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Bibliography on: Symbiosis

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ESP: PubMed Auto Bibliography 01 Apr 2020 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: 2020-03-31

Vangelisti A, Turrini A, Sbrana C, et al (2020)

Gene expression in Rhizoglomus irregulare at two different time points of mycorrhiza establishment in Helianthus annuus roots, as revealed by RNA-seq analysis.

Mycorrhiza pii:10.1007/s00572-020-00950-2 [Epub ahead of print].

Arbuscular mycorrhizal fungi (AMF) play a fundamental role in plant growth and nutrition in natural and agricultural ecosystems. Despite the importance of such symbionts, the different developmental changes occurring during the AMF life cycle have not been fully elucidated at the molecular level. Here, the RNA-seq approach was used to investigate Rhizoglomus irregulare specific and common transcripts at two different time points of mycorrhizal establishment in Helianthus annuus in vivo. Four days after inoculation, transcripts related to cellular remodeling (actin and tubulin), cellular signaling (calmodulin, serine/threonine protein kinase, 14-3-3 protein, and calcium transporting ATPase), lipid metabolism (fatty acid desaturation, steroid hormone, and glycerophospholipid biosynthesis), and biosynthetic processes were detected. In addition to such transcripts, 16 days after inoculation, expressed genes linked to binding and catalytic activities; ion (K+, Ca2+, Fe2+, Zn2+, Mn2+, Pi, ammonia), sugar, and lipid transport; and those involved in vacuolar polyphosphate accumulation were found. Knowledge of transcriptomic changes required for symbiosis establishment and performance is of great importance to understand the functional role of AMF symbionts in food crop nutrition and health, and in plant diversity in natural ecosystems.

RevDate: 2020-03-31

Arcila F, J Meunier (2020)

Friend or foe? The apparent benefits of gregarine (Apicomplexa: Sporozoa) infection in the European earwig.

International journal for parasitology pii:S0020-7519(20)30057-6 [Epub ahead of print].

Studying the costs and benefits of host-parasite interactions is of central importance to shed light on the evolutionary drivers of host life history traits. Although gregarines (Apicomplexa: Sporozoa) are one of the most frequent parasites in the gut of invertebrates, the diversity of its potential impacts on a host remains poorly explored. In this study, we addressed this gap in knowledge by investigating the prevalence of natural infections by the gregarine Gregarina ovata and testing how these infections shape a large set of morphological, behavioural and physiological traits in the European earwig Forficula auricularia. Our results first show that G. ovata was present in 76.8% of 573 field-sampled earwigs, and that its prevalence was both higher in males compared with females and increased between July and September. The load of G. ovata in the infected individuals was higher in males than females, but this sex difference vanished during the season. Our experiments then surprisingly revealed apparent benefits of G. ovata infections. Food-deprived hosts survived longer when they exhibited high compared with low gregarine loads. Moreover, the presence of gregarines was associated with a reduced phenoloxidase activity, indicating a lower immune resistance or a higher immune tolerance of the infected hosts. By contrast, we found no effect of G. ovata presence and number on earwigs' development (eye distance, forceps length), activity, food consumption or resistance against a fungal pathogen. Overall, our findings suggest that G. ovata could be involved in a mutualistic relationship with the European earwig. Given the ubiquitous presence of gregarines among invertebrates, our data also suggest that this common member of insect gut flora could have a broad and positive role in the life history of many host species.

RevDate: 2020-03-31
CmpDate: 2020-03-31

Chuang JS, Frentz Z, S Leibler (2019)

Homeorhesis and ecological succession quantified in synthetic microbial ecosystems.

Proceedings of the National Academy of Sciences of the United States of America, 116(30):14852-14861.

The dynamics of ecological change following a major perturbation, known as succession, are influenced by random processes. Direct quantitation of the degree of contingency in succession requires chronological study of replicate ecosystems. We previously found that population dynamics in carefully controlled, replicated synthetic microbial ecosystems were strongly deterministic over several months. Here, we present simplified, two-species microbial ecosystems consisting of algae and ciliates, imaged in toto at single-cell resolution with fluorescence microscopy over a period of 1 to 2 weeks. To directly study succession in these ecosystems, we deliberately varied the initial cell abundances over replicates and quantified the ensuing dynamics. The distribution of abundance trajectories rapidly converged to a nearly deterministic path, with small fluctuations, despite variations in initial conditions, environmental perturbations, and intrinsic noise, indicative of homeorhesis. Homeorhesis was also observed for certain phenotypic variables, such as partitioning of the ciliates into distinct size classes and clumping of the algae. Although the mechanism of homeorhesis observed in these synthetic ecosystems remains to be elucidated, it is clear that it must emerge from the ways each species controls its own internal states, with respect to a diverse set of environmental conditions and ecological interactions.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Bermúdez-Barrientos JR, Ramírez-Sánchez O, Chow FW, et al (2020)

Disentangling sRNA-Seq data to study RNA communication between species.

Nucleic acids research, 48(4):e21.

Many organisms exchange small RNAs (sRNAs) during their interactions, that can target or bolster defense strategies in host-pathogen systems. Current sRNA-Seq technology can determine the sRNAs present in any symbiotic system, but there are very few bioinformatic tools available to interpret the results. We show that one of the biggest challenges comes from sequences that map equally well to the genomes of both interacting organisms. This arises due to the small size of the sRNAs compared to large genomes, and because a large portion of sequenced sRNAs come from genomic regions that encode highly conserved miRNAs, rRNAs or tRNAs. Here, we present strategies to disentangle sRNA-Seq data from samples of communicating organisms, developed using diverse plant and animal species that are known to receive or exchange RNA with their symbionts. We show that sequence assembly, both de novo and genome-guided, can be used for these sRNA-Seq data, greatly reducing the ambiguity of mapping reads. Even confidently mapped sequences can be misleading, so we further demonstrate the use of differential expression strategies to determine true parasite-derived sRNAs within host cells. We validate our methods on new experiments designed to probe the nature of the extracellular vesicle sRNAs from the parasitic nematode Heligmosomoides bakeri that get into mouse intestinal epithelial cells.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Hein AM, BT Martin (2020)

Information limitation and the dynamics of coupled ecological systems.

Nature ecology & evolution, 4(1):82-90.

The dynamics of large ecological systems result from vast numbers of interactions between individual organisms. Here, we develop mathematical theory to show that the rate of such interactions is inherently limited by the ability of organisms to gain information about one another. This phenomenon, which we call 'information limitation', is likely to be widespread in real ecological systems and can dictate both the rates of ecological interactions and long-run dynamics of interacting populations. We show how information limitation leads to sigmoid interaction rate functions that can stabilize antagonistic interactions and destabilize mutualistic ones; as a species or type becomes rare, information on its whereabouts also becomes rare, weakening coupling with consumers, pathogens and mutualists. This can facilitate persistence of consumer-resource systems, alter the course of pathogen infections within a host and enhance the rates of oceanic productivity and carbon export. Our findings may shed light on phenomena in many living systems where information drives interactions.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Manzano-Marı N A, Coeur d'acier A, Clamens AL, et al (2020)

Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems.

The ISME journal, 14(1):259-273.

Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera's. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera's. Additionally, we found that the Erwinia vitamin-biosynthetic genes not only compensate for Buchnera's deficiencies, but also provide a new nutritional function; whose genes have been horizontally acquired from a Sodalis-related bacterium. A subset of these genes have been subsequently transferred to a new Hamiltonella co-obligate symbiont in one specific Cinara lineage. These results show that the establishment and dynamics of multi-partner endosymbioses can be mediated by lateral gene transfers between co-ocurring symbionts.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Lynch JB, EY Hsiao (2019)

Microbiomes as sources of emergent host phenotypes.

Science (New York, N.Y.), 365(6460):1405-1409.

Microbial communities associated with animals exert powerful influences on host physiology, regulating metabolism and immune function, as well as complex host behaviors. The importance of host-microbiome interactions for maintaining homeostasis and promoting health raises evolutionarily complicated questions about how animals and their microbiomes have coevolved, and how these relationships affect the ways that animals interact with their environment. Here, we review the literature on the contributions of host factors to microbial community structure and corresponding influences of microbiomes on emergent host phenotypes. We focus in particular on animal behaviors as a basis for understanding potential roles for the microbiome in shaping host neurobiology.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Frazão N, Sousa A, Lässig M, et al (2019)

Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut.

Proceedings of the National Academy of Sciences of the United States of America, 116(36):17906-17915.

Bacteria evolve by mutation accumulation in laboratory experiments, but tempo and mode of evolution in natural environments are largely unknown. Here, we study the ubiquitous natural process of host colonization by commensal bacteria. We show, by experimental evolution of Escherichia coli in the mouse intestine, that the ecology of the gut controls the pace and mode of evolution of a new invading bacterial strain. If a resident E. coli strain is present in the gut, the invading strain evolves by rapid horizontal gene transfer (HGT), which precedes and outweighs evolution by accumulation of mutations. HGT is driven by 2 bacteriophages carried by the resident strain, which cause an epidemic phage infection of the invader. These dynamics are followed by subsequent evolution by clonal interference of genetically diverse lineages of phage-carrying (lysogenic) bacteria. We show that the genes uptaken by HGT enhance the metabolism of specific gut carbon sources and provide a fitness advantage to lysogenic invader lineages. A minimal dynamical model explains the temporal pattern of phage epidemics and the complex evolutionary outcome of phage-mediated selection. We conclude that phage-driven HGT is a key eco-evolutionary driving force of gut colonization-it accelerates evolution and promotes genetic diversity of commensal bacteria.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Hehenberger E, Gast RJ, PJ Keeling (2019)

A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis.

Proceedings of the National Academy of Sciences of the United States of America, 116(36):17934-17942.

Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Romero Picazo D, Dagan T, Ansorge R, et al (2019)

Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated.

The ISME journal, 13(12):2954-2968.

Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated subpopulations. The reconstruction of core genome-wide strains from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel life span and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Suzaki T, H Nishida (2019)

Autoregulation of Legume Nodulation by Sophisticated Transcriptional Regulatory Networks.

Molecular plant, 12(9):1179-1181.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Durante MK, Baums IB, Williams DE, et al (2019)

What drives phenotypic divergence among coral clonemates of Acropora palmata?.

Molecular ecology, 28(13):3208-3224.

Evolutionary rescue of populations depends on their ability to produce phenotypic variation that is heritable and adaptive. DNA mutations are the best understood mechanisms to create phenotypic variation, but other, less well-studied mechanisms exist. Marine benthic foundation species provide opportunities to study these mechanisms because many are dominated by isogenic stands produced through asexual reproduction. For example, Caribbean acroporid corals are long lived and reproduce asexually via breakage of branches. Fragmentation is often the dominant mode of local population maintenance. Thus, large genets with many ramets (colonies) are common. Here, we observed phenotypic variation in stress responses within genets following the coral bleaching events in 2014 and 2015 caused by high water temperatures. This was not due to genetic variation in their symbiotic dinoflagellates (Symbiodinium "fitti") because each genet of this coral species typically harbours a single strain of S. "fitti". Characterization of the microbiome via 16S tag sequencing correlated the abundance of only two microbiome members (Tepidiphilus, Endozoicomonas) with a bleaching response. Epigenetic changes were significantly correlated with the host's genetic background, the location of the sampled polyps within the colonies (e.g., branch vs. base of colony), and differences in the colonies' condition during the bleaching event. We conclude that long-term microenvironmental differences led to changes in the way the ramets methylated their genomes, contributing to the differential bleaching response. However, most of the variation in differential bleaching response among clonemates of Acropora palmata remains unexplained. This research provides novel data and hypotheses to help understand intragenet variability in stress phenotypes of sessile marine species.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Wang L, Sun Z, Su C, et al (2019)

A GmNINa-miR172c-NNC1 Regulatory Network Coordinates the Nodulation and Autoregulation of Nodulation Pathways in Soybean.

Molecular plant, 12(9):1211-1226.

Symbiotic root nodules are root lateral organs of plants in which nitrogen-fixing bacteria (rhizobia) convert atmospheric nitrogen to ammonia. The formation and number of nodules in legumes are precisely controlled by a rhizobia-induced signal cascade and host-controlled autoregulation of nodulation (AON). However, how these pathways are integrated and their underlying mechanisms are unclear. Here, we report that microRNA172c (miR172c) activates soybean (Glycine max) Rhizobia-Induced CLE1 (GmRIC1) and GmRIC2 by removing the transcriptional repression of these genes by Nodule Number Control 1 (NNC1), leading to the activation of the AON pathway. NNC1 interacts with GmNINa, the soybean ortholog of Lotus NODULE INCEPTION (NIN), and hampers its transcriptional activation of GmRIC1 and GmRIC2. Importantly, GmNINa acts as a transcriptional activator of miR172c. Intriguingly, NNC1 can transcriptionally repress miR172c expression, adding a negative feedback loop into the NNC1 regulatory network. Moreover, GmNINa interacts with NNC1 and can relieve the NNC1-mediated repression of miR172c transcription. Thus, the GmNINa-miR172c-NNC1 network is a master switch that coordinately regulates and optimizes NF and AON signaling, supporting the balance between nodulation and AON in soybean.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Li F, He X, Tang M, et al (2020)

Adaptation of plants to high-calcium content kart regions: possible involvement of symbiotic microorganisms and underlying mechanisms.

Brazilian journal of biology = Revista brasleira de biologia, 80(1):209-214.

Rhizosphere microorganisms and endophytes can help their hosts absorb nutrients and regulate the levels of plant hormones. Moreover, they can modulate the expressions of host genes, assist hosts in eliminating reactive oxygen species (ROS) and secreting volatile organic compounds. Therefore, rhizosphere microorganisms and endophytes are considered as determinant factors driving processes involved in the growth of host plants. However, the physiological and ecological functions, as well as the molecular mechanism underlying the behavior of rhizosphere microorganisms and endophytes in their role in the adaptive capacity of host plants in the karstic high-calcium environment have not been systematically studied. This review summarizes the physiological and molecular mechanisms of rhizosphere microorganisms and endophytes which help host plants to adapt to various kinds of adverse environments. The adaptive capacities of plants growing in adverse environments, partly, or totally, depends on microorganisms co-existing with the host plants.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Morikawa MK, SR Palumbi (2019)

Using naturally occurring climate resilient corals to construct bleaching-resistant nurseries.

Proceedings of the National Academy of Sciences of the United States of America, 116(21):10586-10591.

Ecological restoration of forests, meadows, reefs, or other foundational ecosystems during climate change depends on the discovery and use of individuals able to withstand future conditions. For coral reefs, climate-tolerant corals might not remain tolerant in different environments because of widespread environmental adjustment of coral physiology and symbionts. Here, we test if parent corals retain their heat tolerance in nursery settings, if simple proxies predict successful colonies, and if heat-tolerant corals suffer lower growth or survival in normal settings. Before the 2015 natural bleaching event in American Samoa, we set out 800 coral fragments from 80 colonies of four species selected by prior tests to have a range of intraspecific natural heat tolerance. After the event, nursery stock from heat-tolerant parents showed two to three times less bleaching across species than nursery stock from less tolerant parents. They also retained higher individual genetic diversity through the bleaching event than did less heat-tolerant corals. The three best proxies for thermal tolerance were response to experimental heat stress, location on the reef, and thermal microclimate. Molecular biomarkers were also predictive but were highly species specific. Colony genotype and symbiont genus played a similarly strong role in predicting bleaching. Combined, our results show that selecting for host and symbiont resilience produced a multispecies coral nursery that withstood multiple bleaching events, that proxies for thermal tolerance in restoration can work across species and be inexpensive, and that different coral clones within species reacted very differently to bleaching.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Lagunas B, Achom M, Bonyadi-Pour R, et al (2019)

Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula.

Molecular plant, 12(6):833-846.

Understanding how plants respond to nitrogen in their environment is crucial for determining how they use it and how the nitrogen use affects other processes related to plant growth and development. Under nitrogen limitation the activity and affinity of uptake systems is increased in roots, and lateral root formation is regulated in order to adapt to low nitrogen levels and scavenge from the soil. Plants in the legume family can form associations with rhizobial nitrogen-fixing bacteria, and this association is tightly regulated by nitrogen levels. The effect of nitrogen on nodulation has been extensively investigated, but the effects of nodulation on plant nitrogen responses remain largely unclear. In this study, we integrated molecular and phenotypic data in the legume Medicago truncatula and determined that genes controlling nitrogen influx are differently expressed depending on whether plants are mock or rhizobia inoculated. We found that a functional autoregulation of nodulation pathway is required for roots to perceive, take up, and mobilize nitrogen as well as for normal root development. Our results together revealed that autoregulation of nodulation, root development, and the location of nitrogen are processes balanced by the whole plant system as part of a resource-partitioning mechanism.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Hager FA, K Krausa (2019)

Acacia Ants Respond to Plant-Borne Vibrations Caused by Mammalian Browsers.

Current biology : CB, 29(5):717-725.e3.

