Viewport Size Code:
Login | Create New Account


About | Classical Genetics | Timelines | What's New | What's Hot

About | Classical Genetics | Timelines | What's New | What's Hot


Bibliography Options Menu

Hide Abstracts   |   Hide Additional Links
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

Bibliography on: Holobiont

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


ESP: PubMed Auto Bibliography 20 Mar 2019 at 01:31 Created: 


Holobionts are assemblages of different species that form ecological units. Lynn Margulis proposed that any physical association between individuals of different species for significant portions of their life history is a symbiosis. All participants in the symbiosis are bionts, and therefore the resulting assemblage was first coined a holobiont by Lynn Margulis in 1991 in the book Symbiosis as a Source of Evolutionary Innovation. Holo is derived from the Ancient Greek word ὅλος (hólos) for “whole”. The entire assemblage of genomes in the holobiont is termed a hologenome.

Created with PubMed® Query: holobiont OR hologenome NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-03-18

Tarquinio F, Hyndes GA, Laverock B, et al (2019)

The seagrass holobiont: understanding seagrass-bacteria interactions and their role in seagrass ecosystem functioning.

FEMS microbiology letters pii:5382495 [Epub ahead of print].

This review shows that the presence of seagrass microbial community is critical for the development of seagrasses; from seed germination, through to phytohormone production and enhanced nutrient availability, and defence against pathogens and saprophytes. The tight seagrass-bacterial relationship highlighted in this review supports the existence of a seagrass holobiont and adds to the growing evidence for the importance of marine eukaryotic microorganisms in sustaining vital ecosystems. Incorporating a micro-scale view on seagrass ecosystems substantially expands our understanding of ecosystem functioning and may have significant implications for future seagrass management and mitigation against human disturbance.

RevDate: 2019-03-14

Thomashow LS, Quak YS, DM Weller (2019)


Pest management science [Epub ahead of print].

Since the discovery of penicillin in 1928 and throughout the "age of antibiotics" from the 1940s until the 1980s, the detection of novel antibiotics was restricted by lack of knowledge about the distribution and ecology of antibiotic producers in nature. The discovery that a phenazine compound produced by Pseudomonas bacteria could suppress soilborne plant pathogens, and its recovery from rhizosphere soil in 1990, provided the first incontrovertible evidence that natural metabolites could control plant pathogens in the environment and opened a new era in biological control by root-associated rhizobacteria. More recently, the advent of genomics, the availability of highly sensitive bioanalytical instrumentation, and the discovery of protective endophytes have accelerated progress toward overcoming many of the impediments that until now have limited the exploitation of beneficial plant-associated microbes to enhance agricultural sustainability. Here, we present key developments that have established the importance of these microbes in the control of pathogens, discuss concepts resulting from the exploration of classical model systems, and highlight advances emerging from ongoing investigations. This article is protected by copyright. All rights reserved.

RevDate: 2019-03-13

Weigel BL, CA Pfister (2019)

Successional Dynamics and Seascape-Level Patterns of Microbial Communities on the Canopy-Forming Kelps Nereocystis luetkeana and Macrocystis pyrifera.

Frontiers in microbiology, 10:346.

Canopy-forming kelps create underwater forests that are among the most productive marine ecosystems. On the Pacific coast of North America, two canopy-forming kelps with contrasting life histories co-occur; Macrocystis pyrifera, a perennial species, and Nereocystis luetkeana, an annual species. Kelp blade-associated microbes were sampled from 12 locations across a spatial gradient in Washington, United States, from the outer Pacific Coast to Puget Sound. Microbial communities were characterized using next-generation Illumina sequencing of 16S rRNA genes. At higher taxonomic levels (bacterial phylum and class), canopy-forming kelps hosted remarkably similar microbial communities, but at the amplicon sequence variant level, microbial communities on M. pyrifera and N. luetkeana were host-specific and distinct from free-living bacteria in the surrounding seawater. Microbial communities associated with blades of each kelp species displayed significant geographic variation. The microbiome of N. luetkeana changed along the spatial gradient and was significantly correlated to salinity, with outer Pacific coast sites enriched in Bacteroidetes (family Saprospiraceae) and Gammaproteobacteria (Granulosicoccus sp.), and southern Puget Sound sites enriched in Alphaproteobacteria (family Hyphomonadaceae). We also examined microbial community development and succession on meristematic and apical N. luetkeana blade tissues throughout the summer growing season on Tatoosh Island, WA. Across all dates, microbial communities were less diverse on younger, meristematic blade tissue compared to the older, apical tissues. In addition, phylogenetic relatedness among microbial taxa increased from meristematic to apical blade tissues, suggesting that the addition of microbial taxa to the community was a non-random process that selected for certain phylogenetic groups of microbes. Microbial communities on older, apical tissues displayed significant temporal variation throughout the summer and microbial taxa that were differentially abundant over time displayed clear patterns of community succession. Overall, we report that host species identity, geographic location, and blade tissue age shape the microbial communities on canopy-forming kelps.

RevDate: 2019-03-04

Reverter M, Tribalat MA, Pérez T, et al (2018)

Metabolome variability for two Mediterranean sponge species of the genus Haliclona: specificity, time, and space.

Metabolomics : Official journal of the Metabolomic Society, 14(9):114 pii:10.1007/s11306-018-1401-5.

INTRODUCTION: The study of natural variation of metabolites brings valuable information on the physiological state of the organisms as well as their phenotypic traits. In marine organisms, metabolome variability has mostly been addressed through targeted studies on metabolites of ecological or pharmaceutical interest. However, comparative metabolomics has demonstrated its potential to address the overall and complex metabolic variability of organisms.

OBJECTIVES: In this study, the intraspecific (temporal and spatial) variability of two Mediterranean Haliclona sponges (H. fulva and H. mucosa) was investigated through an untargeted and then targeted metabolomics approach and further compared to their interspecific variability.

METHODS: Samples of both species were collected monthly during 1 year in the coralligenous habitat of the Northwestern Mediterranean sae at Marseille and Nice. Their metabolomic profiles were obtained by UHPLC-QqToF analyses.

RESULTS: Marked variations were noticed in April and May for both species including a decrease in Shannon's diversity and concentration in specialized metabolites together with an increase in fatty acids and lyso-PAF like molecules. Spatial variations across different sampling sites could also be observed for both species, however in a lesser extent.

CONCLUSIONS: Synchronous metabolic changes possibly triggered by physiological factors like reproduction and/or environmental factors like an increase in the water temperature were highlighted for both Mediterranean Haliclona species inhabiting close habitats but displaying different biosynthetic pathways. Despite significative intraspecific variations, metabolomic variability remains minor when compared to interspecific variations for these congenerous species, therefore suggesting the predominance of genetic information of the holobiont in the observed metabolome.

RevDate: 2019-02-27

Kong HG, Kim HH, Chung JH, et al (2019)

The Galleria mellonella Hologenome Supports Microbiota-Independent Metabolism of Long-Chain Hydrocarbon Beeswax.

Cell reports, 26(9):2451-2464.e5.

The greater wax moth, Galleria mellonella, degrades wax and plastic molecules. Despite much interest, the genetic basis of these hallmark traits remains poorly understood. Herein, we assembled high-quality genome and transcriptome data from G. mellonella to investigate long-chain hydrocarbon wax metabolism strategies. Specific carboxylesterase and lipase and fatty-acid-metabolism-related enzymes in the G. mellonella genome are transcriptionally regulated during feeding on beeswax. Strikingly, G. mellonella lacking intestinal microbiota successfully decomposes long-chain fatty acids following wax metabolism, although the intestinal microbiome performs a supplementary role in short-chain fatty acid degradation. Notably, final wax derivatives were detected by gas chromatography even in the absence of gut microbiota. Our findings provide insight into wax moth adaptation and may assist in the development of unique wax-degradation strategies with a similar metabolic approach for a plastic molecule polyethylene biodegradation using organisms without intestinal microbiota.

RevDate: 2019-02-27

Fuentes A (2019)

Holobionts, Multispecies Ecologies, and the Biopolitics of Care: Emerging Landscapes of Praxis in a Medical Anthropology of the Anthropocene.

Medical anthropology quarterly [Epub ahead of print].

Medical anthropology, given its diversity of practical and historical entanglements with (and outside of) numerous threads of anthropology, is a key site for productive theoretical and methodological confluences in the Anthropocene. Multispecies approaches, ethnographically, theoretically and methodologically, are developing as central locations for the hybridization and mingling of diverse and innovative research questions, particularly those engaging the processes, patterns, and constructs of health.

RevDate: 2019-02-27

Chakravarti LJ, Negri AP, MJH van Oppen (2019)

Thermal and Herbicide Tolerances of Chromerid Algae and Their Ability to Form a Symbiosis With Corals.

Frontiers in microbiology, 10:173.

Reef-building corals form an obligate symbiosis with photosynthetic microalgae in the family Symbiodiniaceae that meet most of their energy requirements. This symbiosis is under threat from the unprecedented rate of ocean warming as well as the simultaneous pressure of local stressors such as poor water quality. Only 1°C above mean summer sea surface temperatures (SSTs) on the Great Barrier Reef (GBR) can trigger the loss of Symbiodiniaceae from the host, and very low concentrations of the most common herbicide, diuron, can disrupt the photosynthetic activity of microalgae. In an era of rapid environmental change, investigation into the assisted evolution of the coral holobiont is underway in an effort to enhance the resilience of corals. Apicomplexan-like microalgae were discovered in 2008 and the Phylum Chromerida (chromerids) was created. Chromerids have been isolated from corals and contain a functional photosynthetic plastid. Their discovery therefore opens a new avenue of research into the use of alternative/additional photosymbionts of corals. However, only two studies to-date have investigated the symbiotic nature of Chromera velia with corals and thus little is known about the coral-chromerid relationship. Furthermore, the response of chromerids to environmental stressors has not been examined. Here we tested the performance of four chromerid strains and the common dinoflagellate symbiont Cladocopium goreaui (formerly Symbiodinium goreaui, ITS2 type C1) in response to elevated temperature, diuron and their combined exposure. Three of the four chromerid strains exhibited high thermal tolerances and two strains showed exceptional herbicide tolerances, greater than observed for any photosynthetic microalgae, including C. goreaui. We also investigated the onset of symbiosis between the chromerids and larvae of two common GBR coral species under ambient and stress conditions. Levels of colonization of coral larvae with the chromerid strains were low compared to colonization with C. goreaui. We did not observe any overall negative or positive larval fitness effects of the inoculation with chromerid algae vs. C. goreaui. However, we cannot exclude the possibility that chromerid algae may have more important roles in later coral life stages and recommend this be the focus of future studies.

