant genes expressed during nodule development and symbiotic nitrogen fixation. Previously, we isolated over one hundred nodulation and nitrogen fixation mutants from a population of Tnt1-insertion mutants of Medigaco truncatula (Pislariu et al., 2011). Using Tnt1 as a tag to identify genetic lesions in these mutants, we discovered that insertions in a nodule-specific PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain-encoding gene, MtNPD1, resulted in development of ineffective nodules. Early stages of nodule development and colonization by the nitrogen fixing bacterium Sinorhizobium meliloti appeared to be normal in the npd1 mutant. However, npd1 nodules ceased to grow after a few days, resulting in abnormally small, ineffective nodules. Rhizobia that colonized developing npd1 nodules did not differentiate completely into nitrogen-fixing bacteroids and quickly degraded. MtNPD1 expression was low in roots but increased significantly in developing nodules four days post-inoculation (DPI), and expression accompanied invading rhizobia in the nodule infection zone and into the distal nitrogen fixation zone. A functional MtNPD1:GFP fusion protein localized in the space surrounding symbiosomes in infected cells. When ectopically expressed in tobacco (Nicotiana tabacum) leaves, MtNPD1 co-localized with vacuoles and the endoplasmic reticulum. MtNPD1 belongs to a cluster of 5 nodule-specific single PLAT domain-encoding genes, with apparent non-redundant functions.

RevDate: 2019-05-07
CmpDate: 2019-05-07

Binetruy F, Bailly X, Chevillon C, et al (2019)

Phylogenetics of the Spiroplasma ixodetis endosymbiont reveals past transfers between ticks and other arthropods.

Ticks and tick-borne diseases, 10(3):575-584.

The bacterium Spiroplasma ixodetis is a maternally inherited endosymbiont primarily described from ticks but also found widespread across other arthropods. While it has been identified as a male-killing agent in some insect species, the consequences of infection with S. ixodetis in ticks are entirely unknown, and it is unclear how this endosymbiont spreads across tick species. Here, we have investigated this aspect through the examination of the diversity and evolutionary history of S. ixodetis infections in 12 tick species and 12 other arthropod species. Using a multi-locus typing approach, we identified that ticks harbor a substantial diversity of divergent S. ixodetis strains. Phylogenetic investigations revealed that these S. ixodetis strains do not cluster within a tick-specific subclade but rather exhibit distinct evolutionary origins. In their past, these strains have undergone repeated horizontal transfers between ticks and other arthropods, including aphids and flies. This diversity pattern strongly suggests that maternal inheritance and horizontal transfers are key drivers of S. ixodetis spread, dictating global incidence of infections across tick communities. We do not, however, detect evidence of S. ixodetis-based male-killing since we observed that infections were widely present in both males and females across populations of the African blue tick Rhipicephalus decoloratus.

RevDate: 2019-05-07
CmpDate: 2019-05-07

Chevrette MG, CR Currie (2019)

Emerging evolutionary paradigms in antibiotic discovery.

Journal of industrial microbiology & biotechnology, 46(3-4):257-271.

Antibiotics revolutionized medicine and remain its cornerstone. Despite their global importance and the continuous threat of resistant pathogens, few antibiotics have been discovered in recent years. Natural products, especially the secondary metabolites of Actinobacteria, have been the traditional discovery source of antibiotics. In nature, the chemistry of antibiotic natural products is shaped by the unique evolution and ecology of their producing organisms, yet these influences remain largely unknown. Here, we highlight the ecology of antibiotics employed by microbes in defensive symbioses and review the evolutionary processes underlying the chemical diversity and activity of microbe-derived antibiotics, including the dynamics of vertical and lateral transmission of biosynthetic pathways and the evolution of efficacy, targeting specificity, and toxicity. We argue that a deeper understanding of the ecology and evolution of microbial interactions and the metabolites that mediate them will allow for an alternative, rational approach to discover new antibiotics.