Living in the African savanna is dangerous, especially for plants. Many plants therefore engage in mutualism with ants, in which plants provide food and shelter in exchange for protection against herbivores. Ants become alarmed when the plant takes on some sort of damage. They immediately emerge from their plant shelter and aggressively defend the plant. Mammalian herbivores can have devastating effects on trees by browsing, breaking tree branches, stripping bark, and pushing over entire trees. However, mutualistic ants substantially reduce the amount of damage. To efficiently protect the tree, ants need to rapidly react together when the tree is under attack. Here, we show that the acacia ant Crematogaster mimosae defends its host tree by exploiting plant-borne vibrations caused by browsers feeding on the tree. Experiments with controlled vibrations show that ants discriminate browser-induced vibrations from those induced by wind, become alarmed, and patrol on the branches. Browser-induced vibrations serve as a long-distance alarm cue. The vibrations propagate through the whole acacia tree and trigger ants' defensive behavior, even on the other side of the tree. Furthermore, the ants make use of tropotactic directional vibration sensing to orient to the attacked part of the tree and fight back the attacker.

RevDate: 2020-03-29

Zhang C, Qi M, Zhang X, et al (2020)

Rhizobial infection triggers systemic transport of endogenous RNAs between shoots and roots in soybean.

Science China. Life sciences pii:10.1007/s11427-019-1608-7 [Epub ahead of print].

Legumes have evolved a symbiotic relationship with rhizobial bacteria and their roots form unique nitrogen-fixing organs called nodules. Studies have shown that abiotic and biotic stresses alter the profile of gene expression and transcript mobility in plants. However, little is known about the systemic transport of RNA between roots and shoots in response to rhizobial infection on a genome-wide scale during the formation of legume-rhizobia symbiosis. In our study, we found that two soybean (Glycine max) cultivars, Peking and Williams, show a high frequency of single nucleotide polymorphisms; this allowed us to characterize the origin and mobility of transcripts in hetero-grafts of these two cultivars. We identified 4,552 genes that produce mobile RNAs in soybean, and found that rhizobial infection triggers mass transport of mRNAs between shoots and roots at the early stage of nodulation. The majority of these mRNAs are of relatively low abundance and their transport occurs in a selective manner in soybean plants. Notably, the mRNAs that moved from shoots to roots at the early stage of nodulation were enriched in many nodule-related responsive processes. Moreover, the transcripts of many known symbiosis-related genes that are induced by rhizobial infection can move between shoots and roots. Our findings provide a deeper understanding of endogenous RNA transport in legume-rhizobia symbiotic processes.

RevDate: 2020-03-28

Roy P, Achom M, Wilkinson H, et al (2020)

Symbiotic Outcome Modified by the Diversification from 7 to over 700 Nodule-Specific Cysteine-Rich Peptides.

Genes, 11(4): pii:genes11040348.

Legume-rhizobium symbiosis represents one of the most successfully co-evolved mutualisms. Within nodules, the bacterial cells undergo distinct metabolic and morphological changes and differentiate into nitrogen-fixing bacteroids. Legumes in the inverted repeat lacking clade (IRLC) employ an array of defensin-like small secreted peptides (SSPs), known as nodule-specific cysteine-rich (NCR) peptides, to regulate bacteroid differentiation and activity. While most NCRs exhibit bactericidal effects in vitro, studies confirm that inside nodules they target the bacterial cell cycle and other cellular pathways to control and extend rhizobial differentiation into an irreversible (or terminal) state where the host gains control over bacteroids. While NCRs are well established as positive regulators of effective symbiosis, more recent findings also suggest that NCRs affect partner compatibility. The extent of bacterial differentiation has been linked to species-specific size and complexity of the NCR gene family that varies even among closely related species, suggesting a more recent origin of NCRs followed by rapid expansion in certain species. NCRs have diversified functionally, as well as in their expression patterns and responsiveness, likely driving further functional specialisation. In this review, we evaluate the functions of NCR peptides and their role as a driving force underlying the outcome of rhizobial symbiosis, where the plant is able to determine the outcome of rhizobial interaction in a temporal and spatial manner.

RevDate: 2020-03-28

Gusmão LC, Van Deusen V, Daly M, et al (2020)

Origin and evolution of the symbiosis between sea anemones (Cnidaria, Anthozoa, Actiniaria) and hermit crabs, with additional notes on anemone-gastropod associations.

Molecular phylogenetics and evolution pii:S1055-7903(20)30077-4 [Epub ahead of print].

The anemone-crab mutualism is ubiquitous in temperate and tropical marine environments. In this symbiosis, one or more anemones live on a shell inhabited by a hermit crab and reciprocal phoretic, trophic, and defensive benefits are exchanged between the partners. Sea anemone-hermit crab symbionts belong to three families: Hormathiidae (Calliactis and Paracalliactis), Sagartiidae (Carcinactis and Verrillactis), and Actiniidae (Stylobates). Hermit crabs establish most partnerships by detaching anemones and placing them on their shell; sea anemones can also mount shells unaided, triggered by a mollusc-derived substance in the periostracum of the shell. At least partial cooperation by the anemones is necessary for successful establishment of the symbiosis. Here, we expand the evolutionary framework provided by Gusmão and Daly (2010) for hormathiid symbionts by generating a phylogeny with at least one member of each actiniarian symbiotic genus with hermit crabs using five molecular markers (16S, 12S, 18S, 28S, CO3). We not only corroborated the results from Gusmão and Daly (2010) by finding two origins of hermit crab symbiosis within Hormathiidae, but also find additional origins for hermit crab symbiosis within Actiniaria. We provide for the first time evidence of a close relationship between symbionts Carcinactis dolosa and V. paguri. The ability to secrete chitin by the ectoderm of the column is inferred to be broadly convergent within Actiniaria whereas the secretion of a chitinous carcinoecium by the pedal disc is a distinct but convergent morphological adaptation of several lineages within Actiniaria. Our finding of multiple origins for both the hermit crab and gastropod symbioses suggests that the shell-mounting behavior might only have been the precursor of the hermit crab association among Calliactis spp.

RevDate: 2020-03-27

Rapport DJ (2007)

Sustainability science: an ecohealth perspective.

Sustainability science, 2(1):77-84.

Sustainability science is emerging as a transdisciplinary effort to come to grips with the much-needed symbiosis between human activity and the environment. While there is recognition that conventional economic growth must yield to policies that foster sustainable development, this has not yet occurred on any broad scale. Rather, there is clear evidence that the Earth's ecosystems and landscapes continue to degrade as a consequence of the cumulative impact of human activities. Taking an ecohealth approach to sustainability science provides a unique perspective on both the goals and the means to achieve sustainability. The goals should be the restoration of full functionality to the Earth's ecosystems and landscapes, as measured by the key indicators of health: resilience, organization, vitality (productivity), and the absence of ecosystem distress syndrome. The means should be the coordinated (spatially and temporally) efforts to modify human behaviors to reduce cumulative stress impacts. Achieving ecosystem health should become the cornerstone of sustainability policy-for healthy ecosystems are the essential precondition for achieving sustainable livelihoods, human health, and many other societal objectives, as reflected in the Millennium Development Goals.

RevDate: 2020-03-27

Velichko NS, Grinev VS, YP Fedonenko (2020)

Characterization of biopolymers produced by planktonic and biofilm cells of Herbaspirillum lusitanum P6-12.

Journal of applied microbiology [Epub ahead of print].

AIMS: The goal of this study was to characterize the Herbaspirillum lusitanum P6-12 biopolymers under various environmental conditions.

METHODS AND RESULTS: Differences in biopolymers composition from planktonic and biofilm cells of H. lusitanum strain P6-12 were analyzed using Fourier transform infrared spectroscopy (FTIR), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and colorimetric and gas-liquid chromatography (GLC). A high degree of polymer separation and purification was achieved by ultracentrifugation, and column chromatography allowed us to identify the chemical differences between biopolymers from biofilm and planktonic Herbaspirillum lusitanum. The planktonic cells of H. lusitanum P6-12 had capsules containing two high-molecular-weight glycoconjugates (CPS-I and CPS-II) of a lipopolysaccharide (LPS) nature and one EPS as a lipid-polysaccharide complex. The EPS, CPS-I, CPS-II had different monosaccharide and lipid compositions. The extracellular polymeric matrix (EPM) produced by the biofilm cells was mostly proteinaceous, with a small amount of carbohydrates (up to 3%). From the biofilm culture medium, a free extracellular polymeric substance (fEPS) was obtained that contained proteins and carbohydrates (up to 7%). The cells outside the biofilm produced capsules (CPSFBC) that consisted of carbohydrates (up to 10%), proteins (up to 16%), and lipids.

CONCLUSIONS: During biofilm formation, the bacteria secreted surface biopolymers that differed from those of the planktonic cells. The heterogeneity of the polysaccharidic polymers of the H. lusitanum P6-12 surface is probably conditioned by their different functions in plant colonization and formation of an efficient symbiosis, as well as in cell adaptation to existence in plant tissues.

The results of the study permit a better understanding of the physiological properties of the biopolymers, e.g., in plant-microbe interactions.

RevDate: 2020-03-26

Dunkley K, Ward AJW, Perkins SE, et al (2020)

To clean or not to clean: Cleaning mutualism breakdown in a tidal environment.

Ecology and evolution, 10(6):3043-3054 pii:ECE36120.

The dynamics and prevalence of mutualistic interactions, which are responsible for the maintenance and structuring of all ecological communities, are vulnerable to changes in abiotic and biotic environmental conditions. Mutualistic outcomes can quickly shift from cooperation to conflict, but it unclear how resilient and stable mutualistic outcomes are to more variable conditions. Tidally controlled coral atoll lagoons that experience extreme diurnal environmental shifts thus provide a model from which to test plasticity in mutualistic behavior of dedicated (formerly obligate) cleaner fish, which acquire all their food resources through client interactions. Here, we investigated cleaning patterns of a model cleaner fish species, the bluestreak wrasse (Labroides dimidiatus), in an isolated tidal lagoon on the Great Barrier Reef. Under tidally restricted conditions, uniquely both adults and juveniles were part-time facultative cleaners, pecking on Isopora palifera coral. The mutualism was not completely abandoned, with adults also wandering across the reef in search of clients, rather than waiting at fixed site cleaning stations, a behavior not yet observed at any other reef. Contrary to well-established patterns for this cleaner, juveniles appeared to exploit the system, by biting ("cheating") their clients more frequently than adults. We show for the first time, that within this variable tidal environment, where mutualistic cleaning might not represent a stable food source, the prevalence and dynamics of this mutualism may be breaking down (through increased cheating and partial abandonment). Environmental variability could thus reduce the pervasiveness of mutualisms within our ecosystems, ultimately reducing the stability of the system.

RevDate: 2020-03-26

Casarrubia S, Martino E, Daghino S, et al (2020)

Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus.

Frontiers in microbiology, 11:341.

The success of Ericaceae in stressful habitats enriched in heavy metals has been ascribed to the distinctive abilities of their mycorrhizal fungal partners to withstand heavy metal stress and to enhance metal tolerance in the host plant. Whereas heavy metal tolerance has been extensively investigated in some ericoid mycorrhizal (ERM) fungi, the molecular and cellular mechanisms that extend tolerance to the host plant are currently unknown. Here, we show a reduced Cd content in Cd-exposed mycorrhizal roots of Vaccinium myrtillus colonized by a metal tolerant isolate of the fungus Oidiodendron maius as compared to non-mycorrhizal roots. To better understand this phenotype, we applied Next Generation Sequencing technologies to analyze gene expression in V. myrtillus and O. maius Zn grown under normal and Cd-stressed conditions, in the free living and in the mycorrhizal status. The results clearly showed that Cd had a stronger impact on plant gene expression than symbiosis, whereas fungal gene expression was mainly regulated by symbiosis. The higher abundance of transcripts coding for stress related proteins in non-mycorrhizal roots may be related to the higher Cd content. Regulated plant metal transporters have been identified that may play a role in reducing Cd content in mycorrhizal roots exposed to this metal.

RevDate: 2020-03-26

Rahman MA, Parvin M, Das U, et al (2020)

Arbuscular Mycorrhizal Symbiosis Mitigates Iron (Fe)-Deficiency Retardation in Alfalfa (Medicago sativa L.) Through the Enhancement of Fe Accumulation and Sulfur-Assisted Antioxidant Defense.

International journal of molecular sciences, 21(6): pii:ijms21062219.

Iron (Fe)-deficiency is one of the major constraints affecting growth, yield and nutritional quality in plants. This study was performed to elucidate how arbuscular mycorrhizal fungi (AMF) alleviate Fe-deficiency retardation in alfalfa (Medicago sativa L.). AMF supplementation improved plant biomass, chlorophyll score, Fv/Fm (quantum efficiency of photosystem II), and Pi_ABS (photosynthesis performance index), and reduced cell death, electrolyte leakage, and hydrogen peroxide accumulation in alfalfa. Moreover, AMF enhanced ferric chelate reductase activity as well as Fe, Zn, S and P in alfalfa under Fe-deficiency. Although Fe-transporters (MsIRT1 and MsNramp1) did not induce in root but MsFRO1 significantly induced by AMF under Fe deficiency in roots, suggesting that AMF-mediated Fe enhancement is related to the bioavailability of Fe at rhizosphere/root apoplast rather than the upregulation of Fe transporters under Fe deficiency in alfalfa. Several S-transporters (MsSULTR1;1, MsSULTR1;2, MsSULTR1;3, and MsSULTR3;1) markedly increased following AMF supplementation with or without Fe-deficiency alfalfa. Our study further suggests that Fe uptake system is independently influenced by AMF regardless of the S status in alfalfa. However, the increase of S in alfalfa is correlated with the elevation of GR and S-metabolites (glutathione and cysteine) associated with antioxidant defense under Fe deficiency.

RevDate: 2020-03-26

Doin de Moura GG, Remigi P, Masson-Boivin C, et al (2020)

Experimental Evolution of Legume Symbionts: What Have We Learnt?.

Genes, 11(3): pii:genes11030339.

Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. They likely emerged and diversified through independent horizontal transfers of key symbiotic genes. To replay the evolution of a new rhizobium genus under laboratory conditions, the symbiotic plasmid of Cupriavidus taiwanensis was introduced in the plant pathogen Ralstonia solanacearum, and the generated proto-rhizobium was submitted to repeated inoculations to the C. taiwanensis host, Mimosa pudica L.. This experiment validated a two-step evolutionary scenario of key symbiotic gene acquisition followed by genome remodeling under plant selection. Nodulation and nodule cell infection were obtained and optimized mainly via the rewiring of regulatory circuits of the recipient bacterium. Symbiotic adaptation was shown to be accelerated by the activity of a mutagenesis cassette conserved in most rhizobia. Investigating mutated genes led us to identify new components of R. solanacearum virulence and C. taiwanensis symbiosis. Nitrogen fixation was not acquired in our short experiment. However, we showed that post-infection sanctions allowed the increase in frequency of nitrogen-fixing variants among a non-fixing population in the M. pudica-C. taiwanensis system and likely allowed the spread of this trait in natura. Experimental evolution thus provided new insights into rhizobium biology and evolution.

RevDate: 2020-03-26

Storey MA, Andreassend SK, Bracegirdle J, et al (2020)

Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts.

mBio, 11(2): pii:mBio.02997-19.

Marine sponges have been a prolific source of unique bioactive compounds that are presumed to act as a deterrent to predation. Many of these compounds have potential therapeutic applications; however, the lack of efficient and sustainable synthetic routes frequently limits clinical development. Here, we describe a metagenomic investigation of Mycale hentscheli, a chemically gifted marine sponge that possesses multiple distinct chemotypes. We applied shotgun metagenomic sequencing, hybrid assembly of short- and long-read data, and metagenomic binning to obtain a comprehensive picture of the microbiome of five specimens, spanning three chemotypes. Our data revealed multiple producing species, each having relatively modest secondary metabolomes, that contribute collectively to the chemical arsenal of the holobiont. We assembled complete genomes for multiple new genera, including two species that produce the cytotoxic polyketides pateamine and mycalamide, as well as a third high-abundance symbiont harboring a proteusin-type biosynthetic pathway that appears to encode a new polytheonamide-like compound. We also identified an additional 188 biosynthetic gene clusters, including a pathway for biosynthesis of peloruside. These results suggest that multiple species cooperatively contribute to defensive symbiosis in M. hentscheli and reveal that the taxonomic diversity of secondary-metabolite-producing sponge symbionts is larger and richer than previously recognized.IMPORTANCEMycale hentscheli is a marine sponge that is rich in bioactive small molecules. Here, we use direct metagenomic sequencing to elucidate highly complete and contiguous genomes for the major symbiotic bacteria of this sponge. We identify complete biosynthetic pathways for the three potent cytotoxic polyketides which have previously been isolated from M. hentscheli Remarkably, and in contrast to previous studies of marine sponges, we attribute each of these metabolites to a different producing microbe. We also find that the microbiome of M. hentscheli is stably maintained among individuals, even over long periods of time. Collectively, our data suggest a cooperative mode of defensive symbiosis in which multiple symbiotic bacterial species cooperatively contribute to the defensive chemical arsenal of the holobiont.

RevDate: 2020-03-26

Clarke DJ (2020)

Photorhabdus: a tale of contrasting interactions.

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

Different model systems have, over the years, contributed to our current understanding of the molecular mechanisms underpinning the various types of interaction between bacteria and their animal hosts. The genus Photorhabdus comprises Gram-negative insect pathogenic bacteria that are normally found as symbionts that colonize the gut of the infective juvenile stage of soil-dwelling nematodes from the family Heterorhabditis. The nematodes infect susceptible insects and release the bacteria into the insect haemolymph where the bacteria grow, resulting in the death of the insect. At this stage the nematodes feed on the bacterial biomass and, following several rounds of reproduction, the nematodes develop into infective juveniles that leave the insect cadaver in search of new hosts. Therefore Photorhabdus has three distinct and obligate roles to play during this life-cycle: (1) Photorhabdus must kill the insect host; (2) Photorhabdus must be capable of supporting nematode growth and development; and (3) Photorhabdus must be able to colonize the gut of the next generation of infective juveniles before they leave the insect cadaver. In this review I will discuss how genetic analysis has identified key genes involved in mediating, and regulating, the interaction between Photorhabdus and each of its invertebrate hosts. These studies have resulted in the characterization of several new families of toxins and a novel inter-kingdom signalling molecule and have also uncovered an important role for phase variation in the regulation of these different roles.