RevDate: 2019-02-18

Estellé J (2019)

Benefits from the joint analysis of host genomes and metagenomes: Select the holobiont.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie, 136(2):75-76.

RevDate: 2019-02-11

Glasl B, Smith CE, Bourne DG, et al (2019)

Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis.

PeerJ, 7:e6377 pii:6377.

Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2 °C), elevated pCO2 (900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research.

RevDate: 2019-02-10

Liu H, LE Brettell (2019)

Plant Defense by VOC-Induced Microbial Priming.

Trends in plant science pii:S1360-1385(19)30023-8 [Epub ahead of print].

The plant holobiont extends the plant's capacity for nutrient acquisition and stress protection. Recent studies show that under biotic stress plants can promote the acquisition of certain beneficial bacteria to their rhizosphere. Active emission of volatile organic compounds (VOCs) is a newly identified mechanism utilized by plants for this process.

RevDate: 2019-02-07

Détrée C, Haddad I, Demey-Thomas E, et al (2019)

Global host molecular perturbations upon in situ loss of bacterial endosymbionts in the deep-sea mussel Bathymodiolus azoricus assessed using proteomics and transcriptomics.

BMC genomics, 20(1):109 pii:10.1186/s12864-019-5456-0.

BACKGROUND: Colonization of deep-sea hydrothermal vents by most invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers in these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. In this study, we proposed to describe, using a proteo-transcriptomic approach, the effects of symbionts loss on the deep-sea mussel Bathymodiolus azoricus' molecular biology. We induced an in situ depletion of symbionts and compared the proteo-transcriptome of the gills of mussels in three conditions: symbiotic mussels (natural population), symbiont-depleted mussels and aposymbiotic mussels.

RESULTS: Global proteomic and transcriptomic results evidenced a global disruption of host machinery in aposymbiotic organisms. We observed that the total number of proteins identified decreased from 1118 in symbiotic mussels to 790 in partially depleted mussels and 761 in aposymbiotic mussels. Using microarrays we identified 4300 transcripts differentially expressed between symbiont-depleted and symbiotic mussels. Among these transcripts, 799 were found differentially expressed in aposymbiotic mussels and almost twice as many in symbiont-depleted mussels as compared to symbiotic mussels. Regarding apoptotic and immune system processes - known to be largely involved in symbiotic interactions - an overall up-regulation of associated proteins and transcripts was observed in symbiont-depleted mussels.

CONCLUSION: Overall, our study showed a global impairment of host machinery and an activation of both the immune and apoptotic system following symbiont-depletion. One of the main assumptions is the involvement of symbiotic bacteria in the inhibition and regulation of immune and apoptotic systems. As such, symbiotic bacteria may increase their lifespan in gill cells while managing the defense of the holobiont against putative pathogens.

RevDate: 2019-02-05

Rosenberg E, I Zilber-Rosenberg (2019)

The Hologenome Concept of Evolution: Medical Implications.

Rambam Maimonides medical journal, 10(1): pii:RMMJ.10359.

All natural animals and plants are holobionts, consisting of the host and microbiome, which is composed of abundant and diverse microorganisms. Health and disease of holobionts depend as much on interactions between host and microbiome and within the microbiome, as on interactions between organs and body parts of the host. Recent evidence indicates that a significant fraction of the microbiome is transferred by a variety of mechanisms from parent to offspring for many generations. Genetic variation in holobionts can occur in the microbiome as well as in the host genome, and it occurs more rapidly and by more mechanisms in genomes of microbiomes than in host genomes (e.g. via acquisition of novel microbes and horizontal gene transfer of microbial genes into host chromosomes). Evidence discussed in this review supports the concept that holobionts with their hologenomes can be considered levels of selection in evolution. Though changes in the microbiome can lead to evolution of the holobiont, it can also lead to dysbiosis and diseases (e.g. obesity, diarrhea, inflammatory bowel disease, and autism). In practice, the possibility of manipulating microbiomes offers the potential to prevent and cure diseases.

RevDate: 2019-02-07

Longford SR, Campbell AH, Nielsen S, et al (2019)

Interactions within the microbiome alter microbial interactions with host chemical defences and affect disease in a marine holobiont.

Scientific reports, 9(1):1363 pii:10.1038/s41598-018-37062-z.

Our understanding of diseases has been transformed by the realisation that people are holobionts, comprised of a host and its associated microbiome(s). Disease can also have devastating effects on populations of marine organisms, including dominant habitat formers such as seaweed holobionts. However, we know very little about how interactions between microorganisms within microbiomes - of humans or marine organisms - affect host health and there is no underpinning theoretical framework for exploring this. We applied ecological models of succession to bacterial communities to understand how interactions within a seaweed microbiome affect the host. We observed succession of surface microbiomes on the red seaweed Delisea pulchra in situ, following a disturbance, with communities 'recovering' to resemble undisturbed states after only 12 days. Further, if this recovery was perturbed, a bleaching disease previously described for this seaweed developed. Early successional strains of bacteria protected the host from colonisation by a pathogenic, later successional strain. Host chemical defences also prevented disease, such that within-microbiome interactions were most important when the host's chemical defences were inhibited. This is the first experimental evidence that interactions within microbiomes have important implications for host health and disease in a dominant marine habitat-forming organism.

RevDate: 2019-01-29

Wemheuer B, Thomas T, F Wemheuer (2019)

Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes.

Microorganisms, 7(2): pii:microorganisms7020037.

Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues of three agriculturally important grass species (Dactylisglomerata L., Festucarubra L. and Loliumperenne L.) over two consecutive years. Our results showed that the management practices influenced fungal communities in the plant holobiont, but observed effects differed between grass species and sampling year. Phylogenetic diversity of fungal endophytes in D. glomerata was significantly affected by mowing frequency in 2010, whereas fertilizer application and the interaction of fertilization with mowing frequency had a significant impact on community composition of L. perenne in 2010 and 2011, respectively. Taken together, our research provides a basis for future studies on responses of fungal endophytes towards management practices. To the best of our knowledge, this is the first study simultaneously assessing fungal endophyte communities in aerial parts of three agriculturally important grass species over two consecutive years.

RevDate: 2019-01-29

Helmkampf M, Bellinger MR, Frazier M, et al (2019)

Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata.

Ecology and evolution, 9(1):378-392 pii:ECE34756.

Reef-building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA-seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai'i Island with contrasting environmental conditions. We found that transcriptome-wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (FST = 0.046) and among corals harboring alternative symbiont clades (FST = 0.036), suggesting that site-related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.

RevDate: 2019-01-23

Töpel M, Pinder MIM, Johansson ON, et al (2019)

Complete Genome Sequence of Novel Sulfitobacter pseudonitzschiae Strain SMR1, Isolated from a Culture of the Marine Diatom Skeletonema marinoi.

Journal of genomics, 7:7-10 pii:jgenv07p0007.

When studying diatoms, an important consideration is the role of associated bacteria in the diatom-microbiome holobiont. To that end, bacteria isolated from a culture of Skeletonema marinoi strain R05AC were sequenced, one of which being bacterial strain SMR1, presented here. The genome consists of a circular chromosome and seven circular plasmids, totalling 5,121,602 bp. After phylotaxonomic analysis and 16S rRNA sequence comparison, we place this strain in the taxon Sulfitobacter pseudonitzschiae on account of similarity to the type strain. The annotated genome suggests similar interactions between strain SMR1 and its host diatom as have been shown previously in diatom-associated Sulfitobacter, for example bacterial production of growth hormone for its host, and breakdown of diatom-derived DMSP by Sulfitobacter for use as a sulfur source.

RevDate: 2019-01-18

Simon JC, Marchesi JR, Mougel C, et al (2019)

Host-microbiota interactions: from holobiont theory to analysis.

Microbiome, 7(1):5 pii:10.1186/s40168-019-0619-4.

In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.

RevDate: 2019-01-09

Osmanovic D, Kessler DA, Rabin Y, et al (2018)

Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole.

Biology direct, 13(1):24 pii:10.1186/s13062-018-0224-7.

BACKGROUND: The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.

RESULTS: To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent ("detox"). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host's offspring. Prolonged exposure to toxin over many host generations promotes anadditional form of emergent adaptation due to selection of hosts based on detox produced by their bacterial community as a whole (as opposed to properties of individual bacteria).

CONCLUSIONS: These findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system.

REVIEWERS: This article was reviewed by Eugene Koonin, Yuri Wolf and Philippe Huneman.

RevDate: 2019-01-10

Huitzil S, Sandoval-Motta S, Frank A, et al (2018)

Modeling the Role of the Microbiome in Evolution.

Frontiers in physiology, 9:1836.

There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.

RevDate: 2019-01-07

Ye S, Bhattacharjee M, E Siemann (2019)

Thermal Tolerance in Green Hydra: Identifying the Roles of Algal Endosymbionts and Hosts in a Freshwater Holobiont Under Stress.

Microbial ecology pii:10.1007/s00248-018-01315-1 [Epub ahead of print].