RevDate: 2019-05-07
CmpDate: 2019-05-07

Zhao D, Hoffmann AA, Zhang Z, et al (2018)

Interactions Between Facultative Symbionts Hamiltonella and Cardinium in Bemisia tabaci (Hemiptera: Aleyrodoidea): Cooperation or Conflict?.

Journal of economic entomology, 111(6):2660-2666.

Maternally-inherited facultative symbionts are widespread in most insect species, and it is common that several symbionts coexist in the same host individual. Hence, the symbionts may compete or share for the limited resources and space in the host. The whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodoidea), harbors a diverse array of facultative symbionts, among which Hamiltonella sp. and Cardinium sp. are abundant species. Hamiltonella alone increases host fitness, while Cardinium alone confers lower fitness. Locking those different partners together creates ideal situations for the evolution of interactions between symbionts. In this study, we compared the fitness effects of whiteflies infected with only Hamiltonella to Hamiltonella-Cardnium co-infected whiteflies and measured the density of Hamiltonella and Cardinium during host aging, aiming to explore Hamiltonella-Cardinium interactions in B. tabaci. Our results illustrated that Hamiltonella-Cardinium coinfection induced lower fecundity, egg hatchability and number of female offspring, leading to a male-biased sex ratio in offspring, while there is no evidence for reproductive incompatibility between the infections. We also found an antagonistic interaction between Hamiltonella and Cardinium given that the density of the latter increased across time and led to a decrease of Hamiltonella density, which may be the underlying causes of the fitness cost in double-infected B. tabaci. Exploring the ecological consequences of co-infections of these different symbionts helps us to understand the nature of host-symbiont interactions in this species and potential for evolutionary conflict.

RevDate: 2019-05-06

Chaubey MG, Patel SNK, Rastogi RP, et al (2019)

Therapeutic potential of cyanobacterial pigment protein phycoerythrin: in silico and in vitro study of BACE1 interaction and in vivo Aβ reduction.

International journal of biological macromolecules pii:S0141-8130(18)37290-8 [Epub ahead of print].

Cyanobacteria are an immense source of innovative classes of pharmacologically active compounds exhibiting various biological activities ranging from antioxidants, antibiotics, anticancer, anti-inflammatory to anti-Alzheimer's disease. In the present study, we primarily targeted the inhibition of Beta-site amyloid precursor protein cleaving enzyme-1 (BACE1) by a naturally occurring cyanobacterial protein phycoerythrin (C-PE). BACE1 cleaves amyloid-β precursor protein (APP) and leads to accumulation of neurotoxic amyloid beta (Aβ) plaques in the brain, as an attribute of Alzheimer's disease (AD). Inhibition of BACE1 was measured in terms of their association and dissociation rate constants, thermodynamics of binding using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). The kinetic parameters for enzyme activity were also measured using synthetic decapeptide as a substrate. We further validated the potential of PE by in-vivo histopathological staining of Aβ aggregate mutant Caenorhabditis elegans CL4176 by Thioflavin-T. The present studies pave the way for the application of naturally occurring C-PE as a putative therapeutic drug for the AD.

RevDate: 2019-05-06

Aasen DM, MN Vergara (2019)

New Drug Discovery Paradigms for Retinal Diseases: A Focus on Retinal Organoids.

Journal of ocular pharmacology and therapeutics : the official journal of the Association for Ocular Pharmacology and Therapeutics [Epub ahead of print].

Retinal disease represents a growing global problem, both in terms of quality of life and economic impact, yet new therapies are not being developed at a sufficient rate to meet this mounting need. In this context, retinal organoids derived from human induced pluripotent stem cells hold significant promise for improving upon the current drug development process, increasing the speed and efficiency of moving potential therapeutic agents from bench to bedside. These organoid systems display the cell-cell and cell-matrix interactions, cellular heterogeneity, and physiological responses reflective of human biology and, thus, have the ability to replicate retinal disease pathology in a way that 2-dimensional cell cultures and animal models have been heretofore unable to achieve. However, organoid technology is not yet mature enough to meet the high-throughput demands of the first stages of drug screening. Hence, the augmentation of the existing drug development pipeline with retinal organoids, rather than the replacement of existing pathway components, may provide a way to harness the benefits of this improved pathological modeling. In this study, we outline the possible benefits of such a symbiosis, discuss other potential uses, and highlight barriers that remain to be overcome.