RevDate: 2020-03-26
CmpDate: 2020-03-26

Blacher E, Bashiardes S, Shapiro H, et al (2019)

Potential roles of gut microbiome and metabolites in modulating ALS in mice.

Nature, 572(7770):474-480.

Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disorder, in which the clinical manifestations may be influenced by genetic and unknown environmental factors. Here we show that ALS-prone Sod1 transgenic (Sod1-Tg) mice have a pre-symptomatic, vivarium-dependent dysbiosis and altered metabolite configuration, coupled with an exacerbated disease under germ-free conditions or after treatment with broad-spectrum antibiotics. We correlate eleven distinct commensal bacteria at our vivarium with the severity of ALS in mice, and by their individual supplementation into antibiotic-treated Sod1-Tg mice we demonstrate that Akkermansia muciniphila (AM) ameliorates whereas Ruminococcus torques and Parabacteroides distasonis exacerbate the symptoms of ALS. Furthermore, Sod1-Tg mice that are administered AM are found to accumulate AM-associated nicotinamide in the central nervous system, and systemic supplementation of nicotinamide improves motor symptoms and gene expression patterns in the spinal cord of Sod1-Tg mice. In humans, we identify distinct microbiome and metabolite configurations-including reduced levels of nicotinamide systemically and in the cerebrospinal fluid-in a small preliminary study that compares patients with ALS with household controls. We suggest that environmentally driven microbiome-brain interactions may modulate ALS in mice, and we call for similar investigations in the human form of the disease.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Kusakabe S, Higasitani N, Kaneko T, et al (2020)

Lotus Accessions Possess Multiple Checkpoints Triggered by Different Type III Secretion System Effectors of the Wide-Host-Range Symbiont Bradyrhizobium elkanii USDA61.

Microbes and environments, 35(1):.

Bradyrhizobium elkanii, a rhizobium with a relatively wide host range, possesses a functional type III secretion system (T3SS) that is involved in symbiotic incompatibility against Rj4-genotype soybean (Glycine max) and some accessions of mung bean (Vigna radiata). To expand our knowledge on the T3SS-mediated partner selection mechanism in the symbiotic legume-rhizobia association, we inoculated three Lotus experimental accessions with wild-type and T3SS-mutant strains of B. elkanii USDA61. Different responses were induced by T3SS in a host genotype-dependent manner. Lotus japonicus Gifu inhibited infection; L. burttii allowed infection, but inhibited nodule maturation at the post-infection stage; and L. burttii and L. japonicus MG-20 both displayed a nodule early senescence-like response. By conducting inoculation tests with mutants of previously reported and newly identified effector protein genes of B. elkanii USDA61, we identified NopF as the effector protein triggering the inhibition of infection, and NopM as the effector protein triggering the nodule early senescence-like response. Consistent with these results, the B. elkanii USDA61 gene for NopF introduced into the Lotus symbiont Mesorhizobium japonicum induced infection inhibition in L. japonicus Gifu, but did not induce any response in L. burttii or L. japonicus MG-20. These results suggest that Lotus accessions possess at least three checkpoints to eliminate unfavorable symbionts, including the post-infection stage, by recognizing different T3SS effector proteins at each checkpoint.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Rejili M, Ruiz-Argueso T, M Mars (2020)

Novel putative Mesorhizobium and Ensifer genomospecies together with a novel symbiovar psoraleae nodulate legumes of agronomic interest grown in Tunisia.

Systematic and applied microbiology, 43(2):126067.

Forty rhizobial strains were isolated from Lotus creticus, L. pusillus and Bituminaria bituminosa endemic to Tunisia, and they belonged to the Mesorhizobium and Ensifer genera based on 16S rDNA sequence phylogeny. According to the concatenated recA and glnII sequence-based phylogeny, four Bituminaria isolates Pb5, Pb12, Pb8 and Pb17 formed a monophyletic group with Mesorhizobium chacoense ICMP14587T, whereas four other strains Pb1, Pb6, Pb13 and Pb15 formed two separate lineages within the Ensifer genus. Among the L. pusillus strains, Lpus9 and Lpus10 showed a 96% identical nucleotide with Ensifer meliloti CCBAU83493T; whereas six other strains could belong to previously undescribed Mesorhizobium and Ensifer species. For L. creticus strains, Lcus37, Lcus39 and Lcus44 showed 98% sequence identity with Ensifer aridi JNVU TP6, and Lcus42 shared a 96% identical nucleotide with Ensifer meliloti CCBAU83493T; whereas another four strains were divergent from all the described Ensifer and Mesorhizobium species. The analysis of the nodC gene-based phylogeny identified four symbiovar groups; Mesorhizobium sp. sv. anthyllidis (Lpus3 and Lpus11 from L. pusillus, Lcus43 from L. creticus), Ensifer medicae sv. meliloti (four strains from L. creticus and two strains from L. pusillus), E. meliloti sv. meliloti (four from L. creticus, four from L. pusillus and four from B. bituminosa). In addition, four B. bituminosa strains (Pb5, Pb8, Pb12, and Pb17) displayed a distinctive nodC sequence distant from those of other symbiovars described to date. According to their symbiotic gene sequences and host range, the B. bituminosa symbionts (Pb5, Pb8, Pb12 and Pb17) would represent a new symbiovar of M. chacoense for which sv. psoraleae is proposed.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Yuan K, Reckling M, Ramirez MDA, et al (2020)

Characterization of Rhizobia for the Improvement of Soybean Cultivation at Cold Conditions in Central Europe.

Microbes and environments, 35(1):.

In central Europe, soybean cultivation is gaining increasing importance to reduce protein imports from overseas and make cropping systems more sustainable. In the field, despite the inoculation of soybean with commercial rhizobia, its nodulation is low. In many parts of Europe, limited information is currently available on the genetic diversity of rhizobia and, thus, biological resources for selecting high nitrogen-fixing rhizobia are inadequate. These resources are urgently needed to improve soybean production in central Europe. The objective of the present study was to identify strains that have the potential to increase nitrogen fixation by and the yield of soybean in German soils. We isolated and characterized 77 soybean rhizobia from 18 different sampling sites. Based on a multilocus sequence analysis (MLSA), 71% of isolates were identified as Bradyrhizobium and 29% as Rhizobium. A comparative analysis of the nodD and nifH genes showed no significant differences, which indicated that the soybean rhizobia symbiotic genes in the present study belong to only one type. One isolate, GMF14 which was tolerant of a low temperature (4°C), exhibited higher nitrogen fixation in root nodules and a greater plant biomass than USDA 110 under cold conditions. These results strongly suggest that some indigenous rhizobia enhance biological nitrogen fixation and soybean yield due to their adaption to local conditions.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Ferraz Helene LC, O'Hara G, M Hungria (2020)

Characterization of Bradyrhizobium strains indigenous to Western Australia and South Africa indicates remarkable genetic diversity and reveals putative new species.

Systematic and applied microbiology, 43(2):126053.

Bradyrhizobium are N2-fixing microsymbionts of legumes with relevant applications in agricultural sustainability, and we investigated the phylogenetic relationships of conserved and symbiotic genes of 21 bradyrhizobial strains. The study included strains from Western Australia (WA), isolated from nodules of Glycine spp. the country is one genetic center for the genus and from nodules of other indigenous legumes grown in WA, and strains isolated from forage Glycine sp. grown in South Africa. The 16S rRNA phylogeny divided the strains in two superclades, of B. japonicum and B. elkanii, but with low discrimination among the species. The multilocus sequence analysis (MLSA) with four protein-coding housekeeping genes (dnaK, glnII, gyrB and recA) pointed out seven groups as putative new species, two within the B. japonicum, and five within the B. elkanii superclades. The remaining eleven strains showed higher similarity with six species, B. lupini, B. liaoningense, B. yuanmingense, B. subterraneum, B. brasilense and B. retamae. Phylogenetic analysis of the nodC symbiotic gene clustered 13 strains in three different symbiovars (sv. vignae, sv. genistearum and sv. retamae), while seven others might compose new symbiovars. The genetic profiles of the strains evaluated by BOX-PCR revealed high intra- and interspecific diversity. The results point out the high level of diversity still to be explored within the Bradyrhizobium genus, and further studies might confirm new species and symbiovars.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Wackett LP (2019)

Rhizobial strains.

Environmental microbiology reports, 11(4):616-617.

RevDate: 2020-03-24

Wang C, Cheng T, Li X, et al (2020)

Metronidazole-Treated Porphyromonas gingivalis Persisters Invade Human Gingival Epithelial Cells and Perturb Innate Responses.

Antimicrobial agents and chemotherapy pii:AAC.02529-19 [Epub ahead of print].

Periodontitis as a biofilm-associated inflammatory disease is highly prevalent worldwide. It severely affects oral health and yet closely links to systemic diseases like diabetes and cardiovascular disease. Porphyromonas gingivalis as a 'keystone' periodontopathogen drives the shift of microbe-host symbiosis to dysbiosis, and critically contributes to the pathogenesis of periodontitis. Persisters are a tiny subset of biofilm-associated microbes highly tolerant to lethal treatment of antimicrobials, and notably metronidazole-tolerant P. gingivalis persisters have recently been identified by our group. This study further explored the interactive profiles of metronidazole-treated P. gingivalis persisters (M-PgPs) with human gingival epithelial cells (HGECs). P. gingivalis cells (ATCC 33277) at stationary phase were treated with lethal dosage of metronidazole (100 μg/ml, 6 hours) for generating M-PgPs. The interaction of M-PgPs with HGECs was assessed by microscopy, flow cytometry, cytokine profiling and qPCR. We demonstrated that the overall morphology and ultra-cellular structure of M-PgPs remained unchanged. Importantly, M-PgPs maintained the capabilities to adhere to and invade into HGECs. Moreover, M-PgPs significantly suppressed pro-inflammatory cytokine expression in HGECs at a comparable level with the untreated P. gingivalis cells, through the thermo-sensitive components. The present study reveals that P. gingivalis persisters induced by lethal treatment of antibiotics could maintain their capabilities to adhere to and invade into human gingival epithelial cells, and perturb the innate host responses. Novel strategies and approaches need to be developed for tackling P. gingivalis and favourably modulating the dysregulated immuno-inflammatory responses for oral/periodontal health and general wellbeing.

RevDate: 2020-03-24

Shitole AA, Raut P, Giram P, et al (2020)

Poly (vinylpyrrolidone)‑iodine engineered poly (ε-caprolactone) nanofibers as potential wound dressing materials.

Materials science & engineering. C, Materials for biological applications, 110:110731.

Facilitating the process of wound healing and effective treatment of wounds remains a serious challenge in healthcare. Wound dressing materials play a major role in the protection of wounds and in accelerating the natural healing process. In the present study, novel core/shell (c/s) nanofibrous mats of poly(vinyl pyrrolidone)‑iodine (PVPI) and polycaprolactone (PCL) were fabricated using a co-axial electrospinning process followed by their surface modification with poly-l-lysine. The developed nanofibrous mats were extensively characterized for their physicochemical properties using various analytical techniques. The core/shell structure of the PVP-I/PCL nanofibers was confirmed using TEM analysis. The PVP-I release studies showed an initial burst phase followed by a sustained release pattern of PVP-I over a period of 30 days. The developed nanofibers exhibited higher BSA and fibrinogen adsorption as compared to pristine PCL. Cytotoxicity studies using MTT assay demonstrated that the PVP-I/PCL (c/s) nanofibers were cytocompatible at optimized PVP-I concentration (3 wt%). The PCL-poly-l-lysine and PVP-I/PCL-poly-l-lysine nanofibers exhibited higher cell viability (24.2% and 21.4% higher at day 7) when compared to uncoated PCL and PVP-I/PCL nanofibers. The PVP-I/PCL nanofibers showed excellent antimicrobial activity against both Gram-positive (S. aureus) and Gram-negative (E. coli) bacteria. The inflammatory response of Mouse RAW 264.7 macrophage cells towards the nanofibers was studied using RT-PCR. It revealed that the pro-inflammatory cytokines (TNF-α and IL-1β) were significantly upregulated on PCL nanofibers, while their expression was comparatively lower on poly-l-lysine coated PCL or PVP-I/PCL(c/s) nanofibers. Overall, the study highlights the ability of poly-l-lysine coated PVP-I/PCL (c/s) nanofibers as potential wound dressing materials effectively facilitating the early stage wound healing and repair process by virtue of their selective modulation of inflammation, cell adhesion and antimicrobial properties.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Živković D, John S, Verin M, et al (2019)

Neutral genomic signatures of host-parasite coevolution.

BMC evolutionary biology, 19(1):230.

BACKGROUND: Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build an eco-evolutionary model, where neutral genomic changes over time are driven by a single selected locus in hosts and parasites via a simple biallelic gene-for-gene or matching-allele interaction. This coevolutionary process may lead to cyclic changes in the sizes of the interacting populations.

RESULTS: We investigate if and when these changes can be observed in the site frequency spectrum of neutral polymorphisms from host and parasite full genome data. We show that changes of the host population size are too smooth to be observable in its polymorphism pattern over the course of time. Conversely, the parasite population may undergo a series of strong bottlenecks occurring on a slower relative time scale, which may lead to observable changes in a time series sample. We also extend our results to cases with 1) several parasites per host accelerating relative time, and 2) multiple parasite generations per host generation slowing down rescaled time.

CONCLUSIONS: Our results show that time series sampling of host and parasite populations with full genome data are crucial to understand if and how coevolution occurs. This model provides therefore a framework to interpret and draw inference from genome-wide polymorphism data of interacting species.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Fazzino L, Anisman J, Chacón JM, et al (2020)

Lytic bacteriophage have diverse indirect effects in a synthetic cross-feeding community.

The ISME journal, 14(1):123-134.

Bacteriophage shape the composition and function of microbial communities. Yet it remains difficult to predict the effect of phage on microbial interactions. Specifically, little is known about how phage influence mutualisms in networks of cross-feeding bacteria. We mathematically modeled the impacts of phage in a synthetic microbial community in which Escherichia coli and Salmonella enterica exchange essential metabolites. In this model, independent phage attack of either species was sufficient to temporarily inhibit both members of the mutualism; however, the evolution of phage resistance facilitated yields similar to those observed in the absence of phage. In laboratory experiments, attack of S. enterica with P22vir phage followed these modeling expectations of delayed community growth with little change in the final yield of bacteria. In contrast, when E. coli was attacked with T7 phage, S. enterica, the nonhost species, reached higher yields compared with no-phage controls. T7 infection increased nonhost yield by releasing consumable cell debris, and by driving evolution of partially resistant E. coli that secreted more carbon. Our results demonstrate that phage can have extensive indirect effects in microbial communities, that the nature of these indirect effects depends on metabolic and evolutionary mechanisms, and that knowing the degree of evolved resistance leads to qualitatively different predictions of bacterial community dynamics in response to phage attack.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Assié A, Leisch N, Meier DV, et al (2020)

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).

The ISME journal, 14(1):104-122.

Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Ogawa M, Takahashi M, Matsutani M, et al (2020)

Obligate intracellular bacteria diversity in unfed Leptotrombidium scutellare larvae highlights novel bacterial endosymbionts of mites.

Microbiology and immunology, 64(1):1-9.

It is well known that the mite Leptotrombidium scutellare carries the pathogen of scrub typhus, Orientia tsutsugamushi. However, our understanding of other bacterial endosymbionts of mites is limited. This study investigated the diversity of the obligate intracellular bacteria carried by L. scutellare using 16S rRNA gene amplicon analysis with next-generation sequencing. The results showed that the detected bacteria were classified into the genera Rickettsia, Wolbachia, and Rickettsiella and an unknown genus of the order Rickettsiales. For further classification of the detected bacteria, a representative read that was most closely related to the assigned taxonomic classification was subjected to homology search and phylogenic analysis. The results showed that some bacteria of the genus Rickettsia were identical or very close to the human pathogens Rickettsia akari, Rickettsia aeschlimannii, Rickettsia felis, and Rickettsia australis. The genetic distance between the genus Wolbachia bacteria in the present study and in previous reports is highly indicative that the bacteria in the present study can be classified as a new taxon of Wolbachia. This study detected obligate intracellular bacteria from unfed mites; thus, the mites did not acquire bacteria from infected animals or any other infectious sources. Finally, the present study demonstrated that various and novel bacterial endosymbionts of mites, in addition to O. tsutsugamushi, might uniquely evolve with the host mites throughout overlapping generations of the mite life cycle. The roles of the bacteria in mites and their pathogenicity should be further examined in studies based on bacterial isolation.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Imai A, Ohtani M, Nara A, et al (2020)

The Lotus japonicus nucleoporin GLE1 is involved in symbiotic association with rhizobia.

Physiologia plantarum, 168(3):590-600.