It has been proposed that holobionts (host-symbiont units) could swap endosymbionts, rapidly alter the hologenome (host plus symbiont genome), and increase their stress tolerance. However, experimental tests of individual and combined contributions of hosts and endosymbionts to holobiont stress tolerance are needed to test this hypothesis. Here, we used six green hydra (Hydra viridissima) strains to tease apart host (hydra) and symbiont (algae) contributions to thermal tolerance. Heat shock experiments with (1) hydra with their original symbionts, (2) aposymbiotic hydra (algae removed), (3) novel associations (a single hydra strain hosting different algae individually), and (4) control hydra (aposymbiotic hydra re-associated with their original algae) showed high variation in thermal tolerance in each group. Relative tolerances of strains were the same within original, aposymbiotic, and control treatments, but reversed in the novel associations group. Aposymbiotic hydra had similar or higher thermal tolerance than hydra with algal symbionts. Selection on the holobiont appears to be stronger than on either partner alone, suggesting endosymbiosis could become an evolutionary trap under climate change. Our results suggest that green hydra thermal tolerance is strongly determined by the host, with a smaller, non-positive role for the algal symbiont. Once temperatures exceed host tolerance limits, swapping symbionts is unlikely to allow these holobionts to persist. Rather, increases in host tolerance through in situ adaptation or migration of pre-adapted host strains appear more likely to increase local thermal tolerance. Overall, our results indicate green hydra is a valuable system for studying aquatic endosymbiosis under changing environmental conditions, and demonstrate how the host and the endosymbiont contribute to holobiont stress tolerance.

RevDate: 2019-01-10

Kamm K, Schierwater B, R DeSalle (2019)

Innate immunity in the simplest animals - placozoans.

BMC genomics, 20(1):5 pii:10.1186/s12864-018-5377-3.

BACKGROUND: Innate immunity provides the core recognition system in animals for preventing infection, but also plays an important role in managing the relationship between an animal host and its symbiont. Most of our knowledge about innate immunity stems from a few animal model systems, but substantial variation between metazoan phyla has been revealed by comparative genomic studies. The exploration of more taxa is still needed to better understand the evolution of immunity related mechanisms. Placozoans are morphologically the simplest organized metazoans and the association between these enigmatic animals and their rickettsial endosymbionts has recently been elucidated. Our analyses of the novel placozoan nuclear genome of Trichoplax sp. H2 and its associated rickettsial endosymbiont genome clearly pointed to a mutualistic and co-evolutionary relationship. This discovery raises the question of how the placozoan holobiont manages symbiosis and, conversely, how it defends against harmful microorganisms. In this study, we examined the annotated genome of Trichoplax sp. H2 for the presence of genes involved in innate immune recognition and downstream signaling.

RESULTS: A rich repertoire of genes belonging to the Toll-like and NOD-like receptor pathways, to scavenger receptors and to secreted fibrinogen-related domain genes was identified in the genome of Trichoplax sp. H2. Nevertheless, the innate immunity related pathways in placozoans deviate in several instances from well investigated vertebrates and invertebrates. While true Toll- and NOD-like receptors are absent, the presence of many genes of the downstream signaling cascade suggests at least primordial Toll-like receptor signaling in Placozoa. An abundance of scavenger receptors, fibrinogen-related domain genes and Apaf-1 genes clearly constitutes an expansion of the immunity related gene repertoire specific to Placozoa.

CONCLUSIONS: The found wealth of immunity related genes present in Placozoa is surprising and quite striking in light of the extremely simple placozoan body plan and their sparse cell type makeup. Research is warranted to reveal how Placozoa utilize this immune repertoire to manage and maintain their associated microbiota as well as to fend-off pathogens.

RevDate: 2019-01-08

Rodriguez-Casariego JA, Ladd MC, Shantz AA, et al (2018)

Coral epigenetic responses to nutrient stress: Histone H2A.X phosphorylation dynamics and DNA methylation in the staghorn coral Acropora cervicornis.

Ecology and evolution, 8(23):12193-12207 pii:ECE34678.

Nutrient pollution and thermal stress constitute two of the main drivers of global change in the coastal oceans. While different studies have addressed the physiological effects and ecological consequences of these stressors in corals, the role of acquired modifications in the coral epigenome during acclimatory and adaptive responses remains unknown. The present work aims to address that gap by monitoring two types of epigenetic mechanisms, namely histone modifications and DNA methylation, during a 7-week-long experiment in which staghorn coral fragments (Acropora cervicornis) were exposed to nutrient stress (nitrogen, nitrogen + phosphorus) in the presence of thermal stress. The major conclusion of this experiment can be summarized by two main results: First, coral holobiont responses to the combined effects of nutrient enrichment and thermal stress involve the post-translational phosphorylation of the histone variant H2A.X (involved in responses to DNA damage), as well as nonsignificant modifications in DNA methylation trends. Second, the reduction in H2A.X phosphorylation (and the subsequent potential impairment of DNA repair mechanisms) observed after prolonged coral exposure to nitrogen enrichment and thermal stress is consistent with the symbiont-driven phosphorus limitation previously observed in corals subject to nitrogen enrichment. The alteration of this epigenetic mechanism could help to explain the synergistic effects of nutrient imbalance and thermal stress on coral fitness (i.e., increased bleaching and mortality) while supporting the positive effect of phosphorus addition to improving coral resilience to thermal stress. Overall, this work provides new insights into the role of epigenetic mechanisms during coral responses to global change, discussing future research directions and the potential benefits for improving restoration, management and conservation of coral reef ecosystems worldwide.

RevDate: 2018-12-19

Esser D, Lange J, Marinos G, et al (2018)

Functions of the Microbiota for the Physiology of Animal Metaorganisms.

Journal of innate immunity pii:000495115 [Epub ahead of print].

Animals are usually regarded as independent entities within their respective environments. However, within an organism, eukaryotes and prokaryotes interact dynamically to form the so-called metaorganism or holobiont, where each partner fulfils its versatile and crucial role. This review focuses on the interplay between microorganisms and multicellular eukaryotes in the context of host physiology, in particular aging and mucus-associated crosstalk. In addition to the interactions between bacteria and the host, we highlight the importance of viruses and nonmodel organisms. Moreover, we discuss current culturing and computational methodologies that allow a deeper understanding of underlying mechanisms controlling the physiology of metaorganisms.

RevDate: 2018-12-21

Proal A, T Marshall (2018)

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity.

Frontiers in pediatrics, 6:373.

The illness ME/CFS has been repeatedly tied to infectious agents such as Epstein Barr Virus. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities. Humans harbor these vast ecosystems of bacteria, viruses and fungi in nearly all tissue and blood. Most well-studied inflammatory conditions are tied to dysbiosis or imbalance of the human microbiome. While gut microbiome dysbiosis has been identified in ME/CFS, microbes and viruses outside the gut can also contribute to the illness. Pathobionts, and their associated proteins/metabolites, often control human metabolism and gene expression in a manner that pushes the body toward a state of illness. Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. Molecular mimicry between host and pathogen proteins/metabolites further complicates this interference. Other human pathogens disable mitochondria or dysregulate host nervous system signaling. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to these persistent microbiome pathogens. Different human pathogens have evolved similar survival mechanisms to disable the host immune response and host metabolic pathways. The metabolic dysfunction driven by these organisms can result in similar clusters of inflammatory symptoms. ME/CFS may be driven by this pathogen-induced dysfunction, with the nature of dysbiosis and symptom presentation varying based on a patient's unique infectious and environmental history. Under such conditions, patients would benefit from treatments that support the human immune system in an effort to reverse the infectious disease process.

RevDate: 2018-12-19

Cernava T, Vasfiu Q, Erlacher A, et al (2018)

Adaptions of Lichen Microbiota Functioning Under Persistent Exposure to Arsenic Contamination.

Frontiers in microbiology, 9:2959.

Host-associated microbiota play an important role in the health and persistence of more complex organisms. In this study, metagenomic analyses were used to reveal microbial community adaptations in three lichen samples as a response to different arsenic concentrations at the sampling sites. Elevated arsenic concentrations at a former mining site expanded the spectrum and number of relevant functions in the lichen-associated microorganisms. Apparent changes affected the abundance of numerous detoxification-related genes, they were substantially enhanced in arsenic-polluted samples. Complementary quantifications of the arsenite S-adenosylmethionine methyltransferase (arsM) gene showed that its abundance is not strictly responding to the environmental arsenic concentrations. The analyzed samples contained rather low numbers of the arsM gene with a maximum of 202 gene copies μl-1 in total community DNA extracts. In addition, bacterial isolates were screened for the presence of arsM. Positive isolates were exposed to different As(III) and As(V) concentrations and tolerated up to 30 mM inorganic arsenic in fluid media, while no substantial biotransformations were observed. Obtained data deepens our understanding related to adaptions of whole microbial communities to adverse environmental conditions. Moreover, this study provides the first evidence that the integrity of bacteria in the lichen holobiont is maintained by acquisition of specific resistances.

RevDate: 2018-12-13

Gibbin E, Gavish A, Krueger T, et al (2018)

Vibrio coralliilyticus infection triggers a behavioural response and perturbs nutritional exchange and tissue integrity in a symbiotic coral.

The ISME journal pii:10.1038/s41396-018-0327-2 [Epub ahead of print].

Under homoeostatic conditions, the relationship between the coral Pocillopora damicornis and Vibrio coralliilyticus is commensal. An increase in temperature, or in the abundance of V. coralliilyticus, can turn this association pathogenic, causing tissue lysis, expulsion of the corals' symbiotic algae (genus Symbiodinium), and eventually coral death. Using a combination of microfluidics, fluorescence microscopy, stable isotopes, electron microscopy and NanoSIMS isotopic imaging, we provide insights into the onset and progression of V. coralliilyticus infection in the daytime and at night, at the tissue and (sub-)cellular level. The objective of our study was to connect the macro-scale behavioural response of the coral to the micro-scale nutritional interactions that occur between the host and its symbiont. In the daytime, polyps enhanced their mucus production, and actively spewed pathogens. Vibrio infection primarily resulted in the formation of tissue lesions in the coenosarc. NanoSIMS analysis revealed infection reduced 13C-assimilation in Symbiodinium, but increased 13C-assimilation in the host. In the night incubations, no mucus spewing was observed, and a mucus film was formed on the coral surface. Vibrio inoculation and infection at night showed reduced 13C-turnover in Symbiodinium, but did not impact host 13C-turnover. Our results show that both the nutritional interactions that occur between the two symbiotic partners and the behavioural response of the host organism play key roles in determining the progression and severity of host-pathogen interactions. More generally, our approach provides a new means of studying interactions (ranging from behavioural to metabolic scales) between partners involved in complex holobiont systems, under both homoeostatic and pathogenic conditions.

RevDate: 2018-12-17

Gobet A, Barbeyron T, Matard-Mann M, et al (2018)

Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches.