RevDate: 2019-05-06

Sorroche F, Walch M, Zou L, et al (2019)

Endosymbiotic Sinorhizobium meliloti modulate Medicago root susceptibility to secondary infection via ethylene.

The New phytologist [Epub ahead of print].

A complex network of pathways coordinates nodulation and epidermal root hair infection in the symbiotic interaction between rhizobia and legume plants. Whereas nodule formation was known to be autoregulated, it was so far unclear whether a similar control is exerted on the infection process. We assessed the capacity of Medicago plants nodulated by Sinorhizobium meliloti to modulate root susceptibility to secondary bacterial infection or to purified Nod factors in split-root and volatile assays using bacterial and plant mutant combinations. Ethylene implication in this process emerged from gas production measurements, use of a chemical inhibitor of ethylene biosynthesis and of a Medicago mutant affected in ethylene signal transduction. We identified a feedback mechanism that we named AOI (for Autoregulation Of Infection) by which endosymbiotic bacteria control secondary infection thread formation by their rhizospheric peers. AOI involves activation of a cAMP cascade in endosymbiotic bacteria, which decreases both root infectiveness and root susceptibility to bacterial Nod factors. These latter two effects are mediated by ethylene. AOI is a novel component of the complex regulatory network controlling the interaction between Sinorhizobium meliloti and its host plants that emphasizes the implication of endosymbiotic bacteria in fine-tuning the interaction. This article is protected by copyright. All rights reserved.

RevDate: 2019-05-06

Zhang L, Yuan L, Staehelin C, et al (2019)

The LYSIN MOTIF-CONTAINING RECEPTOR-LIKE KINASE 1 protein of banana is required for perception of pathogenic and symbiotic signals.

The New phytologist [Epub ahead of print].

● How plants can distinguish pathogenic and symbiotic fungi remains largely unknown. Here, we characterized the role of MaLYK1, a lysin motif receptor kinase of banana. ● Live cell imaging techniques were used in localization studies. RNAi-silenced transgenic banana plants were generated to analyze the biological role of MaLYK1. The MaLYK1 ectodomain, chitin beads, chitooligosaccharides (COs) and mycorrhizal lipochitooligosaccharides (Myc-LCOs) were used in pull-down assays. Ligand-induced MaLYK1 complex formation was tested in immunoprecipitation experiments. Chimeric receptors were expressed in Lotus japonicus to characterize the function of the MaLYK1 kinase domain. ● MaLYK1 was localized to the plasma membrane. MaLYK1 expression was induced by Foc4 (Fusarium oxysporum f. sp. cubense race 4) and diverse microbe-associated molecular patterns. MaLYK1-silenced banana lines showed reduced chitin-triggered defense responses, increased Foc4-induced disease symptoms and reduced mycorrhization. The MaLYK1 ectodomain was pulled-down by chitin beads and LCOs or COs impaired this process. Ligand treatments induced MaLYK1 complex formation in planta. The kinase domain of MaLYK1 could functionally replace that of the chitin elicitor receptor kinase 1 (AtCERK1) in Arabidopsis thaliana and of a rhizobial LCO (Nod factor) receptor (LjNFR1) in L. japonicus. ● MaLYK1 represents a central molecular switch that controls defense- and symbiosis-related signaling. This article is protected by copyright. All rights reserved.

RevDate: 2019-05-06

Gibelin-Viala C, Amblard E, Puech-Pages V, et al (2019)

The Medicago truncatula LysM receptor-like kinase LYK9 plays a dual role in immunity and the arbuscular mycorrhizal symbiosis.

The New phytologist [Epub ahead of print].