Nucleoporins are components of the nuclear pore complexes, channels that regulate the transport of macromolecules between the nucleus and cytoplasm. The nucleoporin GLE1 (GLFG lethal1) functions in the export of messenger RNAs containing poly(A) tails from the nucleus into the cytoplasm. Here we investigated a mutant of the model legume Lotus japonicus that was defective in GLE1, which we designated Ljgle1. The growth of Ljgle1 was retarded under symbiotic association with rhizobia, and the nitrogen-fixation activities of the nodules were around one-third of those in the wild-type plant. The growth of Ljgle1 was not substantialy recovered by supplemention of combined nitrogen. Nodules formed on the Ljgle1 were smaller than those on the wild-type and colored faint pink. The numbers of infected cells of nodules on the Ljgle1 were smaller than on the wild-type plant, and the former cells remained undeveloped. Rhizobia in the cells of the Ljgle1 exhibited disordered forms, and the symbiosome membrane was closely attached to the bacterial membrane. These results indicate that GLE1 plays a distinct role in the symbiotic association between legumes and rhizobia.

RevDate: 2020-03-23

Kikuchi Y, Ohbayashi T, Jang S, et al (2020)

Burkholderia insecticola triggers midgut closure in the bean bug Riptortus pedestris to prevent secondary bacterial infections of midgut crypts.

The ISME journal pii:10.1038/s41396-020-0633-3 [Epub ahead of print].

In addition to abiotic triggers, biotic factors such as microbial symbionts can alter development of multicellular organisms. Symbiont-mediated morphogenesis is well-investigated in plants and marine invertebrates but rarely in insects despite the enormous diversity of insect-microbe symbioses. The bean bug Riptortus pedestris is associated with Burkholderia insecticola which are acquired from the environmental soil and housed in midgut crypts. To sort symbionts from soil microbiota, the bean bug develops a specific organ called the "constricted region" (CR), a narrow and symbiont-selective channel, located in the midgut immediately upstream of the crypt-bearing region. In this study, inoculation of fluorescent protein-labeled symbionts followed by spatiotemporal microscopic observations revealed that after the initial passage of symbionts through the CR, it closes within 12-18 h, blocking any potential subsequent infection events. The "midgut closure" developmental response was irreversible, even after symbiont removal from the crypts by antibiotics. It never occurred in aposymbiotic insects, nor in insects infected with nonsymbiotic bacteria or B. insecticola mutants unable to cross the CR. However, species of the genus Burkholderia and its outgroup Pandoraea that can pass the CR and partially colonize the midgut crypts induce the morphological alteration, suggesting that the molecular trigger signaling the midgut closure is conserved in this bacterial lineage. We propose that this drastic and quick alteration of the midgut morphology in response to symbiont infection is a mechanism for stabilizing the insect-microbe gut symbiosis and contributes to host-symbiont specificity in a symbiosis without vertical transmission.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Araújo JR, Tazi A, Burlen-Defranoux O, et al (2020)

Fermentation Products of Commensal Bacteria Alter Enterocyte Lipid Metabolism.

Cell host & microbe, 27(3):358-375.e7.

Despite the recognized capacity of the gut microbiota to regulate intestinal lipid metabolism, the role of specific commensal species remains undefined. Here, we aimed to understand the bacterial effectors and molecular mechanisms by which Lactobacillus paracasei and Escherichia coli regulate lipid metabolism in enterocytes. We show that L-lactate produced by L. paracasei inhibits chylomicron secretion from enterocytes and promotes lipid storage by a mechanism involving L-lactate absorption by enterocytes, its conversion to malonyl-CoA, and the subsequent inhibition of lipid beta-oxidation. In contrast, acetate produced by E. coli also inhibits chylomicron secretion by enterocytes but promotes lipid oxidation by a mechanism involving acetate absorption by enterocytes, its metabolism to acetyl-CoA and AMP, and the subsequent upregulation of the AMPK/PGC-1α/PPARα pathway. Our study opens perspectives for developing specific bacteria- and metabolite-based therapeutic interventions against obesity, atherosclerosis, and malnutrition by targeting lipid metabolism in enterocytes.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Zhu W, Winter MG, Spiga L, et al (2020)

Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis.

Cell host & microbe, 27(3):376-388.e8.

During short-lived perturbations, such as inflammation, the gut microbiota exhibits resilience and reverts to its original configuration. Although microbial access to the micronutrient iron is decreased during colitis, pathogens can scavenge iron by using siderophores. How commensal bacteria acquire iron during gut inflammation is incompletely understood. Curiously, the human commensal Bacteroides thetaiotaomicron does not produce siderophores but grows under iron-limiting conditions using enterobacterial siderophores. Using RNA-seq, we identify B. thetaiotaomicron genes that were upregulated during Salmonella-induced gut inflammation and were predicted to be involved in iron uptake. Mutants in the xusABC locus (BT2063-2065) were defective for xenosiderophore-mediated iron uptake in vitro. In the normal mouse gut, the XusABC system was dispensable, while a xusA mutant colonized poorly during colitis. This work identifies xenosiderophore utilization as a critical mechanism for B. thetaiotaomicron to sustain colonization during inflammation and suggests a mechanism of how interphylum iron metabolism contributes to gut microbiota resilience.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Parra-Tabla V, Angulo-Pérez D, Albor C, et al (2019)

The role of alien species on plant-floral visitor network structure in invaded communities.

PloS one, 14(11):e0218227.

The interactions between pairs of native and alien plants via shared use of pollinators have been widely studied. Community level studies however, are necessary in order to fully understand the factors and mechanisms that facilitate successful plant invasion, but these are still scarce. Specifically, few community level studies have considered how differences in invasion level (alien flower abundance), and degree of floral trait similarity between native and invasive species, mediate effects on native plant-pollinator communities. Here, we evaluated the role of alien species on overall plant-floral visitor network structure, and on species-level network parameters, across nine invaded coastal communities distributed along 205 km in Yucatán, México that vary in alien species richness and flower abundance. We further assessed the potential the role of alien plant species on plant-floral visitor network structure and robustness via computational simulation of native and invasive plant extinction scenarios. We did not find significant differences between native and alien species in their functional floral phenotypes or in their visitation rate and pollinator community composition in these invaded sites. Variation in the proportion of alien plant species and flower abundance across sites did not influence plant-pollinator network structure. Species-level network parameters (i.e., normalized degree and nestedness contribution) did not differ between native and alien species. Furthermore, our simulation analyses revealed that alien species are functionally equivalent to native species and contribute equally to network structure and robustness. Overall, our results suggest that high levels of floral trait similarity and pollinator use overlap may help facilitate the integration of alien species into native plant-pollinator networks. As a result, alien species may also play a similar role than that of natives in the structure and stability of native plant and pollinator communities in the studied coastal sand dune ecosystem.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Wei Y, X Xia (2019)

Unique Shine-Dalgarno Sequences in Cyanobacteria and Chloroplasts Reveal Evolutionary Differences in Their Translation Initiation.

Genome biology and evolution, 11(11):3194-3206.

Microorganisms require efficient translation to grow and replicate rapidly, and translation is often rate-limited by initiation. A prominent feature that facilitates translation initiation in bacteria is the Shine-Dalgarno (SD) sequence. However, there is much debate over its conservation in Cyanobacteria and in chloroplasts which presumably originated from endosymbiosis of ancient Cyanobacteria. Elucidating the utilization of SD sequences in Cyanobacteria and in chloroplasts is therefore important to understand whether 1) SD role in Cyanobacterial translation has been reduced prior to chloroplast endosymbiosis or 2) translation in Cyanobacteria and in plastid has been subjected to different evolutionary pressures. To test these alternatives, we employed genomic, proteomic, and transcriptomic data to trace differences in SD usage among Synechocystis species, Microcystis aeruginosa, cyanophages, Nicotiana tabacum chloroplast, and Arabidopsis thaliana chloroplast. We corrected their mis-annotated 16S rRNA 3' terminus using an RNA-Seq-based approach to determine their SD/anti-SD locational constraints using an improved measurement DtoStart. We found that cyanophages well-mimic Cyanobacteria in SD usage because both have been under the same selection pressure for SD-mediated initiation. Whereas chloroplasts lost this similarity because the need for SD-facilitated initiation has been reduced in plastids having much reduced genome size and different ribosomal proteins as a result of host-symbiont coevolution. Consequently, SD sequence significantly increases protein expression in Cyanobacteria but not in chloroplasts, and only Cyanobacterial genes compensate for a lack of SD sequence by having weaker secondary structures at the 5' UTR. Our results suggest different evolutionary pressures operate on translation initiation in Cyanobacteria and in chloroplast.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Zheng Y, Shen W, Bi J, et al (2019)

Small RNA analysis provides new insights into cytoplasmic incompatibility in Drosophila melanogaster induced by Wolbachia.

Journal of insect physiology, 118:103938.

Wolbachia is a genus of endosymbiotic bacteria that induce a wide range of effects on their insect hosts. Cytoplasmic incompatibility (CI) is the most common phenotype mediated by Wolbachia and results in embryonic lethality when Wolbachia-infected males mate with uninfected females. Studies have revealed that bacteria can regulate many cellular processes in their hosts using small non-coding RNAs, so we investigated the involvement of small RNAs (sRNAs) in CI. Comparison of sRNA libraries between Wolbachia-infected and uninfected Drosophila melanogaster testes revealed 18 novel microRNAs (miRNAs), of which 12 were expressed specifically in Wolbachia-infected flies and one specifically in Wolbachia-uninfected flies. Furthermore, ten miRNAs showed differential expression, with four upregulated and six downregulated in Wolbachia-infected flies. Of the upregulated miRNAs, nov-miR-12 exhibited the highest upregulation in the testes of D. melanogaster. We then identified pipsqueak (psq) as the target gene of nov-miR-12 with the greatest complementarity in its 3' untranslated region (UTR). Wolbachia infection was correlated with reduced psq expression in D. melanogaster, and luciferase assays demonstrated that nov-miR-12 could downregulate psq through binding to its 3'UTR region. Knockdown of psq in Wolbachia-free fly testes significantly reduced egg hatching rate and mimicked the cellular abnormalities of Wolbachia-induced CI in embryos, including asynchronous nuclear division, chromatin bridging, and chromatin fragmentation. These results suggest that Wolbachia may induce CI in insect hosts by miRNA-mediated changes in host gene expression. Moreover, these findings reveal a potential molecular strategy for elucidating the complex interactions between endosymbionts and their insect hosts, such as Wolbachia-driven CI.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Nakabachi A, M Fujikami (2019)

Concentration and distribution of diaphorin, and expression of diaphorin synthesis genes during Asian citrus psyllid development.

Journal of insect physiology, 118:103931.

The Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Sternorrhyncha: Psylloidea: Liviidae) is an important pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria); the causative agents of an incurable citrus disease known as huanglongbing or greening disease. D. citri possesses a vertically transmitted intracellular symbiont, Candidatus Profftella armatura (Betaproteobacteria), which produces diaphorin; a polyketide that is toxic to various eukaryotic organisms. Our previous study demonstrated that the total amount and average concentration of diaphorin in adult D. citri, when homogeneous distribution is assumed within the insect, are sufficient to exert inhibitory effects on fungi and insects, including the Asian lady beetle Harmonia axyridis (Coleoptera: Coccinellidae); one of the major predators of D. citri. However, diaphorin may be localized to a limited body area within D. citri, and its concentration may change during development. In the present study, to better understand the physiological and ecological function of diaphorin, we assessed the distribution of diaphorin within the D. citri body and analyzed concentrations of diaphorin in various developmental stages. Expression of genes involved in diaphorin synthesis was also analyzed. The results demonstrated that diaphorin is distributed widely in the D. citri body, which appears to be a prerequisite for effective deterrence of natural enemies. The concentration of diaphorin was shown to change significantly during the development of D. citri. It was highest in mature adults, followed by embryos and teneral adults, and lowest in nymphs. The lowest concentrations of diaphorin observed in nymphs are still presumed to be effective in deterring invasive natural enemies, including parasites, parasitoids, and entomopathogenic fungi. Quantitative RT-PCR indicated that amounts of transcripts for diaphorin synthesis genes dipP and dipT were at a minimum in embryos, increased during the nymphal period, and reached a maximum level just after adult eclosion. The alteration pattern of the amounts of transcripts for diaphorin synthesis genes appeared to partially disagree with that of the concentration of diaphorin. The present study provides new insights into the function of diaphorin, which is essential for further investigations that aim to improve the efficacy of D. citri biological control.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Thongpoo P, Tsai S, C Lin (2019)

Assessing the impacts of cryopreservation on the mitochondria of a thermotolerant Symbiodinium lineage: Implications for reef coral conservation.

Cryobiology, 89:96-99.

Earth's coral reefs are threatened by a barrage of anthropogenic insults, and cryopreservation-based conservation measures are warranted. Successfully cryopreserved corals could then thawed and out-planted on reefs when ocean temperatures stabilize. In such efforts, it will be necessary to also cryopreserve the photosynthetic dinoflagellates (genus Symbiodinium) that reside within the corals' gastrodermal cells. Given this need, Symbiodinium (clade D) cells were cryopreserved in 2 M propylene glycol by a two-step freezing protocol herein and then cultured for 42 days post-thaw. To gauge the effect of cryopreservation, mitochondrial DNA content and intracellular ATP concentration were assessed, and the former parameter was nearly 2-fold higher in freeze-thawed cells compared to controls after 14 days of post-thaw culture. In contrast, intracellular ATP concentration was relatively lower in freeze-thawed cells after seven days of post-thaw culture, though returned to control levels in samples cultured for 42 days post-thaw.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Jimenez-Jimenez S, Hashimoto K, Santana O, et al (2019)

Emerging roles of tetraspanins in plant inter-cellular and inter-kingdom communication.

Plant signaling & behavior, 14(4):e1581559.

Inter-cellular and inter-kingdom signaling systems of various levels of complexity regulate pathogenic and mutualistic interactions between bacteria, parasites, and fungi and animal and plant hosts. Inter-kingdom interactions between mutualistic bacteria such as rhizobia and legumes during nodulation and between fungi and plants during mycorrhizal associations, are characterized by the extensive exchange of molecular signals, which allow nitrogen and phosphate assimilation, respectively. A novel aspect of this signaling exchange is the existence of specific structures, the exosomes, that carry important molecules that shape the plant-pathogen interactions. Exosomes contain a wide array of molecules, such as lipids, proteins, messenger RNA, and microRNAs, that play important roles in cell-to-cell communication in animal and plant cells by affecting gene expression and other physiological activity in distant cells within the same organism (e.g., during cancer metastases and neuron injuries). In plant cells, it has been recently reported that exosomes go beyond organism boundaries and inhibit a pathogenic interaction in plants. Plant produce and send exosomes loaded with specific small miRNA which inhibit the pathogen infection, but the pathogen can also produce exosomes carrying pro-pathogenic proteins and microRNAs. Therefore, exosomes are the important bridge regulating the signal exchange. Exosomes are small membrane-bound vesicles derived from multivesicular bodies (MVBs), which carries selected cargos from the cytoplasm (protein, lipids, and microRNAs) and under certain circumstances, they fuse with the plasma membrane, releasing the small vesicles as cargo-carrying exosomes into the extracellular space during intercellular and inter-kingdom communication. Animal and plant proteomic studies have demonstrated that tetraspanin proteins are an integral part of exosome membranes, positioning tetraspanins as essential components for endosome organization, with key roles in membrane fusion, cell trafficking, and membrane recognition. We discuss the similarities and differences between animal tetraspanins and plant tetraspanins formed during plant-microbe interactions and their potential role in mutualistic communication.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Lugli GA, Duranti S, Albert K, et al (2019)

Unveiling Genomic Diversity among Members of the Species Bifidobacterium pseudolongum, a Widely Distributed Gut Commensal of the Animal Kingdom.

Applied and environmental microbiology, 85(8):.

Bifidobacteria are commensals of the animal gut and are commonly found in mammals, birds, and social insects. Specifically, strains of Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium longum, and Bifidobacterium pseudolongum are widely distributed in the mammalian gut. In this context, we investigated the genetic variability and metabolic abilities of the B. pseudolongum taxon, whose genomic characterization has so far not received much attention. Phylogenomic analysis of the genome sequences of 60 B. pseudolongum strains revealed that B. pseudolongum subsp. globosum and B. pseudolongum subsp. pseudolongum may actually represent two distinct bifidobacterial species. Furthermore, our analysis highlighted metabolic differences between members of these two subspecies. Moreover, comparative analyses of genetic strategies to prevent invasion of foreign DNA revealed that the B. pseudolongum subsp. globosum group exhibits greater genome plasticity. In fact, the obtained findings indicate that B. pseudolongum subsp. globosum is more adaptable to different ecological niches such as the mammalian and avian gut than is B. pseudolongum subsp. pseudolongumIMPORTANCE Currently, little information exists on the genetics of the B. pseudolongum taxon due to the limited number of sequenced genomes belonging to this species. In order to survey genome variability within this species and explore how members of this taxon evolved as commensals of the animal gut, we isolated and decoded the genomes of 51 newly isolated strains. Comparative genomics coupled with growth profiles on different carbohydrates has further provided insights concerning the genotype and phenotype of members of the B. pseudolongum taxon.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Eroglu C, Cimen H, Ulug D, et al (2019)

Acaricidal effect of cell-free supernatants from Xenorhabdus and Photorhabdus bacteria against Tetranychus urticae (Acari: Tetranychidae).

Journal of invertebrate pathology, 160:61-66.