Frontiers in microbiology, 9:2740.

About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9T (ATCC 43555T), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface.

RevDate: 2018-12-17

Kenkel CD, LK Bay (2018)

Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition.

PeerJ, 6:e6047.

The coral symbiosis is the linchpin of the reef ecosystem, yet the mechanisms that promote and maintain cooperation between hosts and symbionts have not been fully resolved. We used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism in which symbionts are inherited directly from parents, predicted to enhance cooperation and holobiont fitness. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, which exhibit environmental acquisition of symbionts, were fragmented and subjected to a 2-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological performance and cooperation. All species exhibited similar decreases in symbiont cell density and net photosynthesis in response to elevated temperature, consistent with the onset of bleaching. Yet baseline cooperation, or translocation of photosynthate, in ambient conditions and the reduction in cooperation in response to elevated temperature differed among species. Although Porites lobata and Galaxea acrhelia did exhibit the highest levels of baseline cooperation, we did not observe universally higher levels of cooperation in vertically transmitting species. Post hoc sequencing of the Symbiodinium ITS-2 locus was used to investigate the potential role of differences in symbiont community composition. Interestingly, reductions in cooperation at the onset of bleaching tended to be associated with increased symbiont community diversity among coral species. The theoretical benefits of evolving vertical transmission are based on the underlying assumption that the host-symbiont relationship becomes genetically uniform, thereby reducing competition among symbionts. Taken together, our results suggest that it may not be vertical transmission per se that influences host-symbiont cooperation, but genetic uniformity of the symbiont community, although additional work is needed to test this hypothesis.

RevDate: 2018-12-17

Marasco R, Mosqueira MJ, Fusi M, et al (2018)

Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host.

Microbiome, 6(1):215.

BACKGROUND: The rhizosheath-root system is an adaptive trait of sandy-desert speargrasses in response to unfavourable moisture and nutritional conditions. Under the deserts' polyextreme conditions, plants interact with edaphic microorganisms that positively affect their fitness and resistance. However, the trophic simplicity and environmental harshness of desert ecosystems have previously been shown to strongly influence soil microbial community assembly. We hypothesize that sand-driven ecological filtering constrains the microbial recruitment processes in the speargrass rhizosheath-root niche, prevailing over the plant-induced selection.

METHODS: Bacterial and fungal communities from the rhizosheath-root compartments (endosphere root tissues, rhizosheath and rhizosphere) of three Namib Desert speargrass species (Stipagrostis sabulicola, S. seelyae and Cladoraphis spinosa) along with bulk sand have been studied to test our hypothesis. To minimize the variability determined by edaphic and climatic factors, plants living in a single dune were studied. We assessed the role of plant species vs the sandy substrate on the recruitment and selection, phylogenetic diversity and co-occurrence microbial networks of the rhizosheath-root system microbial communities.

RESULTS: Microorganisms associated with the speargrass rhizosheath-root system were recruited from the surrounding bulk sand population and were significantly enriched in the rhizosheath compartments (105 and 104 of bacterial 16S rRNA and fungal ITS copies per gram of sand to up to 108 and 107 copies per gram, respectively). Furthermore, each rhizosheath-root system compartment hosted a specific microbial community demonstrating strong niche-partitioning. The rhizosheath-root systems of the three speargrass species studied were dominated by desert-adapted Actinobacteria and Alphaproteobacteria (e.g. Lechevalieria, Streptomyces and Microvirga) as well as saprophytic Ascomycota fungi (e.g. Curvularia, Aspergillus and Thielavia). Our results clearly showed a random phylogenetic turnover of rhizosheath-root system associated microbial communities, independent of the plant species, where stochastic factors drive neutral assembly. Co-occurrence network analyses also indicated that the bacterial and fungal community members of the rhizosheath-root systems established a higher number of interactions than those in the barren bulk sand, suggesting that the former are more stable and functional than the latter.

CONCLUSION: Our study demonstrates that the rhizosheath-root system microbial communities of desert dune speargrasses are stochastically assembled and host-independent. This finding supports the concept that the selection determined by the desert sand prevails over that imposed by the genotype of the different plant species.

RevDate: 2019-02-01
CmpDate: 2019-02-01

Baquiran JIP, C Conaco (2018)

Sponge-microbe partnerships are stable under eutrophication pressure from mariculture.

Marine pollution bulletin, 136:125-134.

Sponges harbor a great diversity of symbiotic microorganisms. However, environmental stresses can affect this partnership and influence the health and abundance of the host sponges. In Bolinao, Pangasinan, Philippines, chronic input of organic materials from mariculture activities contributes to a eutrophic coastal environment. To understand how these conditions might affect sponge-microbial partnerships, transplantation experiments were conducted with the marine sponge Gelliodes obtusa. High-throughput sequencing of 16S rRNA revealed that the associated microbial community of the sponges did not exhibit significant shifts after six weeks of transplantation at a eutrophic fish farm site compared to sponges grown at a coral reef or a seagrass area. However, sponges at the fish farm revealed higher abundance of the amoA gene, suggesting that microbiome members are responsive to increased ammonium levels at the site. The stable association between G. obtusa and its microbiome indicates that the sponge holobiont can withstand eutrophication pressure from mariculture.

RevDate: 2018-12-17

Matthews JL, Oakley CA, Lutz A, et al (2018)

Partner switching and metabolic flux in a model cnidarian-dinoflagellate symbiosis.

Proceedings. Biological sciences, 285(1892):.

Metabolite exchange is fundamental to the viability of the cnidarian-Symbiodiniaceae symbiosis and survival of coral reefs. Coral holobiont tolerance to environmental change might be achieved through changes in Symbiodiniaceae species composition, but differences in the metabolites supplied by different Symbiodiniaceae species could influence holobiont fitness. Using 13C stable-isotope labelling coupled to gas chromatography-mass spectrometry, we characterized newly fixed carbon fate in the model cnidarian Exaiptasia pallida (Aiptasia) when experimentally colonized with either native Breviolum minutum or non-native Durusdinium trenchii Relative to anemones containing B. minutum, D. trenchii-colonized hosts exhibited a 4.5-fold reduction in 13C-labelled glucose and reduced abundance and diversity of 13C-labelled carbohydrates and lipogenesis precursors, indicating symbiont species-specific modifications to carbohydrate availability and lipid storage. Mapping carbon fate also revealed significant alterations to host molecular signalling pathways. In particular, D. trenchii-colonized hosts exhibited a 40-fold reduction in 13C-labelled scyllo-inositol, a potential interpartner signalling molecule in symbiosis specificity. 13C-labelling also highlighted differential antioxidant- and ammonium-producing pathway activities, suggesting physiological responses to different symbiont species. Such differences in symbiont metabolite contribution and host utilization may limit the proliferation of stress-driven symbioses; this contributes valuable information towards future scenarios that select in favour of less-competent symbionts in response to environmental change.

RevDate: 2018-12-18

Marangoni LFB, Pinto MMAN, Marques JA, et al (2019)

Copper exposure and seawater acidification interaction: Antagonistic effects on biomarkers in the zooxanthellate scleractinian coral Mussismilia harttii.

Aquatic toxicology (Amsterdam, Netherlands), 206:123-133.

Coral reefs are threatened by global and local impacts, such as ocean acidification (OA) and metal contamination. Toxicity of metals, such as copper (Cu), is expected to be enhanced with OA. However, the interaction between these environmental stressors is still poorly evaluated. In the present study, the interactive effects of seawater acidification and increasing Cu concentrations were evaluated in a zooxanthellate scleractinian coral (Mussismilia harttii), using biochemical biomarkers involved in the coral calcification process and the photosynthetic metabolism of endosymbionts. Corals were kept under control conditions (no seawater acidification and no Cu addition in seawater) or exposed to combined treatments of reduced seawater pH (8.1, 7.8, 7.5 and 7.2) and environmentally relevant concentrations of dissolved Cu (measured: 1.0, 1.6, 2.3 and 3.2 μg/L) in a mesocosm system. After 15- and 35-days exposure, corals were analyzed for photochemical efficiency (Fv/Fm), chlorophyll a content, Ca-ATPase and carbonic anhydrase (CA) activity. Results showed that 76% of the interactions between reduced seawater pH and increasing Cu concentrations were antagonistic. Only 24% of these interactions were additive or synergistic. In general, the combination of stressors had no significant deleterious effects in the photosynthetic metabolism of endosymbionts or Ca-ATPase activity. In fact, the lowest dissolved Cu concentration tested had a consistent positive effect on Ca-ATPase activity in corals facing any of the reduced seawater pH conditions tested. In turn, potentially deleterious effects on acid-base balance in M. harttii, associated with changes in CA activity, were intensified by the combination of stressors. Findings reported here indicate that Cu toxicity in future OA scenarios can be less severe than previously suggested in this coral holobiont.

RevDate: 2018-12-07

Kokou F, Sasson G, Nitzan T, et al (2018)

Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature.

eLife, 7:.

The hologenome concept proposes that microbes and their host organism are an independent unit of selection. Motivated by this concept, we hypothesized that thermal acclimation in poikilothermic organisms, owing to their inability to maintain their body temperature, is connected to their microbiome composition. To test this hypothesis, we used a unique experimental setup with a transgenerational selective breeding scheme for cold tolerance in tropical tilapias. We tested the effects of the selection on the gut microbiome and on host transcriptomic response. Interestingly, we found that host genetic selection for thermal tolerance shapes the microbiome composition and its response to cold. The microbiomes of cold-resistant fish showed higher resilience to temperature changes, indicating that the microbiome is shaped by its host's selection. These findings are consistent with the hologenome concept and highlight the connection between the host and its microbiome's response to the environment.

RevDate: 2018-12-07

O'Brien PA, Smith HA, Fallon S, et al (2018)

Elevated CO2 Has Little Influence on the Bacterial Communities Associated With the pH-Tolerant Coral, Massive Porites spp.

Frontiers in microbiology, 9:2621.