Plant specific lysin-motif receptor-like kinases (LysM-RLKs) are implicated in the perception of N-acetyl glucosamine-containing compounds, some of which are important signal molecules in plant-microbe interactions. Among these, both lipo-chitooligosaccharides (LCOs) and chitooligosaccharides (COs) are proposed as arbuscular mycorrhizal (AM) fungal symbiotic signals. COs can also activate plant defence, although there is scarce data about CO production by pathogens, especially non-fungal pathogens. We tested Medicago truncatula mutants in the LysM-RLK MtLYK9 for their abilities to interact with the AM fungus Rhizophagus irregularis and the oomycete pathogen Aphanomyces euteiches. This prompted us to analyse whether A. euteiches can produce COs. Compared to wild-type plants, Mtlyk9 mutants had fewer infection events and were less colonised by the AM fungus. In contrast, Mtlyk9 mutants were more heavily infected by A. euteiches and showed more disease symptoms. A. euteiches was also shown to produce short COs, mainly CO II, but also CO III and CO IV, and traces of CO V, both ex planta and in planta. MtLYK9 thus has a dual role in plant immunity and the AM symbiosis, which raises questions about the functioning and the ancestral origins of such a receptor protein. This article is protected by copyright. All rights reserved.

RevDate: 2019-05-06

Moreno-Altamirano MMB, Kolstoe SE, FJ Sánchez-García (2019)

Virus Control of Cell Metabolism for Replication and Evasion of Host Immune Responses.

Frontiers in cellular and infection microbiology, 9:95.

Over the last decade, there has been significant advances in the understanding of the cross-talk between metabolism and immune responses. It is now evident that immune cell effector function strongly depends on the metabolic pathway in which cells are engaged in at a particular point in time, the activation conditions, and the cell microenvironment. It is also clear that some metabolic intermediates have signaling as well as effector properties and, hence, topics such as immunometabolism, metabolic reprograming, and metabolic symbiosis (among others) have emerged. Viruses completely rely on their host's cell energy and molecular machinery to enter, multiply, and exit for a new round of infection. This review explores how viruses mimic, exploit or interfere with host cell metabolic pathways and how, in doing so, they may evade immune responses. It offers a brief outline of key metabolic pathways, mitochondrial function and metabolism-related signaling pathways, followed by examples of the mechanisms by which several viral proteins regulate host cell metabolic activity.

RevDate: 2019-05-06

Hossain MS, Hoang NT, Yan Z, et al (2019)

Characterization of the Spatial and Temporal Expression of Two Soybean miRNAs Identifies SCL6 as a Novel Regulator of Soybean Nodulation.

Frontiers in plant science, 10:475.

MicroRNAs (miRNAs) control expression of endogenous target genes through transcript cleavage or translational inhibition. Legume plants can form a specialized organ, the nodule, through interaction with nitrogen fixing soil bacteria. To understand the regulatory roles of miRNAs in the nodulation process, we functionally validated gma-miR171o and gma-miR171q and their target genes in soybean. These two miRNA sequences are identical in sequence but their miRNA genes are divergent and show unique, tissue-specific expression patterns. The expression levels of the two miRNAs are negatively correlated with that of their target genes. Ectopic expression of these miRNAs in transgenic hairy roots resulted in a significant reduction in nodule formation. Both gma-miR171o and gma-miR171q target members of the GRAS transcription factor superfamily, namely GmSCL-6 and GmNSP2. Transient interaction of miRNAs and their target genes in tobacco cells further confirmed their cleavage activity. The results suggest that gma-miR171o and gma-miR171q regulate GmSCL-6 and GmNSP2, which in turn, influence expression of the Nodule inception (NIN), Early Nodulin 40 (ENOD40), and Ethylene Response Factor Required for Nodulation (ERN) genes during the Bradyrhizobium japonicum-soybean nodulation process. Collectively, our data suggest a role for two miRNAs, gma-miR171o and gma-miR171q, in regulating the spatial and temporal aspects of soybean nodulation.