The effects of secondary metabolites produced by the following symbiotic bacteria, Xenorhabdus szentirmaii, X. nematophila, X. bovienii, X. cabanillasii, Photorhabdus luminescens and P. temperata, associated with entomopathogenic nematodes, were investigated against various developmental stages of Tetranychus urticae (Acari: Tetranychidae) using cell-free bacterial supernatants in Petri dishes. In addition, the effects of the most active bacterial supernatant(s) found in Petri dish experiments were tested on T. urticae in pot experiments. All studies were conducted at 25 ± 1 °C temperature, 70 ± 5% relative humidity and a light cycle of 16 h in a climate room. The result of the Petri dish experiments showed that the supernatants had little or no effect on the egg stage, as less than 4% mortality was recorded. Depending on the bacterial supernatant, mortality in the other stages was 46-97% for larvae, 30-96% for protonymphs, 41-92% for deutonymphs, 92-100% for adult males and 46-93% for adult females. Control mortalities ranged from 1-7% for larvae, 2-9% for protonymphs, 4-10% for deutonymphs, 6-10% for adult males and 4-8% for adult females. Among supernatants tested, X. szentirmaii and X. nematophila were the most efficacious with mortality greater than 90% on the mobile stages of T. urticae. According to the results from pot experiments, the supernatants of X. szentirmaii and X. nematophila, singularly and in combination, significantly reduced the T. urticae population. However, the mixture of X. szentirmaii and X. nematophila supernatants did not increase efficiency to reduce T. urticae population compared to each supernatant alone. Further studies are warranted to find the active compound(s) in the supernatants of X. szentirmaii or and X. nematophila and assess whether the supernatant(s) has the potential of being a practical and economical control agent for T. urticae.

RevDate: 2020-03-23
CmpDate: 2020-03-23

De Jaegher K (2019)

Harsh environments: Multi-player cooperation with excludability and congestion.

Journal of theoretical biology, 460:18-36.

The common-enemy hypothesis of by-product mutualism proposes that organisms are more likely to cooperate when facing the common enemy of a harsher environment. Micro-foundations of this hypothesis have so far focused on the case where cooperation consists of the production of a pure public good. In this case, the effect of a harsher environment is ambiguous: not only a common-enemy effect is possible, but also an opposite, competing effect where the harsher environment reduces the probability of cooperation. This paper shows that unambiguous effects of a harsher environment are predicted when considering the realistic case where the collective good produced is excludable (in the sense that whether or not a player benefits from the collective good depends on whether or not he is contributing) and/or congestible (in the sense that the benefits the individual player obtains from the collective good are affected by the number of contributing players). In particular, the competing effect is systematically predicted for club goods, where defectors are excluded from the benefits of the collective good. A common-enemy effect is instead systematically predicted for charity goods, where cooperators are excluded from the benefits of the collective good. These effects are maintained for congestible club goods and for congestible charity goods. As the degree to which a collective good is excludable can be meaningfully compared across different instances of cooperation, these contrasting predictions for public good, charity goods and club goods yield testable hypotheses for the common-enemy hypothesis of by-product mutualism.

RevDate: 2020-03-22

Ferreira DA, da Silva TF, Pylro VS, et al (2020)

Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi.

Microbial ecology pii:10.1007/s00248-020-01502-z [Epub ahead of print].

Terrestrial plants establish symbiosis with arbuscular mycorrhizal fungi (AMF) to exchange water and nutrients. However, the extent to which soil biodiversity influences such association remains still unclear. Here, we manipulated the soil microbial diversity using a "dilution-to-extinction" approach in a controlled pot microcosm system and quantified the root length colonization of maize plants by the AMF Rhizophagus clarus. The experiment was performed by manipulating the soil microbiome within a native and foreign soil having distinct physicochemical properties. Overall, our data revealed significant positive correlations between the soil microbial diversity and AMF colonization. Most importantly, this finding opposes the diversity-invasibility hypothesis and highlights for a potential overall helper effect of the soil biodiversity on plant-AMF symbiosis.

RevDate: 2020-03-21

Botou M, Yalelis V, Lazou P, et al (2020)

Specificity profile of NAT/NCS2 purine transporters in Sinorhizobium (Ensifer) meliloti.

Molecular microbiology [Epub ahead of print].

Sinorhizobium (Ensifer) meliloti is a model example of a soil alpha-proteobacterium which induces the formation of nitrogen-fixing symbiotic nodules on legume roots. In contrast to all other rhizobacterial species, S. meliloti contains multiple homologs of nucleobase transporter genes that belong to NAT/NCS2 family (Nucleobase-Ascorbate Transporter/Nucleobase-Cation Symporter-2). We analyzed functionally all (six) relevant homologs of S. meliloti 1021 using Escherichia coli K-12 as a host and found that five of them are high-affinity transporters for xanthine (SmLL9), uric acid (SmLL8, SmLL9, SmX28), adenine (SmVC3, SmYE1), guanine (SmVC3) or hypoxanthine (SmVC3). Detailed analysis of substrate profiles showed that two of these transporters display enlarged specificity (SmLL9, SmVC3). SmLL9 is closely related in sequence with the xanthine-specific XanQ of E. coli. We subjected SmLL9 to rationally designed site-directed mutagenesis and found that the role of key binding-site residues of XanQ is conserved in SmLL9 whereas a single amino-acid change (S93N) converts the xanthine/uric-acid transporter SmLL9 to a xanthine-preferring variant, due to disruption of an essential hydrogen bond with the C8 oxygen of uric acid. The results highlight the presence of several different purine nucleobase transporters in S. meliloti and imply that purine transport might be important in nodule symbiosis involving S. meliloti.

RevDate: 2020-03-21

Dolgikh EA, Kusakin PG, Kitaeva AB, et al (2020)

Mutational analysis indicates that abnormalities in rhizobial infection and subsequent plant cell and bacteroid differentiation in pea (Pisum sativum) nodules coincide with abnormal cytokinin responses and localization.

Annals of botany pii:5810737 [Epub ahead of print].

BACKGROUND AND AIMS: Recent findings indicate that Nod factor signalling is tightly interconnected with phytohormonal regulation that affects the development of nodules. Since the mechanisms of this interaction are still far from understood, here the distribution of cytokinin and auxin in pea (Pisum sativum) nodules was investigated. In addition, the effect of certain mutations blocking rhizobial infection and subsequent plant cell and bacteroid differentiation on cytokinin distribution in nodules was analysed.

METHODS: Patterns of cytokinin and auxin in pea nodules were profiled using both responsive genetic constructs and antibodies.

KEY RESULTS: In wild-type nodules, cytokinins were found in the meristem, infection zone and apical part of the nitrogen fixation zone, whereas auxin localization was restricted to the meristem and peripheral tissues. We found significantly altered cytokinin distribution in sym33 and sym40 pea mutants defective in IPD3/CYCLOPS and EFD transcription factors, respectively. In the sym33 mutants impaired in bacterial accommodation and subsequent nodule differentiation, cytokinin localization was mostly limited to the meristem. In addition, we found significantly decreased expression of LOG1 and A-type RR11 as well as KNOX3 and NIN genes in the sym33 mutants, which correlated with low cellular cytokinin levels. In the sym40 mutant, cytokinins were detected in the nodule infection zone but, in contrast to the wild type, they were absent in infection droplets.

CONCLUSIONS: In conclusion, our findings suggest that enhanced cytokinin accumulation during the late stages of symbiosis development may be associated with bacterial penetration into the plant cells and subsequent plant cell and bacteroid differentiation.

RevDate: 2020-03-20

Feng S, Liu F, Zhu S, et al (2020)

Performance of a microalgal-bacterial consortium system for the treatment of dairy-derived liquid digestate and biomass production.

Bioresource technology, 306:123101 pii:S0960-8524(20)30370-9 [Epub ahead of print].

To enhance the treatment performance of dairy-derived liquid digestate (DLD) using microalgal-bacterial consortium system composed of Chlorella vulgaris and indigenous bacteria (CV), activated sludge was introduced to form a new microalgal-bacterial consortium system (Co-culture). The activated sludge shortened the lag phase and increased the specific growth rate of C. vulgaris (0.56 d-1). The biomass yield in the Co-culture was 2.72 g L-1, which was lower than that in the CV (3.24 g L-1), but the Co-culture had an improved COD (chemical oxygen demand) removal (25.26%) compared to the CV (13.59%). Quantitative PCR and metagenomic analyses demonstrated that microalgae also promoted bacterial growth, but influenced differently on the bacterial communities of indigenous bacteria and activated sludge. Compared with indigenous bacteria, activated sludge was more prone to forming a favorable symbiosis with C. vulgaris. These findings contribute to the construction of efficient microalgal-bacterial consortium system in wastewater treatment.

RevDate: 2020-03-20

Souza SCR, Souza LA, Schiavinato MA, et al (2020)

Zinc toxicity in seedlings of three trees from the Fabaceae associated with arbuscular mycorrhizal fungi.

Ecotoxicology and environmental safety, 195:110450 pii:S0147-6513(20)30289-X [Epub ahead of print].

Due to diverse human activities zinc (Zn) may reach phytotoxic levels in the soil. Here, we evaluated the differential sensibility of three Brazilian tree species from the Fabaceae to increasing soil Zn concentrations and its physiological response to cope with excess Zn. A greenhouse experiment was conducted with the species: Mimosa caesalpiniaefolia, Erythrina speciosa and Schizolobium parahyba, and the addition of 0, 200, 400 and 600 mg Zn kg-1 to the soil. Plants were harvested after three months of cultivation, and growth, root symbiosis, biochemical markers and elemental composition were analyzed. Soil Zn addition reduced seedling growth, irrespective of the species, with a strong reduction in M. caesalpiniaefolia. Regarding root symbiosis, in N2-fixing species, nitrogenase activity was reduced by the highest Zn concentrations. Zn addition caused plants nutritional imbalances, mainly in roots. The content of photosynthetic pigments in leaves decreased up to 40%, suggesting that high Zn contents interfered with its biosynthesis, and altered the content of foliar polyamines and free amino acids, depending on the species and the soil Zn concentration. Zn toxicity in M. caesalpiniaefolia plants was observed at available soil Zn concentrations greater than 100 mg kg-1 (DTPA-extractable), being the most sensitive species and E. speciosa was moderately sensitive. S. parahyba was a moderately tolerant species, which seems to be related to polyamines accumulation and to mycorrhizal association. This last species has the potential for revegetation of areas with moderately high soil Zn concentration and for phytostabilization purposes. Future research evaluating the tolerance to multiple metal stress under field conditions should confirm S. parayba suitability in Zn contaminated areas of tropical regions.

RevDate: 2020-03-20

Raudenska M, Gumulec J, Balvan J, et al (2020)

Caveolin-1 in oncogenic metabolic symbiosis.

International journal of cancer [Epub ahead of print].

Metabolic phenotypes of cancer cells are heterogeneous and flexible as a tumour mass is a hurriedly evolving system capable of constant adaptation to oxygen and nutrient availability. The exact type of cancer metabolism arises from the combined effects of factors intrinsic to the cancer cells and factors proposed by the tumour microenvironment. As a result, a condition termed oncogenic metabolic symbiosis in which components of the tumour microenvironment (TME) promote tumour growth often occurs. Understanding how oncogenic metabolic symbiosis emerges and evolves is crucial for perceiving tumorigenesis. The process by which tumour cells reprogram their TME involves many mechanisms, including changes in intercellular communication, alterations in metabolic phenotypes of TME cells, and rearrangement of the extracellular matrix. It is possible that one molecule with a pleiotropic effect such as Caveolin-1 may affect many of these pathways. Here, we discuss the significance of Caveolin-1 in establishing metabolic symbiosis in TME. This article is protected by copyright. All rights reserved.

RevDate: 2020-03-20
CmpDate: 2020-03-20

Sanchez JA, López-Gallego E, M La-Spina (2020)

The impact of ant mutualistic and antagonistic interactions on the population dynamics of sap-sucking hemipterans in pear orchards.

Pest management science, 76(4):1422-1434.

BACKGROUND: Ants are known to establish antagonistic and mutualistic interactions with honeydew-producing hemipterans, depending on the species involved and the ecological context. The aim of this work was to infer the role that such interactions play in the population dynamics of psyllids and aphids in pear orchards. Interactions were inferred from field data and periodical sampling along a 4-year study, and from interaction assays performed under controlled conditions.

RESULTS: A decline in the abundance of the pear psyllid (Cacopsylla pyri L.), parallel to an increase in the abundance of aphids, was registered over 4 years. Ants were the dominant species, representing about 90% of the predators, followed by spiders and predatory hemipterans (namely Pilophorus gallicus Remane). Ant abundance increased over the 4 years, matching the population dynamics of aphids. Evidence of mutualistic and antagonistic interactions were found for ant-aphid and ant-psyllid, respectively: (i) ant-aphid abundances on pear trees were positively correlated, and ants reduced predation on aphids by generalist predators, and (ii) ant-psyllid abundances were negatively correlated, ants have a negative effect on the psyllid population growth rates, and ants were found to prey on the psyllid.

CONCLUSIONS: Because of their high abundance in comparison with other predators and the mutualistic-antagonistic relationships with aphids-psyllids, ants are considered to be the principal force behind the decline of pear psyllid populations and the increase in aphid numbers. In summary, ants contribute positively to biological control by the suppresion of pests (i.e. the psyllid) which are more damaging than those they protect (i.e. aphids). © 2019 Society of Chemical Industry.

RevDate: 2020-03-19

Brahme RG, Godbole SV, Gangakhedkar RR, et al (2019)

Evaluation of key survey components of bio-behavioral surveillance among HIV high-risk subpopulation in Western India.

Indian journal of public health, 63(4):305-312.

Background: High-quality data are of prime importance in any health survey because survey data are considered as a gold standard for nationally representative data. The quality of data collection largely depends on the design of the questionnaire, training, and skills of the interviewer.

Objectives: In the present study, we tried to evaluate three key components, such as questionnaire design, human resource and training of the field staff for Integrated Biological and Behavioural Surveillance carried out among the HIV high-risk subpopulation.

Methods: A mixed-methods approach was used. Qualitative and quantitative data collection was carried out in the year 2015 with cross-sectional survey design in western states of India. The in-depth interviews of 10 stakeholders, structured interviews of the survey respondents (n = 560), and field investigators (n = 71) were conducted. Data triangulation was used to find out the concurrence of the qualitative and quantitative data.

Results: Comprehensive and standardized survey questionnaire, structured training agenda, and strategic preparation for recruiting human resources were the overall strengths of the survey. However, during the implementation of the survey, there were some difficulties reported in data collection process. Overall, the respondents and investigators felt that the questionnaire was long and exhaustive. Difficulties were faced while collecting data on sexual history. The field staffs were not adequately experienced to work with sensitive population.

Conclusions: In order to have accurate, reliable data, especially on sexual behavior; emphasis should be given on simple questionnaire with the use of community-friendly language, skilled and experienced interviewers for data collection, and extensive field training.

RevDate: 2020-03-19

Hamilton LA, ML Behal (2020)

Altering Routine Intensive Care Unit Practices to Support Commensalism.

Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition [Epub ahead of print].

The gastrointestinal (GI) tract consists of trillions of organisms that support multiple functions in the body, from immunity, digestion, and absorption to drug metabolism. These microbes form an overall collection of microorganisms that form the body's microbiome. In critical illness, many of these functions are aberrant, and the microbiome is altered, leading to untoward effects. Some of the most common medications received by patients include antibiotics and proton pump inhibitors, which affect particular changes in the microbiome. In addition, patients receiving prolonged enteral and parenteral nutrition experience changes in the microbiological composition and diversity of their GI tracts. Research is ongoing to characterize the crosstalk between the microbiome and immune function as targets for drug and nutrition therapy.

RevDate: 2020-03-19

Banerjee J, Dhas Y, N Mishra (2020)

HOMA-Adiponectin Closely Associates with Cardiometabolic Risk Markers in Middle-Aged Indians with Metabolic Syndrome.

Experimental and clinical endocrinology & diabetes : official journal, German Society of Endocrinology [and] German Diabetes Association [Epub ahead of print].

BACKGROUND: Unhealthy dietary habits and sedentary lifestyles have raised alarming concerns for the rising prevalence of metabolic syndrome (MetS) and associated cardiometabolic risk among Indians at an early age. Insulin resistance and adiposity are the important risk factors associated with MetS. The present study aimed to investigate the relationship between a modified marker of insulin resistance (homeostatic model assessment-adiponectin (HOMA-AD)) and cardiometabolic risk among middle-aged Indians.

METHODS: The study comprised of 144 subjects of age-group 31-50 years, where 83 subjects were diagnosed for MetS according to the guidelines given by the International Diabetes Federation. We measured cardiometabolic risk indicators such as fasting blood glucose (FPG), fasting plasma insulin (FPI), homeostatic model assessment- insulin resistance (HOMA-IR), adiponectin, high sensitivity C-reactive protein (hs-CRP), oxidized LDL (oxLDL), monocyte chemoattractant protein-1 (MCP-1), and atherogenic index, among others. We calculated HOMA-AD by the formula: [FPG (mmol/l) × FPI (µIU/ml)] / [22.5 × Adiponectin (µg/ml)].