Ocean acidification (OA) as a result of increased anthropogenic CO2 input into the atmosphere carries consequences for all ocean life. Low pH can cause a shift in coral-associated microbial communities of pCO2-sensitive corals, however, it remains unknown whether the microbial community is also influenced in corals known to be more tolerant to high pCO2/low pH. This study profiles the bacterial communities associated with the tissues of the pCO2-tolerant coral, massive Porites spp., from two natural CO2 seep sites in Papua New Guinea. Amplicon sequencing of the hypervariable V3-V4 regions of the 16S rRNA gene revealed that microbial communities remained stable across CO2 seep sites (pH = 7.44-7.85) and adjacent control sites (ambient pH = 8.0-8.1). Microbial communities were more significantly influenced by reef location than pH, with the relative abundance of dominant microbial taxa differing between reefs. These results directly contrast with previous findings that increased CO2 has a strong effect on structuring microbial communities. The stable structure of microbial communities associated with the tissues of massive Porites spp. under high pCO2/low pH conditions confirms a high degree of tolerance by the whole Porites holobiont to OA, and suggest that pH tolerant corals such as Porites may dominate reef assemblages in an increasingly acidic ocean.

RevDate: 2019-01-01

Goüy de Bellocq J, Wasimuddin , Ribas A, et al (2018)

Holobiont suture zones: Parasite evidence across the European house mouse hybrid zone.

Molecular ecology, 27(24):5214-5227.

Parasite hybrid zones resulting from host secondary contact have never been described in nature although parasite hybridization is well known and secondary contact should affect them similarly to free-living organisms. When host populations are isolated, diverge and recontact, intimate parasites (host specific, direct life cycle) carried during isolation will also meet and so may form parasite hybrid zones. If so, we hypothesize these should be narrower than the host's hybrid zone as shorter parasite generation time allows potentially higher divergence. We investigate multilocus genetics of two parasites across the European house mouse hybrid zone. We find each host taxon harbours its own parasite taxa. These also hybridize: Parasite hybrid zones are significantly narrower than the host's. Here, we show a host hybrid zone is a suture zone for a subset of its parasite community and highlight the potential of such systems as windows on the evolutionary processes of host-parasite interactions and recombinant pathogen emergence.

RevDate: 2019-02-03

Castillo-Álvarez F, ME Marzo-Sola (2019)

Disease of the holobiont, the example of multiple sclerosis.

Medicina clinica, 152(4):147-153.

In recent years there has been a revolution regarding the role of the microbiota in different diseases, most of them within the spectrum of inflammatory and autoimmune diseases, associated with the development of metagenomics and the concept of holobiont, a large organism together with its microbiota. Specifically, in Multiple Sclerosis, multiple evidence points to the role of the microbiota in experimental autoimmune encephalomyelitis, animal model of the disease, and several articles have been published in recent years about differences in intestinal microbiota among patients with multiple sclerosis and control subjects. We review in this article the concept of holobiont and the gut microbiota functions, as well as the evidence accumulated about the role of the microbiota in experimental autoimmune encephalomyelitis and multiple sclerosis. Nowadays, there is a lot of evidence showing the role of the microbiota in the genesis, prevention and treatment of experimental autoimmune encephalomyelitis based mainly on three immunological pillars, the Th1-Th17 / Th2 balance, the Treg cells and the humoral immunity. It is also well documented that there are differences in the microbiota of patients with MS that are associated with a different expression of genes related to inflammation.

RevDate: 2018-12-07

Galand PE, Chapron L, Meistertzheim AL, et al (2018)

The Effect of Captivity on the Dynamics of Active Bacterial Communities Differs Between Two Deep-Sea Coral Species.

Frontiers in microbiology, 9:2565.

Microbes play a crucial role in sustaining the coral holobiont's functions and in particular under the pressure of environmental stressors. The effect of a changing environment on coral health is now a major branch of research that relies heavily on aquarium experiments. However, the effect of captivity on the coral microbiome remains poorly known. Here we show that different cold-water corals species have different microbiome responses to captivity. For both the DNA and the RNA fraction, Madrepora oculata bacterial communities were maintained for at least 6 months of aquarium rearing, while Lophelia pertusa bacteria changed within a day. Interestingly, bacteria from the genus Endozoicomonas, a ubiquitous symbiont of numerous marine hosts, were resilient and remained active in M. oculata for several months. Our results demonstrate that a good knowledge of the coral microbiome and an understanding of the ecological strategy of the holobiont is needed before designing aquarium experiments.

RevDate: 2018-12-07

Ochsenkühn MA, Schmitt-Kopplin P, Harir M, et al (2018)

Coral metabolite gradients affect microbial community structures and act as a disease cue.

Communications biology, 1:184.

Corals are threatened worldwide due to prevalence of disease and bleaching. Recent studies suggest the ability of corals to resist disease is dependent on maintaining healthy microbiomes that span coral tissues and surfaces, the holobiont. Although our understanding of the role endosymbiotic microbes play in coral health has advanced, the role surface-associated microbes and their chemical signatures play in coral health is limited. Using minimally invasive water sampling, we show that the corals Acropora and Platygyra harbor unique bacteria and metabolites at their surface, distinctly different from surrounding seawater. The surface metabolites released by the holobiont create concentration gradients at 0-5 cm away from the coral surface. These molecules are identified as chemo-attractants, antibacterials, and infochemicals, suggesting they may structure coral surface-associated microbes. Further, we detect surface-associated metabolites characteristic of healthy or white syndrome disease infected corals, a finding which may aid in describing effects of diseases.

RevDate: 2018-12-07

Mazel F, Davis KM, Loudon A, et al (2018)

Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?.

mSystems, 3(5):.

Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.

RevDate: 2018-11-10

Villegas-Plazas M, Wos-Oxley ML, Sanchez JA, et al (2018)

Variations in Microbial Diversity and Metabolite Profiles of the Tropical Marine Sponge Xestospongia muta with Season and Depth.

Microbial ecology pii:10.1007/s00248-018-1285-y [Epub ahead of print].

Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.

RevDate: 2018-12-26

Morris JJ (2018)

What is the hologenome concept of evolution?.

F1000Research, 7:.

All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host-microbiome ecosystem as a "holobiont". Because natural selection acts on an organism's realized phenotype, and the phenotype of a holobiont is the result of the integrated activities of both the host and all of its microbiome inhabitants, it is reasonable to think that evolution can act at the level of the holobiont and cause changes in the "hologenome", or the collective genomic content of all the individual bionts within the holobiont. This relatively simple assertion has nevertheless been controversial within the microbiome community. Here, I provide a review of recent work on the hologenome concept of evolution. I attempt to provide a clear definition of the concept and its implications and to clarify common points of disagreement.

RevDate: 2018-11-14

Backer R, Rokem JS, Ilangumaran G, et al (2018)

Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture.

Frontiers in plant science, 9:1473.

Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology.

RevDate: 2018-12-17

Pasquaretta C, Gómez-Moracho T, Heeb P, et al (2018)

Exploring Interactions between the Gut Microbiota and Social Behavior through Nutrition.

Genes, 9(11):.

Microbes influence a wide range of host social behaviors and vice versa. So far, however, the mechanisms underpinning these complex interactions remain poorly understood. In social animals, where individuals share microbes and interact around foods, the gut microbiota may have considerable consequences on host social interactions by acting upon the nutritional behavior of individual animals. Here we illustrate how conceptual advances in nutritional ecology can help the study of these processes and allow the formulation of new empirically testable predictions. First, we review key evidence showing that gut microbes influence the nutrition of individual animals, through modifications of their nutritional state and feeding decisions. Next, we describe how these microbial influences and their social consequences can be studied by modelling populations of hosts and their gut microbiota into a single conceptual framework derived from nutritional geometry. Our approach raises new perspectives for the study of holobiont nutrition and will facilitate theoretical and experimental research on the role of the gut microbiota in the mechanisms and evolution of social behavior.

RevDate: 2018-11-02

Sewell AK, Han M, B Qi (2018)

An unexpected benefit from E. coli: how enterobactin benefits host health.

Microbial cell (Graz, Austria), 5(10):469-471 pii:MIC0178E160.

Iron plays many critical roles in human biology, such as aiding the transport of oxygen and mediating redox reactions. Iron is essential for life, yet little is known about how iron is taken up into mitochondria to impact the labile iron pool. Iron deficiency is one of the most prevalent human nutrient-deficiency diseases in the world and is a major cause of anemia that affects >25% of the world's population, but unfortunately the current treatment (oral iron supplementation) is inefficient and has many side effects. A greater understanding of iron uptake, and discovery of molecules that aid in this process, may lead to more effective treatments for iron deficiency. In this study, we uncovered a unique and surprising role for an Escherichia coli-produced siderophore enterobactin (Ent) that facilitates iron uptake by the host, observed in both C. elegans and mammalian cells. Although siderophores are well-known Fe+3 scavengers, this activity has previously been described to only benefit iron acquisition by bacteria, not the host. This unexpected function is dependent on the binding of Ent to the host's ATP synthase α-subunit but is independent of other subunits of the ATP synthase. This finding marks a major shift regarding the role of this siderophore in the "iron tug-of-war" paradigm, which is often used to describe the fight between the bacteria and the host for this essential micronutrient. Instead, this study presents E. coli as a commensal "friend" that provides a molecule that supports the host's iron homeostasis. This work reveals a novel, beneficial role of a bacteria-generated molecule in aiding the host's iron homeostasis, and points to surprising new benefits from commensal bacteria.

RevDate: 2018-10-31

Miller WB, Torday JS, F Baluška (2018)

Biological evolution as defense of 'self'.

Progress in biophysics and molecular biology pii:S0079-6107(18)30151-2 [Epub ahead of print].

Although the origin of self-referential consciousness is unknown, it can be argued that the instantiation of self-reference was the commencement of the living state as phenomenal experientiality. As self-referential cognition is demonstrated by all living organisms, life can be equated with the sustenance of cellular homeostasis in the continuous defense of 'self'. It is proposed that the epicenter of 'self' is perpetually embodied within the basic cellular form in which it was instantiated. Cognition-Based Evolution argues that all of biological and evolutionary development represents the perpetual autopoietic defense of self-referential basal cellular states of homeostatic preference. The means by which these states are attained and maintained is through self-referential measurement of information and its communication. The multicellular forms, either as biofilms or holobionts, represent the cellular attempt to achieve maximum states of informational distinction and energy efficiency through individual and collective means. In this frame, consciousness, self-consciousness and intelligence can be identified as forms of collective cellular phenotype directed towards the defense of fundamental cellular self-reference.