RevDate: 2019-05-06

Methou P, Hernández-Ávila I, Aube J, et al (2019)

Is It First the Egg or the Shrimp? - Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development.

Frontiers in microbiology, 10:808.

Rimicaris exoculata is one of the most well-known and emblematic species of endemic vent fauna. Like many other species from these ecosystems, Rimicaris shrimps host important communities of chemosynthetic bacteria living in symbiosis with their host inside the cephalothorax and gut. For many of these symbiotic partners, the mode of transmission remains to be elucidated and the starting point of the symbiotic relationship is not yet defined, but could begin with the egg. In this study, we explored the proliferation of microbial communities on R. exoculata broods through embryonic development using a combination of NGS sequencing and microscopy approaches. Variations in abundance and diversity of egg microbial communities were analyzed in broods at different developmental stages and collected from mothers at two distinct vent fields on the Mid-Atlantic Ridge (TAG and Snake Pit). We also assessed the specificity of the egg microbiome by comparing communities developing on egg surfaces with those developing on the cuticle of pleopods, which are thought to be exposed to similar environmental conditions because the brood is held under the female's abdomen. In terms of abundance, bacterial colonization clearly increases with both egg developmental stage and the position of the egg within the brood: those closest to the exterior having a higher bacterial coverage. Bacterial biomass increase also accompanies an increase of mineral precipitations and thus clearly relates to the degree of exposure to vent fluids. In terms of diversity, most bacterial lineages were found in all samples and were also those found in the cephalothorax of adults. However, significant variation occurs in the relative abundance of these lineages, most of this variation being explained by body surface (egg vs. pleopod), vent field, and developmental stage. The occurrence of symbiont-related lineages of Epsilonbacteraeota, Gammaproteobacteria, Zetaproteobacteria, and Mollicutes provide a basis for discussion on both the acquisition of symbionts and the potential roles of these bacterial communities during egg development.

RevDate: 2019-05-06

Rebollar EA, RN Harris (2019)

Editorial: Ecology of Amphibian-Microbial Symbioses.

Frontiers in microbiology, 10:766.

RevDate: 2019-05-06

Skaljac M, Vogel H, Wielsch N, et al (2019)

Transmission of a Protease-Secreting Bacterial Symbiont Among Pea Aphids via Host Plants.

Frontiers in physiology, 10:438.

Aphids are economically important pest insects that damage plants by phloem feeding and the transmission of plant viruses. Their ability to feed exclusively on nutritionally poor phloem sap is dependent on the obligatory symbiotic bacterium Buchnera aphidicola, but additional facultative symbionts may also be present, a common example of which is Serratia symbiotica. Many Serratia species secrete extracellular enzymes, so we hypothesised that S. symbiotica may produce proteases that help aphids to feed on plants. Molecular analysis, including fluorescence in situ hybridization (FISH), revealed that S. symbiotica colonises the gut, salivary glands and mouthparts (including the stylet) of the pea aphid Acyrthosiphon pisum, providing a mechanism to transfer the symbiont into host plants. S. symbiotica was also detected in plant tissues wounded by the penetrating stylet and was transferred to naïve aphids feeding on plants containing this symbiont. The maintenance of S. symbiotica by repeated transmission via plants may explain the high frequency of this symbiont in aphid populations. Proteomic analysis of the supernatant from a related but cultivable S. symbiotica strain cultured in liquid medium revealed the presence of known and novel proteases including metalloproteases. The corresponding transcripts encoding these S. symbiotica enzymes were detected in A. pisum and in plants carrying the symbiont, although the mRNA was much more abundant in the aphids. Our data suggest that enzymes from S. symbiotica may facilitate the digestion of plant proteins, thereby helping to suppress plant defense, and that the symbionts are important mediators of aphid-plant interactions.

RevDate: 2019-05-05

Carotenuto G, Sciascia I, Oddi L, et al (2019)

Size matters: three methods for estimating nuclear size in mycorrhizal roots of Medicago truncatula by image analysis.