RESULTS: HOMA-IR and HOMA-AD were highly increased (p<0.001) in the MetS subjects than controls. Adiponectin was significantly (p<0.01) lower whereas cardiac risk markers such as atherogenic index, hs-CRP, oxLDL, and MCP-1 were significantly (p<0.01) elevated in MetS group than controls. Linear regression showed positive and significant associations (p<0.01) of HOMA-AD with all the cardiometabolic risk markers except MCP-1. HOMA-AD showed higher AUC (0.806) than HOMA-IR (0.791) for predicting MetS.

CONCLUSION: HOMA-AD could be a surrogate adipokine-based marker correlated significantly with components of MetS and cardiometabolic risk indicators. It appeared to be a better predictor of MetS among middle-aged Indians than HOMA-IR.

RevDate: 2020-03-19

Fallon AM (2020)

Computational evidence for antitoxins associated with RelE/ParE, RatA, Fic, and AbiEii-family toxins in Wolbachia genomes.

Molecular genetics and genomics : MGG pii:10.1007/s00438-020-01662-0 [Epub ahead of print].

Wolbachia is an obligate intracellular Gram-negative alpha-proteobacterium that has diverse effects on reproduction of arthropod hosts, including cytoplasmic incompatibility, male killing, feminization, and parthenogenesis. Some of these effects have important potential for control of insect pests, including mosquitoes that vector pathogens of humans. In mosquitoes, and in most other arthropods, elimination of Wolbachia by antibiotic treatment has no effect on host survival and reverses the Wolbachia-associated phenotype. Elimination of Wolbachia strain wFol, which enables parthenogenetic reproduction of the Collembolan, Folsomia candida, would result in population extinction. However, F. candida adults remain viable and resume reproduction when antibiotics are removed, suggesting that wFol survives antibiotic treatment in a quiescent persister state similar to that induced by chromosomally encoded toxin-antitoxin (TA) modules in free-living bacteria. Computational approaches were used to document the presence of antitoxin genes upstream of Wolbachia RelE/ParE, Fic, and AbiEii toxin genes. Moreover, this analysis revealed that Wolbachia RatA toxin is encoded by a single copy gene associated with an ssrS noncoding RNA gene. Documentation of potentially functional TA modules expands our understanding of the metabolic capabilities of Wolbachia, and provides an explanation for variable and sometimes contradictory results of antibiotic treatments. The presence of chromosomal TA modules in Wolbachia genomes suggests that wFol, and potentially other strains of Wolbachia, can enter a quiescent persister state.

RevDate: 2020-03-19
CmpDate: 2020-03-19

Thirkell TJ, Pastok D, KJ Field (2020)

Carbon for nutrient exchange between arbuscular mycorrhizal fungi and wheat varies according to cultivar and changes in atmospheric carbon dioxide concentration.

Global change biology, 26(3):1725-1738.

Arbuscular mycorrhizal fungi (AMF) form symbioses with most crops, potentially improving their nutrient assimilation and growth. The effects of cultivar and atmospheric CO2 concentration ([CO2 ]) on wheat-AMF carbon-for-nutrient exchange remain critical knowledge gaps in the exploitation of AMF for future sustainable agricultural practices within the context of global climate change. We used stable and radioisotope tracers (15 N, 33 P, 14 C) to quantify AMF-mediated nutrient uptake and fungal acquisition of plant carbon in three wheat (Triticum aestivum L.) cultivars. We grew plants under current ambient (440 ppm) and projected future atmospheric CO2 concentrations (800 ppm). We found significant 15 N transfer from fungus to plant in all cultivars, and cultivar-specific differences in total N content. There was a trend for reduced N uptake under elevated atmospheric [CO2 ]. Similarly, 33 P uptake via AMF was affected by cultivar and atmospheric [CO2 ]. Total P uptake varied significantly among wheat cultivars and was greater at the future than current atmospheric [CO2 ]. We found limited evidence of cultivar or atmospheric [CO2 ] effects on plant-fixed carbon transfer to the mycorrhizal fungi. Our results suggest that AMF will continue to provide a route for nutrient uptake by wheat in the future, despite predicted rises in atmospheric [CO2 ]. Consideration should therefore be paid to cultivar-specific AMF receptivity and function in the development of climate smart germplasm for the future.

RevDate: 2020-03-19
CmpDate: 2020-03-19

Yamada T, Hino S, Iijima H, et al (2019)

Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis.

EBioMedicine, 48:513-525.

BACKGROUND: The dysbiosis of gut microbiota has been implicated in the pathogenesis of inflammatory bowel diseases; however, the underlying mechanisms have not yet been elucidated. Heavily glycosylated mucin establishes a first-line barrier against pathogens and serves as a niche for microbial growth.

METHODS: To elucidate relationships among dysbiosis, abnormal mucin utilisation, and microbial metabolic dysfunction, we analysed short-chain fatty acids (SCFAs) and mucin components in stool samples of 40 healthy subjects, 49 ulcerative colitis (UC) patients, and 44 Crohn's disease (CD) patients from Japan.

FINDINGS: Levels of n-butyrate were significantly lower in stools of both CD and UC patients than in stools of healthy subjects. Correlation analysis identified seven bacterial species positively correlated with n-butyrate levels; the major n-butyrate producer, Faecalibacterium prausnitzii, was particularly underrepresented in CD patients, but not in UC patients. In UC patients, there were inverse correlations between mucin O-glycan levels and the production of SCFAs, such as n-butyrate, suggesting that mucin O-glycans serve as an endogenous fermentation substrate for n-butyrate production. Indeed, mucin-fed rodents exhibited enhanced n-butyrate production, leading to the expansion of RORgt+Treg cells and IgA-producing cells in colonic lamina propria. Microbial utilisation of mucin-associated O-glycans was significantly reduced in n-butyrate-deficient UC patients.

INTERPRETATION: Mucin O-glycans facilitate symbiosynthesis of n-butyrate by gut microbiota. Abnormal mucin utilisation may lead to reduced n-butyrate production in UC patients. FUND: Japan Society for the Promotion of Science, Health Labour Sciences Research Grant, AMED-Crest, AMED, Yakult Foundation, Keio Gijuku Academic Development Funds, The Aashi Grass Foundation, and The Canon Foundation.

RevDate: 2020-03-18

Xiao A, Yu H, Fan Y, et al (2020)

Transcriptional regulation of NIN expression by IPN2 is required for root nodule symbiosis in Lotus japonicus.

The New phytologist [Epub ahead of print].

Expression of Nodule Inception (NIN) is essential for initiation of legume-rhizobial symbiosis. An existing model regarding the regulation of NIN expression involves two GRAS transcription factors, i.e., NSP1 and NSP2. NSP2 forms a complex with NSP1 to directly bind to NIN promoter. However, rhizobial treatment-induced NIN expression could still be detected in the nsp1 mutant plants, suggesting other proteins must be involved in regulation of NIN expression. A combination of molecular, biochemical and genetic analyses was used to investigate the molecular basis of IPN2 in regulating root development and NIN expression in L. japonicus. In this study, we identified that IPN2 is a close homolog of Arabidopsis APL with essential function in root development. However, Lotus IPN2 has a different expression pattern compared with Arabidopsis APL gene. IPN2 binds to the IPN2-responsive cis element (IPN2-RE) of NIN promoter and activates NIN expression. IPN2,NSP1, and NSP2 form a protein complex to directly target NIN promoter and activate NIN expression in the legume-rhizobial symbiosis. Our data refine the regulatory model of NIN expression, i.e., NSP2 works together with NSP1 and IPN2 to activate NIN gene allowing nodulation in L. japonicus.

RevDate: 2020-03-18

Shi Y, Zhang Z, Wen Y, et al (2020)

RNA sequencing-associated study identifies GmDRR1 as positively regulating the establishment of symbiosis in soybean.

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

In the soybean (Glycine max)-rhizobium interactions, the type III secretion system (T3SS) of the rhizobium plays a key role in regulating host specificity. However, the lack of information on the role of T3SS in signaling networks limits our understanding of symbiosis. Here, we conducted an RNA sequencing analysis of three soybean chromosome segment substituted lines, one female parent and two derived lines with different chromosome substituted segments of wild soybean and opposite nodulation patterns. By analyzing chromosome-linked differentially expressed genes in the substituted segments and quantitative trail loci-assisted selection in the substituted segment region, genes that may respond to type III effectors to mediate plant immunity-related signaling were identified. To narrow down the candidate genes number, QTL assistant was used to identify the candidate region consistent with the substituted segments. Furthermore, one candidate gene, GmDRR1, was identified in the substituted segment. To investigate the role of GmDRR1 in symbiosis establishment, GmDRR1-overexpression and RNA interference soybean lines were constructed. The nodule number increased in the former compared with in wild type soybean. Additionally, the T3SS-regulated effectors appeared to interact with the GmDDR1 signaling pathway. This finding will allow the detection of T3SS-regulated effectors involved in legume-rhizobium interactions.

RevDate: 2020-03-18

Stavru F, Riemer J, Jex A, et al (2020)

When bacteria meet mitochondria: The strange case of the tick symbiont Midichloria mitochondrii†.

Cellular microbiology, 22(4):e13189.

Mitochondria are key eukaryotic organelles that perform several essential functions. Not surprisingly, many intracellular bacteria directly or indirectly target mitochondria, interfering with innate immunity, energy production or apoptosis, to make the host cell a more hospitable niche for bacterial replication. The alphaproteobacterium Midichloria mitochondrii has taken mitochondrial targeting to another level by physically colonising mitochondria, as shown by transmission electron micrographs of bacteria residing in the mitochondrial intermembrane space. This unique localization provokes a number of questions around the mechanisms allowing, and reasons driving intramitochondrial tropism. We suggest possible scenarios that could lead to this peculiar localization and hypothesize potential costs and benefits of mitochondrial colonisation for the bacterium and its host.

RevDate: 2020-03-18

Hereme R, Morales-Navarro S, Ballesteros G, et al (2020)

Fungal Endophytes Exert Positive Effects on Colobanthus quitensis Under Water Stress but Neutral Under a Projected Climate Change Scenario in Antarctica.

Frontiers in microbiology, 11:264.

Functional symbiosis is considered one of the successful mechanisms by which plants that inhabit extreme environment improve their ability to tolerate different types of stress. One of the most conspicuous type of symbiosis is the endophyticism. This interaction has been noted to play a role in the adaptation of the native vascular plant Colobanthus quitensis to the stressful environments of Antarctica, characterized by low temperatures and extreme aridity. Projections of climate change for this ecosystem indicate that abiotic conditions will be less limiting due to an increase in temperature and water availability in the soil. Due to this decrease in stress induced by the climate change, it has been suggested that the positive role of fungal endophytes on performance of C. quitensis plants would decrease. In this study, we evaluated the role of endophytic fungi on osmoprotective molecules (sugar production, proline, oxidative stress) and gene expression (CqNCED1, CqABCG25, and CqRD22) as well as physiological traits (stomatal opening, net photosynthesis, and stomatal conductance) in individuals of C. quitensis. Individual plants of C. quitensis with (E+) and without (E-) endophytic fungi were exposed to simulated conditions of increased water availability (W+), having the current limiting water condition (W-) in Antarctica as control. The results reveal an endophyte-mediated lower oxidative stress, higher production of sugars and proline in plants. In addition, E+ plants showed differential expressions in genes related with drought stress response, which was more evident in W- than in W+. These parameters corresponded with increased physiological mechanisms such as higher net photosynthesis, stomatal opening and conductance under presence of endophytes (E+) as well as the projected water condition (W+) for Antarctica. These results suggest that the presence of fungal endophytes plays a positive role in favoring tolerance to drought in C. quitensis. However, this positive role would be diminished if the stress factor is relaxed, suggesting that the role of endophytes could be less important under a future scenario of climate change in Antarctica with higher soil water availability.

RevDate: 2020-03-18

Ortega-Ortega Y, Carrasco-Castilla J, Juárez-Verdayes MA, et al (2020)

Actin Depolymerizing Factor Modulates Rhizobial Infection and Nodule Organogenesis in Common Bean.

International journal of molecular sciences, 21(6): pii:ijms21061970.

Actin plays a critical role in the rhizobium-legume symbiosis. Cytoskeletal rearrangements and changes in actin occur in response to Nod factors secreted by rhizobia during symbiotic interactions with legumes. These cytoskeletal rearrangements are mediated by diverse actin-binding proteins, such as actin depolymerization factors (ADFs). We examined the function of an ADF in the Phaseolus vulgaris-rhizobia symbiotic interaction (PvADFE). PvADFE was preferentially expressed in rhizobia-inoculated roots and nodules. PvADFE promoter activity was associated with root hairs harbouring growing infection threads, cortical cell divisions beneath root hairs, and vascular bundles in mature nodules. Silencing of PvADFE using RNA interference increased the number of infection threads in the transgenic roots, resulting in increased nodule number, nitrogen fixation activity, and average nodule diameter. Conversely, overexpression of PvADFE reduced the nodule number, nitrogen fixation activity, average nodule diameter, as well as NODULE INCEPTION (NIN) and EARLY NODULIN2 (ENOD2) transcript accumulation. Hence, changes in ADFE transcript levels affect rhizobial infection and nodulation, suggesting that ADFE is fine-tuning these processes.

RevDate: 2020-03-18
CmpDate: 2020-03-18

Sarath E, Ezaki K, Sasaki T, et al (2020)

Morphological characterization of domatium development in Callicarpa saccata.

Annals of botany, 125(3):521-532.

BACKGROUND AND AIMS: Domatia are plant structures within which organisms reside. Callicarpa saccata (Lamiaceae) is the sole myrmecophyte, or 'ant plant', that develops foliar (leaf-borne) myrmeco-domatia in this genus. In this work we examined domatium development in C. saccata to understand the developmental processes behind pouch-like domatia.

METHODS: Scanning electron microscopy, sectioning and microcomputed tomography were carried out to compare the leaves of C. saccata with those of the closely related but domatia-less myrmecophyte Callicarpa subaequalis, both under cultivation without ants.

KEY RESULTS: Callicarpa saccata domatia are formed as a result of excess cell proliferation at the blade/petiole junctions of leaf primordia. Blade/petiole junctions are important meristematic sites in simple leaf organogenesis. We also found that the mesophyll tissue of domatia does not clearly differentiate into palisade and spongy layers.

CONCLUSIONS: Rather than curling of the leaf margins, a perturbation of the normal functioning of the blade/petiole junction results in the formation of domatium tissue. Excess cell proliferation warps the shape of the blade and disturbs the development of the proximal-distal axis. This process leads to the generation of distinct structures that facilitate interaction between C. saccata and ants.

RevDate: 2020-03-17

van Winden JF, Talbot HM, Reichart GJ, et al (2020)

Influence of temperature on the δ13 C values and distribution of methanotroph-related hopanoids in Sphagnum-dominated peat bogs.

Geobiology [Epub ahead of print].

Methane emissions from peat bogs are mitigated by methanotrophs, which live in symbiosis with peat moss (e.g. Sphagnum). Here, we investigate the influence of temperature and resultant changes in methane fluxes on Sphagnum and methanotroph-related biomarkers, evaluating their potential as proxies in ancient bogs. A pulse-chase experiment using 13 C-labelled methane in the field clearly showed label uptake in diploptene, a biomarker for methanotrophs, demonstrating in situ methanotrophic activity in Sphagnum under natural conditions. Peat cores containing live Sphagnum were incubated at 5, 10, 15, 20 and 25°C for two months, causing differences in net methane fluxes. The natural δ13 C values of diploptene extracted from Sphagnum showed a strong correlation with temperature and methane production. The δ13 C values ranged from -34‰ at 5°C to -41‰ at 25°C. These results are best explained by enhanced expression of the methanotrophic enzymatic isotope effect at higher methane concentrations. Hence, δ13 C values of diploptene, or its diagenetic products, potentially provide a useful tool to assess methanotrophic activity in past environments. Increased methane fluxes towards Sphagnum did not affect δ13 C values of bulk Sphagnum and its specific marker, the C23 n-alkane. The concentration of methanotroph-specific bacteriohopanepolyols (BHPs), aminobacteriohopanetetrol (aminotetrol, characteristic for type II and to a lesser extent type I methanotrophs) and aminobacteriohopanepentol (aminopentol, a marker for type I methanotrophs) showed a non-linear response to increased methane fluxes, with relatively high abundances at 25°C compared to those at 20°C or below. Aminotetrol was more abundant than aminopentol, in contrast to similar abundances of aminotetrol and aminopentol in fresh Sphagnum. This probably indicates that type II methanotrophs became prevalent under the experimental conditions relative to type I methanotrophs. Even though BHP concentrations may not directly reflect bacterial activity, they may provide insight into the presence of different types of methanotrophs.

RevDate: 2020-03-16

Cavassim MIA, Moeskjær S, Moslemi C, et al (2020)

Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

Microbial genomics [Epub ahead of print].

Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression using de novo assembly of 196 Rhizobium leguminosarum sv. trifolii genomes. The 196 strains constituted a five-species complex, and we calculated introgression scores based on gene-tree traversal to identify 171 genes that frequently cross species boundaries. Rather than relying on the gene order of a single reference strain, we clustered the introgressing genes into four blocks based on population structure-corrected linkage disequilibrium patterns. The two largest blocks comprised 125 genes and included the symbiosis genes, a smaller block contained 43 mainly chromosomal genes, and the last block consisted of three genes with variable genomic location. All introgression events were likely mediated by conjugation, but only the genes in the symbiosis linkage blocks displayed overrepresentation of distinct, high-frequency haplotypes. The three genes in the last block were core genes essential for symbiosis that had, in some cases, been mobilized on symbiosis plasmids. Inter-species introgression is thus not limited to symbiosis genes and plasmids, but other cases are infrequent and show distinct selection signatures.