RevDate: 2019-01-31

Thomashow LS, LeTourneau MK, Kwak YS, et al (2019)

The soil-borne legacy in the age of the holobiont.

Microbial biotechnology, 12(1):51-54.

Future efforts to increase agricultural productivity will focus on crops as functional units comprised of plants and their associated microflora in the context of the various environments in which they are grown. It is suggested that future efforts to increase agricultural productivity will focus on crops as functional units comprised of plants and their associated beneficial microorganisms in the context in which they are grown. Scientists, industry, and farmers must work closely together to develop, adapt, and apply new technologies to a wide range of cropping systems. Consumer education is needed help grow public awareness that 'plant probiotics' offer a safe and environmentally friendly alternative to dependence on the use of chemical pesticides.

RevDate: 2018-11-21

Leftwich PT, Hutchings MI, T Chapman (2018)

Diet, Gut Microbes and Host Mate Choice: Understanding the significance of microbiome effects on host mate choice requires a case by case evaluation.

BioEssays : news and reviews in molecular, cellular and developmental biology, 40(12):e1800053.

All organisms live in close association with microbes. However, not all such associations are meaningful in an evolutionary context. Current debate concerns whether hosts and microbes are best described as communities of individuals or as holobionts (selective units of hosts plus their microbes). Recent reports that assortative mating of hosts by diet can be mediated by commensal gut microbes have attracted interest as a potential route to host reproductive isolation (RI). Here, the authors discuss logical problems with this line of argument. The authors briefly review how microbes can affect host mating preferences and evaluate recent findings from fruitflies. Endosymbionts can potentially influence host RI given stable and recurrent co-association of hosts and microbes over evolutionary time. However, observations of co-occurrence of microbes and hosts are ripe for misinterpretation and such associations will rarely represent a meaningful holobiont. A framework in which hosts and their microbes are independent evolutionary units provides the only satisfactory explanation for the observed range of effects and associations.

RevDate: 2019-01-20

Cernava T, Aschenbrenner IA, Soh J, et al (2019)

Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota.

The ISME journal, 13(2):547-556.

The role of host-associated microbiota in enduring dehydration and drought is largely unknown. We have used lichens to study this increasingly important problem because they are the organisms that are optimally adapted to reoccurring hydration/dehydration cycles, and they host a defined and persistent bacterial community. The analysis of metatranscriptomic datasets from bacterial communities of the lung lichen (Lobaria pulmonaria (L.) Hoffm.), sampled under representative hydration stages, revealed significant structural shifts and functional specialization to host conditions. The hydrated samples showed upregulated transcription of transport systems, tRNA modification and various porins (Omp2b by Rhizobiales), whereas the desiccated samples showed different functions related to stress adaption prominently. Carbohydrate metabolism was activated under both conditions. Under dry conditions, upregulation of a specialized ketone metabolism indicated a switch to lipid-based nutrition. Several bacterial lineages were involved in a functional transition that was reminiscent of a 'fasting metaorganism'. Similar functional adaptions were assigned to taxonomically unrelated groups, indicating hydration-related specialization of the microbiota. We were able to show that host-associated bacterial communities are well adapted to dehydration by stress protection and changes of the metabolism. Moreover, our results indicate an intense interplay in holobiont functioning under drought stress.

RevDate: 2019-01-03
CmpDate: 2019-01-03

Zepeda Mendoza ML, Roggenbuck M, Manzano Vargas K, et al (2018)

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.

Acta veterinaria Scandinavica, 60(1):61.

BACKGROUND: Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut.

RESULTS: We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut.

CONCLUSIONS: Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.

RevDate: 2019-01-30

Guyomar C, Legeai F, Jousselin E, et al (2018)

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.

Microbiome, 6(1):181.

BACKGROUND: Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact.

RESULTS: We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host.

CONCLUSIONS: We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.

RevDate: 2019-01-23

Hernandez-Agreda A, Leggat W, Bongaerts P, et al (2018)

Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere.

mBio, 9(5):.

Studies of the coral microbiome predominantly characterize the microbial community of the host species as a collective, rather than that of the individual. This ecological perspective on the coral microbiome has led to the conclusion that the coral holobiont is the most diverse microbial biosphere studied thus far. However, investigating the microbiome of the individual, rather than that of the species, highlights common and conserved community attributes which can provide insights into the significance of microbial associations to the host. Here, we show there are consistent characteristics between individuals in the proposed three components of the coral microbiome (i.e., "environmentally responsive community," "resident or individual microbiome," and "core microbiome"). We found that the resident microbiome of a photoendosymbiotic coral harbored <3% (∼605 phylotypes) of the 16S rRNA phylotypes associated with all investigated individuals of that species ("species-specific microbiome") (∼21,654 phylotypes; individuals from Pachyseris speciosa [n = 123], Mycedium elephantotus [n = 95], and Acropora aculeus [n = 91] from 10 reef locations). The remaining bacterial phylotypes (>96%) (environmentally responsive community) of the species-specific microbiome were in fact not found in association with the majority of individuals of the species. Only 0.1% (∼21 phylotypes) of the species-specific microbiome of each species was shared among all individuals of the species (core microbiome), equating to ∼3.4% of the resident microbiome. We found taxonomic redundancy and consistent patterns of composition, structure, and taxonomic breadth across individual microbiomes from the three coral species. Our results demonstrate that the coral microbiome is structured at the individual level.IMPORTANCE We propose that the coral holobiont should be conceptualized as a diverse transient microbial community that is responsive to the surrounding environment and encompasses a simple, redundant, resident microbiome and a small conserved core microbiome. Most importantly, we show that the coral microbiome is comparable to the microbiomes of other organisms studied thus far. Accurately characterizing the coral-microbe interactions provides an important baseline from which the functional roles and the functional niches within which microbes reside can be deciphered.

RevDate: 2019-02-03

Mancini MV, Damiani C, Accoti A, et al (2018)

Estimating bacteria diversity in different organs of nine species of mosquito by next generation sequencing.

BMC microbiology, 18(1):126.

BACKGROUND: Symbiosis in insects is accumulating significant amount of studies: the description of a wide array of mutualistic associations across the evolutionary history of insects suggests that resident microbiota acts as a driving force by affecting several aspects of hosts biology. Among arthropods, mosquito midgut microbiota has been largely investigated, providing crucial insights on the role and implications of host-symbiont relationships. However, limited amount of studies addressed their efforts on the investigation of microbiota colonizing salivary glands and reproductive tracts, crucial organs for pathogen invasion and vertical transmission of symbiotic microorganisms. Using 16S rRNA gene sequencing-based approach, we analysed the microbiota of gut, salivary glands and reproductive tracts of several mosquito species, representing some of the main vectors of diseases, aiming at describing the dynamics of bacterial communities within the individual.

RESULTS: We identified a shared core microbiota between different mosquito species, although interesting inter- and intra-species differences were detected. Additionally, our results showed deep divergences between genera, underlining microbiota specificity and adaptation to their host.

CONCLUSIONS: The comprehensive landscape of the bacterial microbiota components may ultimately provide crucial insights and novel targets for possible application of symbionts in innovative strategies for the control of vector borne diseases, globally named Symbiotic Control (SC), and suggesting that the holobiont of different mosquito species may significantly vary. Moreover, mosquito species are characterized by distinctive microbiota in different organs, likely reflecting different functions and/or adaptation processes.

RevDate: 2018-11-14

Palmer CV (2018)

Immunity and the coral crisis.

Communications biology, 1:91.

Climate change is killing coral at an unprecedented rate. As immune systems promote homeostasis and survival of adverse conditions I propose we explore coral health in the context of holobiont immunity.

RevDate: 2018-12-11

Løvendahl P, Difford GF, Li B, et al (2018)

Review: Selecting for improved feed efficiency and reduced methane emissions in dairy cattle.

Animal : an international journal of animal bioscience, 12(s2):s336-s349.

It may be possible for dairy farms to improve profitability and reduce environmental impacts by selecting for higher feed efficiency and lower methane (CH4) emission traits. It remains to be clarified how CH4 emission and feed efficiency traits are related to each other, which will require direct and accurate measurements of both of these traits in large numbers of animals under the conditions in which they are expected to perform. The ranking of animals for feed efficiency and CH4 emission traits can differ depending upon the type and duration of measurement used, the trait definitions and calculations used, the period in lactation examined and the production system, as well as interactions among these factors. Because the correlation values obtained between feed efficiency and CH4 emission data are likely to be biased when either or both are expressed as ratios, therefore researchers would be well advised to maintain weighted components of the ratios in the selection index. Nutrition studies indicate that selecting low emitting animals may result in reduced efficiency of cell wall digestion, that is NDF, a key ruminant characteristic in human food production. Moreover, many interacting biological factors that are not measured directly, including digestion rate, passage rate, the rumen microbiome and rumen fermentation, may influence feed efficiency and CH4 emission. Elucidating these mechanisms may improve dairy farmers ability to select for feed efficiency and reduced CH4 emission.

RevDate: 2018-11-20
CmpDate: 2018-11-20

Cavalcanti GS, Shukla P, Morris M, et al (2018)

Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification.

BMC genomics, 19(1):701.

BACKGROUND: Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) that are photosynthesizers, calcifiers, and ecosystem engineers and therefore represent important targets for ocean acidification (OA) research. Here, we exposed live rhodoliths to near-future OA conditions to investigate responses in their photosynthetic capacity, calcium carbonate production, and associated microbiome using carbon uptake, decalcification assays, and whole genome shotgun sequencing metagenomic analysis, respectively. The results from our live rhodolith assays were compared to similar manipulations on dead rhodolith (calcareous skeleton) biofilms and water column microbial communities, thereby enabling the assessment of host-microbiome interaction under climate-driven environmental perturbations.

RESULTS: Under high pCO2 conditions, live rhodoliths exhibited positive physiological responses, i.e. increased photosynthetic activity, and no calcium carbonate biomass loss over time. Further, whereas the microbiome associated with live rhodoliths remained stable and resembled a healthy holobiont, the microbial community associated with the water column changed after exposure to elevated pCO2.