BMC plant biology, 19(1):180 pii:10.1186/s12870-019-1791-1.

BACKGROUND: The intracellular accommodation of arbuscular mycorrhizal (AM) fungi involves a profound molecular reprogramming of the host cell architecture and metabolism, based on the activation of a symbiotic signaling pathway. In analogy with other plant biotrophs, AM fungi are reported to trigger cell cycle reactivation in their host tissues, possibly in support of the enhanced metabolic demand required for the symbiosis.

RESULTS: We here compare the efficiency of three Fiji/ImageJ image analysis plugins in localizing and quantifying the increase in nuclear size - a hallmark of recursive events of endoreduplication - in M. truncatula roots colonized by the AM fungus Gigaspora margarita. All three approaches proved to be versatile and upgradeable, allowing the investigation of nuclear changes in a complex tissue; 3D Object Counter provided more detailed information than both TrackMate and Round Surface Detector plugins. On this base we challenged 3D Object Counter with two case studies: verifying the lack of endoreduplication-triggering responses in Medicago truncatula mutants with a known non-symbiotic phenotype; and analysing the correlation in space and time between the induction of cortical cell division and endoreduplication upon AM colonization. Both case studies revealed important biological aspects. Mutant phenotype analyses have demonstrated that the knock-out mutation of different key genes in the symbiotic signaling pathway block AM-associated endoreduplication. Furthermore, our data show that cell divisions occur during initial stages of root colonization and are followed by recursive activation of the endocycle in preparation for arbuscule accommodation.

CONCLUSIONS: In conclusion, our results indicate 3D Object Counter as the best performing Fiji/ImageJ image analysis script in plant root thick sections and its application highlighted endoreduplication as a major feature of the AM pre-penetration response in root cortical cells.

RevDate: 2019-05-04

Kelsey R (2019)

Magnetotactic symbiosis in marine sediments.

Nature reviews. Microbiology pii:10.1038/s41579-019-0210-9 [Epub ahead of print].

RevDate: 2019-05-04

Poinar G, FE Vega (2019)

A mid-Cretaceous trichomycete, Priscadvena corymbosa gen. et sp. nov., in Burmese amber.

Fungal biology, 123(5):393-396.

Priscadvena corymbosa gen. et sp. nov., is described from thalli and sporangia emerging from the oral cavity of a click beetle (Coleoptera: Elateridae) in mid-Cretaceous Burmese amber. The fossil contains several features unknown in extant Trichomycetes including a click beetle (Coleoptera: Elateridae) host, spiny, aerial thalli with the entire thallus bearing numerous small uninucleate globular spores and stalks attached to the oral cavity of its host. Based on these features, P. corymbosa gen. et sp. nov. is placed in a new family, Priscadvenaceae fam. nov., and new order, Priscadvenales ord. nov. The new morphological and behavioral features of the fossil add to the diversity of the trichomycetes as currently defined.

RevDate: 2019-05-06

Moshiri F, Ebrahimi H, Ardakani MR, et al (2019)

Biogeochemical distribution of Pb and Zn forms in two calcareous soils affected by mycorrhizal symbiosis and alfalfa rhizosphere.

Ecotoxicology and environmental safety, 179:241-248 pii:S0147-6513(19)30488-9 [Epub ahead of print].