RevDate: 2020-03-16

Dovrat G, Bakhshian H, Masci T, et al (2020)

The nitrogen economic spectrum of legume stoichiometry and fixation strategy.

The New phytologist [Epub ahead of print].

Leaf nitrogen concentration often is higher in leguminous plants, which associate with dinitrogen-fixing bacteria, compared to non-legume plants. However, the range of nitrogen concentrations in legumes is wide, likely related to the range of nitrogen fixation strategies. We evaluated how carbon and nitrogen allocation to roots, stems and leaves is influenced by the type of strategy of nitrogen fixation regulation. We grew herbaceous annual legumes (Medicago truncatula, Hymenocarpus circinnatus, and Vicia palaestina) under two nitrogen availability treatments (none/sufficient), with and without bacterial inoculation. We found facultative downregulation of the rate of nitrogen fixation when nitrogen was available in H. circinnatus, and an obligate similar fixation rate in both nitrogen treatments in M. truncatula and V. palaestina. Uninoculated plants invested more biomass in roots and contained lower nitrogen concentrations. However, nitrogen concentration in the entire plant and in the leaves was lower and more plastic in the species with a facultative fixation strategy, whereas species with an obligate fixation strategy also maintained high nitrogen concentrations. Our results suggest a suite of functional traits associated with the strategies of allocation and symbiotic nitrogen fixation. This suite of traits probably shapes successional and functional niches of different leguminous species in specious plant communities.

RevDate: 2020-03-16

Harper CJ, Taylor EL, M Krings (2020)

Filamentous cyanobacteria preserved in masses of fungal hyphae from the Triassic of Antarctica.

PeerJ, 8:e8660 pii:8660.

Permineralized peat from the central Transantarctic Mountains of Antarctica has provided a wealth of information on plant and fungal diversity in Middle Triassic high-latitude forest paleoecosystems; however, there are no reports as yet of algae or cyanobacteria. The first record of a fossil filamentous cyanobacterium in this peat consists of wide, uniseriate trichomes composed of discoid cells up to 25 µm wide, and enveloped in a distinct sheath. Filament morphology, structurally preserved by permineralization and mineral replacement, corresponds to the fossil genus Palaeo-lyngbya, a predominantly Precambrian equivalent of the extant Lyngbya sensu lato (Oscillatoriaceae, Oscillatoriales). Specimens occur exclusively in masses of interwoven hyphae produced by the fungus Endochaetophora antarctica, suggesting that a special micro-environmental setting was required to preserve the filaments. Whether some form of symbiotic relationship existed between the fungus and cyanobacterium remains unknown.

RevDate: 2020-03-16

Das D, Torabi S, Chapman P, et al (2020)

A Flexible, Low-Cost Hydroponic Co-Cultivation System for Studying Arbuscular Mycorrhiza Symbiosis.

Frontiers in plant science, 11:63.

Arbuscular mycorrhiza (AM) is a widespread symbiosis between plant roots and fungi of the Glomeromycotina, which improves nutrient uptake by plants. The molecular mechanisms underlying development and function of the symbiosis are subject to increasing research activity. Since AM occurs in the soil, most studies targeting a molecular understanding of AM development and function, use solid substrates for co-cultivating plants and AM fungi. However, for some experiments very clean roots, highly controlled nutrient conditions or applications of defined concentrations of signaling molecules (such as hormones) or other small chemicals (such as synthetic inhibitors or signaling agonists) are needed. To this end, hydroponics has been widely used in research on mechanisms of plant nutrition and some hydroponic systems were developed for AM fungal spore amplification. Here, we present a hydroponics set-up, which can be successfully utilized for experimental root colonization assays. We established a "tip-wick" system based on pipette tips and rock wool wicks for co-cultivation of AM fungi with small model plants such as Lotus japonicus. A larger "Falcon-wick" system using Falcon tubes and rockwool wicks was developed for larger model plants such as rice. The hydroponic system can also be employed for growing L. japonicus hairy roots after transformation by Agrobacterium rhizogenes, thus circumventing the laborious cultivation on agar medium-containing Petri dishes during hairy root development. The tip-wick and Falcon-wick systems are easy to use and can be built with low cost, conventional and reusable lab plastic ware and a simple aquarium pump.

RevDate: 2020-03-15

Suetsugu K, Matsubayashi J, Ogawa NO, et al (2020)

Isotopic evidence of arbuscular mycorrhizal cheating in a grassland gentian species.

Oecologia pii:10.1007/s00442-020-04631-x [Epub ahead of print].

All orchids and pyroloids are mycoheterotrophic at least in the early stage. Many species are predisposed to mycoheterotrophic nutrition even in the adult stage, due to the initial mycoheterotrophy during germination. Although other green plants, such as gentian species, also produce numerous minute seeds, whose germination may depend on fungal associations to meet C demands, physiological evidence for partial mycoheterotrophy in the adult stage is lacking for most candidate taxa. Here, we compared the natural abundances of 13C and 15N isotopes in the AM-associated gentian species Pterygocalyx volubilis growing in high-light-intensity habitats with those of co-occurring autotrophic C3 and C4 plants and AM fungal spores. We found that P. volubilis was significantly enriched in 13C compared with the surrounding C3 plants, which suggests the transfer of some C from the surrounding autotrophic plants through shared AM networks. In addition, the intermediate δ15N values of P. volubilis, between those of autotrophic plants and AM fungal spores, provide further evidence for partial mycoheterotrophy in P. volubilis. Although it is often considered that light deficiency selects partial mycoheterotrophy, we show that partial mycoheterotrophy in AM-forming plants can evolve even under light-saturated conditions. The fact that there have been relatively few descriptions of partial mycoheterotrophy in AM plants may not necessarily reflect the rarity of such associations. In conclusion, partial mycoheterotrophy in AM plants may be more common than hitherto believed.

RevDate: 2020-03-17
CmpDate: 2020-03-17

Joshi M, J Royet (2020)

Uridine Catabolism Breaks the Bonds of Commensalism.

Cell host & microbe, 27(3):312-314.

How gut cells distinguish between beneficial symbionts and deleterious pathobionts is a central question. In this issue of Cell Host & Microbe, Kim et al. (2020) demonstrate that the nucleoside catabolism pathway controlling bacterial uracil and ribose production is an essential trigger of the commensal to pathogen transition.

RevDate: 2020-03-16
CmpDate: 2020-03-16

Dicke M, Cusumano A, EH Poelman (2020)

Microbial Symbionts of Parasitoids.

Annual review of entomology, 65:171-190.

Parasitoids depend on other insects for the development of their offspring. Their eggs are laid in or on a host insect that is consumed during juvenile development. Parasitoids harbor a diversity of microbial symbionts including viruses, bacteria, and fungi. In contrast to symbionts of herbivorous and hematophagous insects, parasitoid symbionts do not provide nutrients. Instead, they are involved in parasitoid reproduction, suppression of host immune responses, and manipulation of the behavior of herbivorous hosts. Moreover, recent research has shown that parasitoid symbionts such as polydnaviruses may also influence plant-mediated interactions among members of plant-associated communities at different trophic levels, such as herbivores, parasitoids, and hyperparasitoids. This implies that these symbionts have a much more extended phenotype than previously thought. This review focuses on the effects of parasitoid symbionts on direct and indirect species interactions and the consequences for community ecology.

RevDate: 2020-03-16
CmpDate: 2020-03-16

Cobian GM, Egan CP, AS Amend (2019)

Plant-microbe specificity varies as a function of elevation.

The ISME journal, 13(11):2778-2788.

Specialized associations between interacting species fundamentally determine the diversity and distribution of both partners. How the specialization of guilds of organisms varies along environmental gradients underpins popular theories of biogeography and macroecology, whereas the degree of specialization of a species is typically considered fixed. However, the extent to which environmental context impacts specialization dynamics is seldom examined empirically. In this study, we examine how specialization within a bipartite network consisting of three co-occurring plant species and their foliar fungal endophyte symbionts changes along a 1000-meter elevation gradient where host species were held constant. The gradient, along the slope of Mauna Loa shield volcano, represents almost the entire elevational range of two of the three plants. Network and plant specialization values displayed a parabolic relationship with elevation, and were highest at middle elevations, whereas bipartite associations were least specific at low and high elevations. Shannon's diversity of fungal endophytes correlated negatively with specificity, and was highest at the ends of the transects. Although plant host was a strong determinant of fungal community composition within sites, fungal species turnover was high among sites. There was no evidence of spatial or elevational patterning in fungal community compositon. Our work demonstrates that specificity can be a plastic trait, which is influenced by the environment and centrality of the host within its natural range.

RevDate: 2020-03-17
CmpDate: 2020-03-17

Wen Z, Li H, Shen Q, et al (2019)

Tradeoffs among root morphology, exudation and mycorrhizal symbioses for phosphorus-acquisition strategies of 16 crop species.

The New phytologist, 223(2):882-895.

Plant roots exhibit diverse root functional traits to enable soil phosphorus (P) acquisition, including changes in root morphology, root exudation and mycorrhizal symbioses. Yet, whether these traits are differently coordinated among crop species to enhance P acquisition is unclear. Here, eight root functional traits for P acquisition were characterized in 16 major herbaceous crop species grown in a glasshouse under limiting and adequate soil P availability. We found substantial interspecific variation in root functional traits among species. Those with thinner roots showed more root branching and less first-order root length, and had consistently lower colonization by arbuscular mycorrhizal fungi (AMF), fewer rhizosheath carboxylates and reduced acid phosphatase activity. In response to limiting soil P, species with thinner roots showed a stronger response in root branching, first-order root length and specific root length of the whole root system, Conversely, species with thicker roots exhibited higher colonization by AMF and/or more P-mobilizing exudates in the rhizosheath. We conclude that, at the species level, tradeoffs occur among the three groups of root functional traits we examined. Root diameter is a good predictor of the relative expression of these traits and how they change when P is limiting.

RevDate: 2020-03-14

Porcelli R, Dotto F, Pezzolesi L, et al (2020)

Comparative life cycle assessment of microalgae cultivation for non-energy purposes using different carbon dioxide sources.

The Science of the total environment, 721:137714 pii:S0048-9697(20)31225-0 [Epub ahead of print].

The ability of microalgae to sequester carbon and at the same time synthesise valuable compounds with potential applications in nutraceutical, pharmaceutical and cosmetic industries makes them attractive for commercial deployment, especially in view of a blue bioeconomy. Among microalgae, the diatom Phaeodactylum tricornutum is considered as an important potential source of omega-3 polyunsaturated fatty acids, such as eicosapentanoic acid, an essential polyunsaturated fatty acid with anti-inflammatory and antimicrobial properties. The aim of this study was to perform the Life Cycle Assessment of the cultivation of P. tricornutum - at semi-industrial scale in photobioreactor - for the production of high-quality bioactive compounds comparing synthetic carbon dioxide supply to a supply with waste carbon dioxide from a biogas upgrading process hypothesizing industrial symbiosis network. The effect of renewable energy use instead of the European electricity mix was also examined. Primary data on the production process, including the stages of cleaning and sterilisation, cultivation, harvesting and freeze-drying, were used. The midpoint impact categories recommended in the ILCD Handbook were used for performing the impact assessment. A sensitivity analysis was also performed on algal productivity, culture medium recirculation factor and amount of solvents per cleaning cycle. Firstly, results indicate in general cultivation and freeze-drying as the most contributing stages to the impacts. Secondly, they demonstrate in the comparative assessment that the use of carbon dioxide from the biogas upgrading is a feasible and attractive alternative to the synthetic one, as it allows for the improvement of the environmental performance of the production process in all the analysed impact categories. Finally, sensitivity analysis suggests that the environmental performance could be further improved by acting on other key factors, such as electricity source, nutrients culture medium and cleaning solutions.

RevDate: 2020-03-14

Czubinska G (2020)

Difference - is it hated or desired? Reflections on the totalitarian state of mind.

The Journal of analytical psychology, 65(2):325-344.

In an age of polarized political views and growing nationalism it is vital that the psychoanalytic profession offers its contribution. The author makes a link between early infant development and social and political behaviour. Psychoanalytic, Jungian and Relational ideas are explored. Starting from Freud and his theory of 'minor differences', a dichotomy between closeness and separateness is investigated. The writer argues that difference is at the centre of human identity and human development and explores why we struggle to accept it. The totalitarian political system is described as one that eliminates difference. A case study is offered as an illustration of a patient's struggle to move from a symbiotic, undifferentiated state towards object relating and individuation.

RevDate: 2020-03-14

Li FW, Nishiyama T, Waller M, et al (2020)

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts.

Nature plants, 6(3):259-272.

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

RevDate: 2020-03-14

Boudehouche W, Parker MA, F Boulila (2020)

Relationships of Bradyrhizobium strains nodulating three Algerian Genista species.

Systematic and applied microbiology pii:S0723-2020(20)30022-9 [Epub ahead of print].

The Mediterranean world is the cradle for the diversification of a large number of plant species, including legumes belonging to the Tribe Genisteae. Nodule bacteria from three species of Genista legumes indigenous to northwestern Africa (G. ferox, G. numidica, G. tricuspidata) were sampled across a 150km region of Algeria in order to investigate symbiotic relationships. Partial 23S rRNA sequences from 107 isolates indicated that Bradyrhizobium was the predominant symbiont genus (96% of isolates), with the remainder belonging to Rhizobium or Mesorhizobium. A multilocus sequence analysis on 46 Bradyrhizobium strains using seven housekeeping (HK) genes showed that strains were differentiated into multiple clades with affinities to seven species: B. canariense (17 isolates), B. japonicum (2), B. ottawaense (2), B. cytisi/B. rifense (9), 'B. valentinum' (5), and B. algeriense (11). Extensive discordance between the HK gene phylogeny and a tree for four loci in the symbiosis island (SI) region implied that horizontal transfer of SI loci has been common. Cases of close symbiont relationship across pairs of legumes hosts were evident, with 33% of isolates having as their closest relative a strain sampled from a different Genista species. Nevertheless, tree permutation tests also showed that there was substantial host-related phylogenetic clustering. Thus, each of the three Genista hosts utilized a measurably different array of bacterial lineages.

RevDate: 2020-03-13

Yu L, Wang L, Yi H, et al (2020)

Beneficial effects of LRP6-CRISPR on prevention of alcohol-related liver injury surpassed fecal microbiota transplant in a rat model.

Gut microbes [Epub ahead of print].

Alcohol intake can modify gut microbiota composition, increase gut permeability, and promote liver fibrogenesis. LRP6 is a signal transmembrane protein and a co-receptor for the canonical Wnt signaling pathway. This study compared the curative effect of LRP6-CRISPR on alcohol-related liver injury with that of traditional fecal microbiota transplant (FMT) and investigated the alteration of the gut microbiome following the treatment. A rat model of alcohol-related liver injury was established and injected with lentiviral vectors expressing LRP6-CRISPR or administered with fecal filtrate from healthy rats, with healthy rat served as the control. Liver tissues of rats were examined by HE staining, Sirius staining, and Oil red O staining, respectively. The expression of LRP6 and fibrosis biomarkers were tested by PCR. The fecal sample of rats was collected and examined by 16S rRNA sequencing. Our data indicated that LRP6-CRISPR was more efficient in the prevention of alcohol-related liver injury than FMT. Microbiome analysis showed that alcohol-related liver injury related to gut microbiota dysbiosis, while treatment with LRP6-CRISPR or FMT increased gut microflora diversity and improved gut symbiosis. Further, bacteria specific to the disease stages were identified. Genera Romboutsia, Escherichia-Shigella, Pseudomonas, Turicibacter, and Helicobacter were prevalent in the intestine of rats with alcohol-related liver injury, while the domination of Lactobacillus was found in rats treated with LRP6-CRISPR or FMT. Besides, Lactobacillus and genera belonging to family Lachnospiraceae, Bacteroidales S24-7 group, and Ruminococcaceae were enriched in healthy rats. LRP6-CRISPR and FMT have beneficial effects on the prevention of alcohol-related liver injury, and correspondently, both treatments altered the disrupted gut microflora to a healthy one.

RevDate: 2020-03-13

Zilli JÉ, Simoes-Araujo JL, Rouws LFM, et al (2020)

Draft Genome Sequence of Bradyrhizobium elkanii BR 2003, an Efficient Rhizobium Strain for Cajanus, Canavalia, Crotalaria, and Indigofera.

Microbiology resource announcements, 9(11): pii:9/11/e01565-19.

We report here the annotated draft genome sequence of the rhizobium strain BR 2003. This strain is able to establish symbiosis and to fix nitrogen with a broad range of leguminous species. The estimation of the average nucleotide identity confirmed the strain as a member of Bradyrhizobium elkanii.

RevDate: 2020-03-13

Vohsen SA, Anderson KE, Gade AM, et al (2020)

Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans.

Microbiome, 8(1):34 pii:10.1186/s40168-020-00798-w.

BACKGROUND: Apicomplexans are the causative agents of major human diseases such as malaria and toxoplasmosis. A novel group of apicomplexans, recently named corallicolids, have been detected in corals inhabiting tropical shallow reefs. These apicomplexans may represent a transitional lifestyle between free-living phototrophs and obligate parasites. To shed light on the evolutionary history of apicomplexans and to investigate their ecology in association with corals, we screened scleractinians, antipatharians, alcyonaceans, and zoantharians from shallow, mesophotic, and deep-sea communities. We detected corallicolid plastids using 16S metabarcoding, sequenced the nuclear 18S rRNA gene of corallicolids from selected samples, assembled and annotated the plastid and mitochondrial genomes from a corallicolid that associates with a deep-sea coral, and screened the metagenomes of four coral species for corallicolids.