CONCLUSIONS: Our results suggest that a tightly regulated microbial-host interaction, as evidenced by the stability of the rhodolith microbiome recorded here under OA-like conditions, is important for host resilience to environmental stress. This study extends the scarce comprehension of microbes associated with rhodolith beds and their reaction to increased pCO2, providing a more comprehensive approach to OA studies by assessing the host holobiont.

RevDate: 2018-11-14

Stencel A, DM Wloch-Salamon (2018)

Correction to: Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation.

Theory in biosciences = Theorie in den Biowissenschaften, 137(2):207-208.

The original version of this article unfortunately contained a mistake.

RevDate: 2018-11-14

Clerissi C, Brunet S, Vidal-Dupiol J, et al (2018)

Protists Within Corals: The Hidden Diversity.

Frontiers in microbiology, 9:2043.

Previous observations suggested that microbial communities contribute to coral health and the ecological resilience of coral reefs. However, most studies of coral microbiology focused on prokaryotes and the endosymbiotic algae Symbiodinium. In contrast, knowledge concerning diversity of other protists is still lacking, possibly due to methodological constraints. As most eukaryotic DNA in coral samples was derived from hosts, protist diversity was missed in metagenome analyses. To tackle this issue, we designed blocking primers for Scleractinia sequences amplified with two primer sets that targeted variable loops of the 18S rRNA gene (18SV1V2 and 18SV4). These blocking primers were used on environmental colonies of Pocillopora damicornis sensu lato from two regions with contrasting thermal regimes (Djibouti and New Caledonia). In addition to Symbiodinium clades A/C/D, Licnophora and unidentified coccidia genera were found in many samples. In particular, coccidian sequences formed a robust monophyletic clade with other protists identified in Agaricia, Favia, Montastraea, Mycetophyllia, Porites, and Siderastrea coral colonies. Moreover, Licnophora and coccidians had different distributions between the two geographic regions. A similar pattern was observed between Symbiodinium clades C and A/D. Although we were unable to identify factors responsible for this pattern, nor were we able to confirm that these taxa were closely associated with corals, we believe that these primer sets and the associated blocking primers offer new possibilities to describe the hidden diversity of protists within different coral species.

RevDate: 2018-10-26

Carthey AJR, Gillings MR, DT Blumstein (2018)

The Extended Genotype: Microbially Mediated Olfactory Communication.

Trends in ecology & evolution, 33(11):885-894.

Microbes are now known to influence inter- and intraspecific olfactory signaling systems. They do so by producing metabolites that function as odorants. A unique attribute of such odorants is that they arise as a product of microbial-host interactions. These interactions need not be mutualistic, and indeed can be antagonistic. We develop an integrated ecoevolutionary model to explore microbially mediated olfactory communication and a process model that illustrates the various ways that microbial products might contribute to odorants. This novel approach generates testable predictions, including that selection to incorporate microbial products should be a common feature of infochemicals that communicate identity but not those that communicate fitness or quality. Microbes extend an individual's genotype, but also enhance vulnerability to environmental change.

RevDate: 2019-02-07

Bredon M, Dittmer J, Noël C, et al (2018)

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate.

Microbiome, 6(1):162.

BACKGROUND: Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action. Some invertebrates express a few endogenous lignocellulose-degrading enzymes but in most species, an efficient degradation and digestion of lignocellulose can only be achieved through mutualistic associations with endosymbionts. Similar to termites, it has been suspected that several bacterial symbionts may be involved in lignocellulose degradation in terrestrial isopods, by completing the CAZyme repertoire of their hosts.

RESULTS: To test this hypothesis, host transcriptomic and microbiome shotgun metagenomic datasets were obtained and investigated from the pill bug Armadillidium vulgare. Many genes of bacterial and archaeal origin coding for CAZymes were identified in the metagenomes of several host tissues and the gut content of specimens from both laboratory lineages and a natural population of A. vulgare. Some of them may be involved in the degradation of cellulose, hemicellulose, and lignin. Reconstructing a lignocellulose-degrading microbial community based on the prokaryotic taxa contributing relevant CAZymes revealed two taxonomically distinct but functionally redundant microbial communities depending on host origin. In parallel, endogenous CAZymes were identified from the transcriptome of the host and their expression in digestive tissues was demonstrated by RT-qPCR, demonstrating a complementary enzyme repertoire for lignocellulose degradation from both the host and the microbiome in A. vulgare.

CONCLUSIONS: Our results provide new insights into the role of the microbiome in the evolution of terrestrial isopods and their adaptive radiation in terrestrial habitats.

RevDate: 2019-02-07

Sitaraman R (2018)

Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.

Microbiome, 6(1):163.

The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.

RevDate: 2018-09-15

Bernasconi R, Stat M, Koenders A, et al (2018)

Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont.

Microbial ecology pii:10.1007/s00248-018-1255-4 [Epub ahead of print].

Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the co-occurrence of multiple partners within the coral 'holobiont' and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus Symbiodinium and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and Symbiodinium with 13 coral genera across six water basins. The majority of the bacteria-Symbiodinium co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and Symbiodinium that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.

RevDate: 2019-01-28

Wenzel MA, Douglas A, SB Piertney (2018)

Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons).

PloS one, 13(8):e0202212.

The increasingly recognised effects of microbiomes on the eco-evolutionary dynamics of their hosts are promoting a view of the "hologenome" as an integral host-symbiont evolutionary entity. For example, sex-ratio distorting reproductive parasites such as Wolbachia are well-studied pivotal drivers of invertebrate reproductive processes, and more recent work is highlighting novel effects of microbiome assemblages on host mating behaviour and developmental incompatibilities that underpin or reinforce reproductive isolation processes. However, examining the hologenome and its eco-evolutionary effects in natural populations is challenging because microbiome composition is considerably influenced by environmental factors. Here we illustrate these challenges in a sympatric species complex of intertidal isopods (Jaera albifrons spp.) with pervasive sex-ratio distortion and ecological and behavioural reproductive isolation mechanisms. We deep-sequence the bacterial 16S rRNA gene among males and females collected in spring and summer from two coasts in north-east Scotland, and examine microbiome composition with a particular focus on reproductive parasites. Microbiomes of all species were diverse (overall 3,317 unique sequences among 3.8 million reads) and comprised mainly Proteobacteria and Bacteroidetes taxa typical of the marine intertidal zone, in particular Vibrio spp. However, we found little evidence of the reproductive parasites Wolbachia, Rickettsia, Spiroplasma and Cardinium, suggesting alternative causes of sex-ratio distortion. Notwithstanding, a significant proportion of the variance in microbiome composition among samples was explained by sex (14.1 %), nested within geographic (26.9 %) and seasonal (39.6 %) variance components. The functional relevance of this sex signal was difficult to ascertain given the absence of reproductive parasites, the ephemeral nature of the species assemblages and substantial environmental variability. These results establish the Jaera albifrons species complex as an intriguing system for examining the effects of microbiomes on reproductive processes and speciation, and highlight the difficulties associated with snapshot assays of microbiome composition in dynamic and complex environments.

RevDate: 2018-08-29

Basso V, De Freitas Pereira M, Maillard F, et al (2018)

Facing global change: the millennium challenge for plant scientists: 41st New Phytologist Symposium 'Plant sciences for the future', Nancy, France, April 2018.

The New phytologist, 220(1):25-29.

RevDate: 2018-10-10

Allard SM, Ottesen AR, Brown EW, et al (2018)

Insect exclusion limits variation in bacterial microbiomes of tomato flowers and fruit.

Journal of applied microbiology [Epub ahead of print].

AIMS: The effect of insect exclusion via netting on bacterial microbiota associated with field-grown tomato fruit and flowers was evaluated.

METHODS AND RESULTS: Amplicon-based bacterial community profiling from insect-exposed plants and plants wrapped in nylon mosquito netting was conducted on total DNA extracted from tomato flower and mature unripe fruit washes. The V1-V3 region of the 16S rRNA gene was sequenced using Illumina MiSeq and analysed using qiime ver. 1.8. The carposphere supported significantly more phylogenetic diversity (PD) compared to the anthosphere, as measured by operational taxonomic unit richness (P = 0·001) and Faith's PD (P = 0·004). Flowers and fruit hosted distinct bacterial community structures (R2 = 0·27, P = 0·001), with specific taxonomic differences in taxa that included the Xanthomonadaceae (higher in flowers), and the Pseudomonadaceae, Methylobacteriaceae and Rhizobiales (higher in fruit) (FDR-P < 0·05). Bacterial community profiles of netted plants were overall statistically similar to non-netted plants for both flowers and fruit (P > 0·10). However, less variation between samples was observed among flowers (~50% less, P = 0·004) and green fruit (~10% less, P = 0·038) collected from netted than non-netted plants.

CONCLUSION: Insects may introduce or augment variability in bacterial diversity associated with tomato flowers and potentially green fruit surfaces.

This work contributes to knowledge on microbiome dynamics of the tomato holobiont. Deciphering drivers of bacterial diversity and community structure of fruit crops could reveal processes important to agricultural management, such as competitive exclusion of pathogens and priming of plant defense mechanisms.

RevDate: 2018-12-11
CmpDate: 2018-12-11

Stabili L, Parisi MG, Parrinello D, et al (2018)

Cnidarian Interaction with Microbial Communities: From Aid to Animal's Health to Rejection Responses.

Marine drugs, 16(9):.

The phylum Cnidaria is an ancient branch in the tree of metazoans. Several species exert a remarkable longevity, suggesting the existence of a developed and consistent defense mechanism of the innate immunity capable to overcome the potential repeated exposure to microbial pathogenic agents. Increasing evidence indicates that the innate immune system in Cnidarians is not only involved in the disruption of harmful microorganisms, but also is crucial in structuring tissue-associated microbial communities that are essential components of the Cnidarian holobiont and useful to the animal's health for several functions, including metabolism, immune defense, development, and behavior. Sometimes, the shifts in the normal microbiota may be used as "early" bio-indicators of both environmental changes and/or animal disease. Here the Cnidarians relationships with microbial communities and the potential biotechnological applications are summarized and discussed.