Using of arbuscular mycorrhizal fungi (AMF) has emerged as a new technique to alleviate the toxic metals stress through changing their chemical behavior. The present work was conducted as a factorial arrangement based on a completely randomized design to study the inoculation effects of Glomus intraradices, Glomus mosseae and Glomus etunicatum, on Pb and Zn fractions in the rhizosphere of alfalfa by using rhizobox technique in two agricultural soils with different Zn and Pb concentrations [with low (LH) and high (HH) concentration levels]. The results showed that AMF colonization promoted plant growth and lowered the shoot and root Pb and shoot Zn concentrations in the studied soils compared to uninoculated treatments. Mycorrhizal colonization significantly increased the Ca(NO3)2- extractable Zn and ORG-Zn (respectively 500 and 59.6% more than the uninoculated treatment) and decreased the OXI-Zn (20.32% less than the none inoculated treatment) in the HH soil. By contrast, mycorrhizae slightly increased the CARB, OXI and ORG-Zn forms in the LH soil compared to the uninoculation condition. In the AMF- treated HH soil, an increase was recorded in the Ca(NO3)2- extractable Pb, EXCH-Pb and CARB-Pb (respectively, 17.65, 3.09 and 14.22% compared to the none inoculated treatment) and a decrease in the OXI and ORG-Pb forms (respectively, 28.79 and 13.51% compared to the uninoculated treatment). A reverse status was observed for Pb changes in the LH soil. Depending on the contamination level, the mycorrhizal inoculation differentially affected the Pb and Zn fractions at different distances from the root surface. In the LH soil, at <5 mm distance (i.e. rhizospheric soil), the mycorrhizal inoculation decreased the CARB (about 17.99%) and OXI -Zn (about 29.63%) forms compared to bulk soil (i.e. > 5 mm distance) while ORG-Zn was increased up to 48.63%. However, Ca(NO3)2- extractable, CARB and ORG-Pb was increased in rhizosphere soil (respectively, 89.33, 3.84 and 6.14%) and OXI-Pb was decreased up to 10.36% compared to the bulk soil. In the HH soil, mycorrhizal inoculation increased the CARB and OXI-Zn (respectively, 1.76 and 5.71%) and OXI-Pb fractions (11.56%) compared to the <5 mm distances. Whereas, it reduced the Ca(NO3)2- extractable, EXCH, and ORG-Zn (Respectively, 52.70, 19.19 and 30.16%) and Ca(NO3)2- extractable, CARB and ORG-Pb (respectively, 47.18, 3.70 and 5.79%). These results revealed that depending on the soil contamination level and nature of the element, AMF colonization affects biogeochemical fractions of the metals and their accumulation in the plant tissues.

RevDate: 2019-05-06

Molinero-Rosales N, Martín-Rodríguez JÁ, Ho-Plágaro T, et al (2019)

Identification and expression analysis of the arbuscular mycorrhiza-inducible Rieske non-heme oxygenase Ptc52 gene from tomato.

Journal of plant physiology, 237:95-103 pii:S0176-1617(19)30054-9 [Epub ahead of print].

Arbuscular mycorrhizal (AM) formation enhances plant growth and fitness through improved uptake of water and mineral nutrients in exchange for carbon compounds to the AM fungus. The fungal structure for the reciprocal exchange of nutrients in the symbiosis is the arbuscule, and defence genes expressed in cells containing arbuscules could play a role in the control of hyphal spread and arbuscule formation in the root. We characterized and analyzed the Ptc52 gene from tomato (SlPtc52), a member of the gene family of non-heme oxygenases, whose function has been related to the lethal leaf spot 1 (Lls1) lesion mimic phenotype in plants which is sometimes associated with enhanced disease resistance. Sequence analysis of the SlPTC52 protein revealed conserved typical motifs from non-heme oxygenases, including a Rieske [2Fe-2S] motif, a mononuclear non-heme iron-binding motif and a C-terminal CxxC motif. The level of transcript accumulation was low in stem, flower and green fruits, and high in leaves. Although SlPtc52 expression was perceptible at low levels in roots, its expression increased concomitantly with AM fungus root colonization. Tomato non-mycorrhizal hairy roots expressing the GUS protein under the control of promoter SlPtc52 exhibited GUS activity in the endodermis, the apical meristem of the root tip and in the lateral root primordium. AM fungal colonization also resulted in intensive GUS activity that clearly corresponds to cortical cells containing arbuscules. SlPtc52 gene silencing led to a delay in root colonization and a decrease in arbuscular abundance, suggesting that SlPTC52 plays a regulatory role during AM symbiosis.

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RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

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