RESULTS: We detected 23 corallicolid plastotypes that were associated with 14 coral species from three orders and depths down to 1400 m. Individual plastotypes were restricted to coral hosts within a single depth zone and within a single taxonomic order of corals. Some clusters of closely related corallicolids were revealed that associated with closely related coral species. However, the presence of divergent corallicolid lineages that associated with similar coral species and depths suggests that corallicolid/coral relations are flexible over evolutionary timescales and that a large diversity of apicomplexans may remain undiscovered. The corallicolid plastid genome from a deep-sea coral contained four genes involved in chlorophyll biosynthesis: the three genes of the LIPOR complex and acsF.

CONCLUSIONS: The presence of corallicolid apicomplexans in corals below the photic zone demonstrates that they are not restricted to shallow-water reefs and are more general anthozoan symbionts. The presence of LIPOR genes in the deep-sea corallicolid precludes a role involving photosynthesis and suggests they may be involved in a different function. Thus, these genes may represent another set of genetic tools whose function was adapted from photosynthesis as the ancestors of apicomplexans evolved towards parasitic lifestyles. Video abstract.

RevDate: 2020-03-13
CmpDate: 2020-03-13

Kiaeian Moosavi F, Cargnus E, Torelli E, et al (2020)

Is the existence of a mutualistic relationship between Lobesia botrana and Botrytis cinerea well-founded?.

Archives of insect biochemistry and physiology, 103(4):e21655.

Some studies have highlighted benefits for Lobesia botrana by adding Botrytis cinerea mycelium to an artificial larval diet and have suggested a mutualistic relationship between the two organisms on grapevine, hypothesizing that fungal sterols were the nutritional factor involved. Because the nutritional quality of an artificial diet should be similar to grapes to allow extrapolation of the results to the field conditions, in the current study L. botrana larval performance was compared when larvae were fed on grapes (berries) or two artificial diets either with or without enrichment with B. cinerea. Based on sterol analysis, the two artificial diets had high cholesterol content, but relative to berries showed comparable and low phytosterol contents, respectively (high- and low-phytosterol, HPh, and LPh). While larval fitness on the HPh diet was similar to berries, the LPh diet led to higher mortality and worse larval performance. The addition of the fungus compensated for the shortage in the LPh diet but did not improve the HPh diet. Supplementing the LPh diet with linoleic acid, which is supplied also from B. cinerea, partially improved larval performance. In a field experiment, females did not show any egg-laying preferences towards naturally botrytized bunches. The positive effect of B. cinerea on the moth's next generation that is reported in the literature could be a consequence of fungus developed inside berry tunnels bored by larvae. Therefore, based on our data and previous reports the existence of a mutualistic relationship between L. botrana and B. cinerea is not well-founded.

RevDate: 2020-03-13
CmpDate: 2020-03-13

Shipway JR, Rosenberg G, Concepcion GP, et al (2019)

Shipworm bioerosion of lithic substrates in a freshwater setting, Abatan River, Philippines: Ichnologic, paleoenvironmental and biogeomorphical implications.

PloS one, 14(10):e0224551.

Teredinid bivalves, commonly referred to as shipworms, are known for their propensity to inhabit, bioerode, and digest woody substrates across a range of brackish and fully marine settings. Shipworm body fossils and/or their borings, which are most allied with the ichnotaxon Teredolites longissimus, are found in wood preserved in sedimentary sequences ranging in age from Early Cretaceous to Recent and traditionally they have been regarded as evidence of marginal marine or marine depositional environments. Recent studies associated with the Philippine Mollusk Symbiont International Collaboration Biodiversity Group (PMS-ICBG) expedition on the island of Bohol, Philippines, have identified a new shipworm taxon (Lithoredo abatanica) that is responsible for macrobioerosion of a moderately indurated Neogene foraminiferal packstone cropping out along a freshwater reach of the Abatan River. In the process of drilling into and ingesting the limestone, these shipworms produce elongate borings that expand in diameter very gradually toward distal termini, exhibit sinuous or highly contorted axes and circular transverse outlines, and are lined along most of their length by a calcite tube. Given their strong resemblance to T. longissimus produced in wood but their unusual occurrence in a lithic substrate, these shipworm borings can be regarded as incipient Gastrochaenolites or, alternatively, as Apectoichnus. The alternate names reflect that the borings provide a testbed for ideas of the appropriateness of substrate as an ichnotaxobasis. The discovery of previously unrecognized shipworm borings in lithic substrates and the co-occurrence of another shipworm (Nausitora) in submerged logs in the same freshwater setting have implications for interpreting depositional conditions based on fossil teredinids or their ichnofossils. Of equal significance, the Abatan River study demonstrates that macrobioerosion in freshwater systems may be just as important as it is in marine systems with regard to habitat creation and landscape development. L. abatanica serve as ecosystems engineers in the sense that networks of their abandoned borings provide habitats for a variety of nestling invertebrates, and associated bioerosion undoubtedly enhances rates of mechanical and chemical degradation, thus influencing the Abatan River profile.

RevDate: 2020-03-13
CmpDate: 2020-03-13

Bueno CG, Aldrich-Wolfe L, Chaudhary VB, et al (2019)

Misdiagnosis and uncritical use of plant mycorrhizal data are not the only elephants in the room.

The New phytologist, 224(4):1415-1418.

RevDate: 2020-03-12

Hoang NT, Tóth K, G Stacey (2020)

The role of microRNAs in the legume-Rhizobium nitrogen-fixing symbiosis.

Journal of experimental botany, 71(5):1668-1680.

Under nitrogen starvation, most legume plants form a nitrogen-fixing symbiosis with Rhizobium bacteria. The bacteria induce the formation of a novel organ called the nodule in which rhizobia reside as intracellular symbionts and convert atmospheric nitrogen into ammonia. During this symbiosis, miRNAs are essential for coordinating the various plant processes required for nodule formation and function. miRNAs are non-coding, endogenous RNA molecules, typically 20-24 nucleotides long, that negatively regulate the expression of their target mRNAs. Some miRNAs can move systemically within plant tissues through the vascular system, which mediates, for example, communication between the stem/leaf tissues and the roots. In this review, we summarize the growing number of miRNAs that function during legume nodulation focusing on two model legumes, Lotus japonicus and Medicago truncatula, and two important legume crops, soybean (Glycine max) and common bean (Phaseolus vulgaris). This regulation impacts a variety of physiological processes including hormone signaling and spatial regulation of gene expression. The role of mobile miRNAs in regulating legume nodule number is also highlighted.

RevDate: 2020-03-12

Morrow JL, Schneider DI, Klasson L, et al (2020)

Parallel sequencing of Wolbachia wCer2 from donor and novel hosts reveals multiple incompatibility factors and genome stability after host transfers.

Genome biology and evolution pii:5803650 [Epub ahead of print].

The application of Wolbachia in insect pest and vector control requires the establishment of genotypically stable host associations. The cytoplasmic incompatibility (CI) inducing Wolbachia strain wCer2 naturally occurs in the cherry fruit fly Rhagoletis cerasi as co-infection with other strains and was transferred to other fruit flies by embryonic microinjections. We obtained wCer2 genome data from its native and three novel hosts, Drosophila simulans, Drosophila melanogaster and Ceratitis capitata and assessed its genome stability, characteristics and CI factor (cif) genes. De novo assembly was successful from Wolbachia cell-enriched singly infected D. simulans embryos, with minimal host and other bacterial genome traces. The low yield of Wolbachia sequence reads from total genomic extracts of one multiply infected R. cerasi pupa and one singly infected C. capitata adult limited de novo assemblies but was sufficient for comparative analyses. Across hosts wCer2 was stable in genome synteny and content. Polymorphic nucleotide sites were found in wCer2 of each host, however only one nucleotide was different between R. cerasi and C. capitata, and none between replicated D. simulans lines. The wCer2 genome is highly similar to wAu (D. simulans), wMel (D. melanogaster) and wRec (Drosophila recens). In contrast to wMel and wRec (each with one cif gene pair) and wAu (without any cif genes), wCer2 has three pairs of Type I cif genes and one Type IV cifB gene without a cifA complement. This may explain previously reported CI patterns of wCer2, including incomplete rescue of its own CI modification in three novel host species.

RevDate: 2020-03-12

Greshake Tzovaras B, Segers FHID, Bicker A, et al (2020)

What is in Umbilicaria pustulata? A metagenomic approach to reconstruct the holo-genome of a lichen.

Genome biology and evolution pii:5803651 [Epub ahead of print].

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high quality genomes for such symbiotic communities is technically challenging. Here we present the first assembly of a lichen holo-genome from metagenomic whole genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis - the fungus Umbilicaria pustulata (33 Mbp) and the green alga Trebouxia sp. (53 Mbp) - were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of approximately 20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae, and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with non-random sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

RevDate: 2020-03-12

Noh HJ, Lee YM, Park CH, et al (2020)

Microbiome in Cladonia squamosa Is Vertically Stratified According to Microclimatic Conditions.

Frontiers in microbiology, 11:268.

Lichens are miniature ecosystems that contain fungi, microalgae, and bacteria. It is generally accepted that symbiosis between mycobiont and photobiont and microbial contribution to the ecosystem support the wide distribution of lichens in terrestrial ecosystems, including polar areas. The composition of symbiotic components can be affected by subtle microenvironmental differences within a thallus, as well as large-scale climate differences. In this study, we investigated fine-scale profiles of algal, fungal, and bacterial compositions through horizontal and vertical positions of the Antarctic lichen Cladonia squamosa colonies by next-generation sequencing of the nuclear large subunit rRNA gene (nucLSU) of eukaryotes and the 16S rRNA gene of bacteria. Apical parts of thalli were exposed to strong light, low moisture, and high variability of temperature compared with basal parts. Microbial diversity increased from apical parts to basal parts of thalli. Asterochloris erici was the major photobiont in apical positions of thalli, but other microalgal operational taxonomic units (OTUs) of Trebouxiophyceae and Ulvophyceae were major microalgal components in basal positions. Photochemical responses of algal components from apical and basal parts of thalli were quite different under variable temperature and humidity conditions. Several fungal OTUs that belonged to Arthoniomycetes and Lecanoromycetes, and diverse bacterial OTUs that belonged to Alphaproteobacteria, Acidobacteria_Gp1, and candidate division WPS-2 showed a clear distribution pattern according to their vertical positions within thalli. The overall lichen microbiome was significantly differentiated by the vertical position within a thallus. These results imply that different microclimate are formed at different lichen thallus parts, which can affect microbial compositions and physiological responses according to positions within the thalli.

RevDate: 2020-03-12

Claar DC, Tietjen KL, Cox KD, et al (2020)

Chronic disturbance modulates symbiont (Symbiodiniaceae) beta diversity on a coral reef.

Scientific reports, 10(1):4492 pii:10.1038/s41598-020-60929-z.

Chronic disturbance can disrupt ecological interactions including the foundational symbiosis between reef-building corals and the dinoflagellate family Symbiodiniaceae. Symbiodiniaceae are photosynthetic endosymbionts necessary for coral survival, but many Symbiodiniaceae can also be found free-living in the environment. Since most coral species acquire new Symbiodiniaceae from the environment each generation, free-living Symbiodiniaceae represent important pools for coral symbiont acquisition. Yet, little is known about the diversity of, or impacts of disturbance on, free-living Symbiodiniaceae. To determine how chronic and pulse disturbances influence Symbiodiniaceae communities, we sampled three reef habitat compartments - sediment, water, and coral (Pocillopora grandis, Montipora aequituberculata, Porites lobata) - at sites exposed to different levels of chronic anthropogenic disturbance, before, during, and after a major storm. Almost no (4%) Symbiodiniaceae amplicon sequence variants (ASVs) were found in all three compartments, and over half were found uniquely in coral. Sites experiencing chronic disturbance were typically associated with higher symbiont beta diversity (i.e., variability and turnover) across reef habitat compartments. Pulse stress, from the storm, exhibited some influence on symbiont beta diversity but the effect was inconsistent. This suggests that in this ecosystem, the effects of chronic disturbance are more prominent than temporal variability during a pulse disturbance for shaping symbiont communities.

RevDate: 2020-03-11

Salomaki ED, CE Lane (2020)

Response to Preuss and Zuccarello (2020): Biological definitions that can be unambiguously applied for red algal parasites.

In response to a comment in this issue on our proposal of new terminology to distinguish red algal parasites, we clarify a few key issues. The terms adelphoparasite and alloparasite were previously used to identify parasites that infected close or distant relatives, respectively. However, most red algal parasites have only been studied morphologically, and molecular tools have shown that these binary terms do a poor job at representing the range of parasite-host relationships. We recognize the need to clarify inferred misconceptions that appear to be drawing from historical terminology to contaminate our new definitions. We did not intend to replace the term adelphoparasite with neoplastic parasites and the term alloparasites with archaeplastic parasites. Rather, we seek to establish new terms for discussing red algal parasites, based on the retention of a native plastid, a binary biological trait that is relatively easy to identify using modern methods and has biological implications for the interactions between a parasite and its host. The new terminology can better account for the spectrum of relationships and developmental patterns found among the many independently evolved red algal parasites, and is intended to inspire new research, particularly the role of plastids in the survival and evolution of red algal parasites.

RevDate: 2020-03-11

Nelson CA, Pérez-Chada LM, Creadore A, et al (2020)

Patient Perspectives on the Use of Artificial Intelligence for Skin Cancer Screening: A Qualitative Study.

JAMA dermatology pii:2762711 [Epub ahead of print].

Importance: The use of artificial intelligence (AI) is expanding throughout the field of medicine. In dermatology, researchers are evaluating the potential for direct-to-patient and clinician decision-support AI tools to classify skin lesions. Although AI is poised to change how patients engage in health care, patient perspectives remain poorly understood.

Objective: To explore how patients conceptualize AI and perceive the use of AI for skin cancer screening.

A qualitative study using a grounded theory approach to semistructured interview analysis was conducted in general dermatology clinics at the Brigham and Women's Hospital and melanoma clinics at the Dana-Farber Cancer Institute. Forty-eight patients were enrolled. Each interview was independently coded by 2 researchers with interrater reliability measurement; reconciled codes were used to assess code frequency. The study was conducted from May 6 to July 8, 2019.

Main Outcomes and Measures: Artificial intelligence concept, perceived benefits and risks of AI, strengths and weaknesses of AI, AI implementation, response to conflict between human and AI clinical decision-making, and recommendation for or against AI.

Results: Of 48 patients enrolled, 26 participants (54%) were women; mean (SD) age was 53.3 (21.7) years. Sixteen patients (33%) had a history of melanoma, 16 patients (33%) had a history of nonmelanoma skin cancer only, and 16 patients (33%) had no history of skin cancer. Twenty-four patients were interviewed about a direct-to-patient AI tool and 24 patients were interviewed about a clinician decision-support AI tool. Interrater reliability ratings for the 2 coding teams were κ = 0.94 and κ = 0.89. Patients primarily conceptualized AI in terms of cognition. Increased diagnostic speed (29 participants [60%]) and health care access (29 [60%]) were the most commonly perceived benefits of AI for skin cancer screening; increased patient anxiety was the most commonly perceived risk (19 [40%]). Patients perceived both more accurate diagnosis (33 [69%]) and less accurate diagnosis (41 [85%]) to be the greatest strength and weakness of AI, respectively. The dominant theme that emerged was the importance of symbiosis between humans and AI (45 [94%]). Seeking biopsy was the most common response to conflict between human and AI clinical decision-making (32 [67%]). Overall, 36 patients (75%) would recommend AI to family members and friends.

Conclusions and Relevance: In this qualitative study, patients appeared to be receptive to the use of AI for skin cancer screening if implemented in a manner that preserves the integrity of the human physician-patient relationship.

RevDate: 2020-03-11

Speijer D (2020)

Debating Eukaryogenesis: Part 2: How Anachronistic Reasoning Can Lure Us into Inventing Intermediates.

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

Eukaryotic origins are inextricably linked with the arrival of a pre-mitochondrion of alphaproteobacterial-like ancestry. However, the nature of the "host" cell and the mode of entry are subject to heavy debate. It is becoming clear that the mutual adaptation of a relatively simple, archaeal host and the endosymbiont has been the defining influence at the beginning of the eukaryotic lineage; however, many still resist such symbiogenic models. In part 1, it is posited that a symbiotic stage before uptake ("pre-symbiosis") seems essential to allow further metabolic integration of the two partners ending in endosymbiosis. Thus, the author argued against phagocytic mechanisms (in which the bacterium is prey or parasite) as the mode of entry. Such positions are still broadly unpopular. Here it is explained why. Evolutionary thinking, especially in the case of eukaryogenesis, is still dominated by anachronistic reasoning, in which highly derived protozoan organisms are seen as in some way representative of intermediate steps during eukaryotic evolution, hence poisoning the debate. This reasoning reflects a mind-set that ignores that Darwinian evolution is a fundamentally historic process. Numerous examples of this kind of erroneous reasoning are given, and some basic precautions against its use are formulated.

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ESP Quick Facts

ESP Origins

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

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

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

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

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

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