RevDate: 2018-11-14

Van Duyl FC, Mueller B, EH Meesters (2018)

Spatio-temporal variation in stable isotope signatures (δ13C and δ15N) of sponges on the Saba Bank.

PeerJ, 6:e5460.

Sponges are ubiquitous on coral reefs, mostly long lived and therefore adaptive to changing environmental conditions. They feed on organic matter withdrawn from the passing water and they may harbor microorganisms (endosymbionts), which contribute to their nutrition. Their diets and stable isotope (SI) fractionation determine the SI signature of the sponge holobiont. Little is known of spatio-temporal variations in SI signatures of δ13C and δ15N in tropical sponges and whether they reflect variations in the environment. We investigated the SI signatures of seven common sponge species with different functional traits and their potential food sources between 15 and 32 m depth along the S-SE and E-NE side of the Saba Bank, Eastern Caribbean, in October 2011 and October 2013. SI signatures differed significantly between most sponge species, both in mean values and in variation, indicating different food preferences and/or fractionation, inferring sponge species-specific isotopic niche spaces. In 2011, all sponge species at the S-SE side were enriched in d13C compared to the E-NE side. In 2013, SI signatures of sponges did not differ between the two sides and were overall lighter in δ13C and δ15N than in 2011. Observed spatio-temporal changes in SI in sponges could not be attributed to changes in the SI signatures of their potential food sources, which remained stable with different SI signatures of pelagic (particulate organic matter (POM): δ13C -24.9‰, δ15N +4.3‰) and benthic-derived food (macroalgae: δ13C -15.4‰, δ15N +0.8‰). Enriched δ13C signatures in sponges at the S-SE side in 2011 are proposed to be attributed to predominantly feeding on benthic-derived C. This interpretation was supported by significant differences in water mass constituents between sides in October 2011. Elevated NO3 and dissolved organic matter concentrations point toward a stronger reef signal in reef overlying water at the S-SE than N-NE side of the Bank in 2011. The depletions of δ13C and δ15N in sponges in October 2013 compared to October 2011 concurred with significantly elevated POM concentrations. The contemporaneous decrease in δ15N suggests that sponges obtain their N mostly from benthic-derived food with a lower δ15N than pelagic food. Average proportional feeding on available sources varied between sponge species and ranged from 20% to 50% for benthic and 50% to 80% for pelagic-derived food, assuming trophic enrichment factors of 0.5‰ ± sd 0.5 for δ13C and 3‰ ± sd 0.5 for δ15N for sponges. We suggest that observed variation of SI in sponges between sides and years were the result of shifts in the proportion of ingested benthic- and pelagic-derived organic matter driven by environmental changes. We show that sponge SI signatures reflect environmental variability in space and time on the Saba Bank and that SI of sponges irrespective of their species-specific traits move in a similar direction in response to these environmental changes.

RevDate: 2018-11-29

Kranabetter JM, Harman-Denhoed R, BJ Hawkins (2019)

Saprotrophic and ectomycorrhizal fungal sporocarp stoichiometry (C : N : P) across temperate rainforests as evidence of shared nutrient constraints among symbionts.

The New phytologist, 221(1):482-492.

Quantifying nutritional dynamics of free-living saprotrophs and symbiotic ectomycorrhizal fungi in the field is challenging, but the stoichiometry of fruiting bodies (sporocarps) may be an effective methodology for this purpose. Carbon (C), nitrogen (N) and phosphorus (P) concentrations of soils, foliage and 146 sporocarp collections were analyzed from 14 Pseudotsuga menziesii var. menziesii stands across a podzolization gradient on Vancouver Island (Canada). N and P concentrations were considerably higher in saprotrophic fungi. Fungal N% increased with soil N content at a greater rate for saprotrophs than ectomycorrhizal fungi, while fungal P% of saprotrophs was more constrained. Fungal N : P was more responsive to soil N : P for ectomycorrhizal fungi (homeostatic regulation coefficient 'H' = 2.9) than saprotrophs (H = 5.9), while N : P of ectomycorrhizal fungi and host tree foliage scaled almost identically. Results underscore the role of ectomycorrhizal fungi as nutrient conduits, supporting host trees, whereas saprotrophs maintain a greater degree of nutritional homeostasis. Site nutrient constraints were shared in equal measure between ectomycorrhizal fungi and host trees, particularly for P, suggesting neither partner benefits from enhanced nutrition at the expense of the other. Sporocarp stoichiometry provides new insights into mycorrhizal relationships and illustrates pervasive P deficiencies across temperate rainforests of the Pacific Northwest.

RevDate: 2018-11-06

Godoy-Vitorino F, C Toledo-Hernandez (2018)

Reef-Building Corals as a Tool for Climate Change Research in the Genomics Era.

Results and problems in cell differentiation, 65:529-546.

Coral reef ecosystems are among the most biodiverse habitats in the marine realm. They not only contribute with a plethora of ecosystem services, but they also are beneficial to humankind via nurturing marine fisheries and sustaining recreational activities. We will discuss the biology of coral reefs and their ecophysiology including the complex bacterial microbiota associated with them.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Stencel A, DM Wloch-Salamon (2018)

Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation.

Theory in biosciences = Theorie in den Biowissenschaften, 137(2):197-206.

Research on symbiotic communities (microbiomes) of multicellular organisms seems to be changing our understanding of how species of plants and animals have evolved over millions of years. The quintessence of these discoveries is the emergence of the hologenome theory of evolution, founded on the concept that a holobiont (a host along with all of its associated symbiotic microorganisms) acts a single unit of selection in the process of evolution. Although the hologenome theory has become very popular among certain scientific circles, its principles are still being debated. In this paper, we argue, firstly, that only a very small number of symbiotic microorganisms are sufficiently integrated into multicellular organisms to act in concert with them as units of selection, thus rendering claims that holobionts are units of selection invalid. Secondly, even though holobionts are not units of selection, they can still constitute genuine units from an evolutionary perspective, provided we accept certain constraints: mainly, they should be considered units of co-operation. Thirdly, we propose a reconciliation of the role of symbiotic microorganisms with the theory of speciation through the use of a developed framework. Mainly, we will argue that, in order to understand the role of microorganisms in the speciation of multicellular organisms, it is not necessary to consider holobionts units of selection; it is sufficient to consider them units of co-operation.

RevDate: 2018-09-28

Armstrong EJ, Roa JN, Stillman JH, et al (2018)

Symbiont photosynthesis in giant clams is promoted by V-type H+-ATPase from host cells.

The Journal of experimental biology, 221(Pt 18): pii:jeb.177220.

Giant clams (genus Tridacna) are the largest living bivalves and, like reef-building corals, host symbiotic dinoflagellate algae (Symbiodinium) that significantly contribute to their energy budget. In turn, Symbiodinium rely on the host to supply inorganic carbon (Ci) for photosynthesis. In corals, host 'proton pump' vacuolar-type H+-ATPase (VHA) is part of a carbon-concentrating mechanism (CCM) that promotes Symbiodinium photosynthesis. Here, we report that VHA in the small giant clam (Tridacna maxima) similarly promotes Symbiodinium photosynthesis. VHA was abundantly expressed in the apical membrane of epithelial cells of T. maxima's siphonal mantle tubule system, which harbors Symbiodinium Furthermore, application of the highly specific pharmacological VHA inhibitors bafilomycin A1 and concanamycin A significantly reduced photosynthetic O2 production by ∼40%. Together with our observation that exposure to light increased holobiont aerobic metabolism ∼5-fold, and earlier estimates that translocated fixed carbon exceeds metabolic demand, we conclude that VHA activity in the siphonal mantle confers strong energetic benefits to the host clam through increased supply of Ci to algal symbionts and subsequent photosynthetic activity. The convergent role of VHA in promoting Symbiodinium photosynthesis in the giant clam siphonal mantle tubule system and coral symbiosome suggests that VHA-driven CCM is a common exaptation in marine photosymbioses that deserves further investigation in other taxa.

RevDate: 2018-08-07

Berg M, B Koskella (2018)

Nutrient- and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen.

Current biology : CB, 28(15):2487-2492.e3.

Plant-associated microbial communities can promote plant nutrient uptake, growth, and resistance to pathogens [1-3]. Host resistance to infection can increase directly through commensal-pathogen interactions or indirectly through modulation of host defenses [4-6], the mechanisms of which are best described for rhizosphere-associated bacteria. For example, Arabidopsis plants infected with the foliar pathogen, Pseudomonas syringae pathovar tomato (Pst), increase their root secretion of malate, which attracts Bacillus subtillis to the roots and leads to a stronger host response against Pst [7]. Although there are numerous examples of individual defensive symbionts (e.g., [8]), it is less clear whether this type of protection is an emergent property of whole microbial communities. In particular, relatively little is known about whether and how the presence of phyllosphere (above-ground) microbial communities can increase host resistance against pathogens. In this study, we examined the ability of augmented tomato phyllosphere microbiomes to confer resistance against the causal agent of bacterial speck, Pst. Across five independent experiments, the augmented phyllosphere microbiome was found to decrease pathogen colonization. Furthermore, the dose of commensal bacteria applied affected the degree of protection conferred, and although the effect is dependent on microbial composition, it is not clearly related to overall bacterial diversity. Finally, our results suggest that resources available to the phyllosphere microbial community may play an important role in protection, as the addition of fertilizer abolished the observed microbiome-mediated protection. Together, these results have clear relevance to microbiome-mediated protection within agricultural settings and the use of plant probiotics to increase disease resistance.

RevDate: 2018-11-14

Garcia J, J Kao-Kniffin (2018)

Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling.

Frontiers in microbiology, 9:1516.

Plant rhizospheres encompass a dynamic zone of interactions between microorganisms and their respective plant hosts. For decades, researchers have worked to understand how these complex interactions influence different aspects of plant growth, development, and evolution. Studies of plant-microbial interactions in the root zone have typically focused on the effect of single microbial species or strains on a plant host. These studies, however, provide only a snapshot of the complex interactions that occur in the rhizosphere, leaving researchers with a limited understanding of how the complex microbiome influences the biology of the plant host. To better understand how rhizosphere interactions influence plant growth and development, novel frameworks and research methodologies could be implemented. In this perspective, we propose applying concepts in evolutionary biology to microbiome experiments for improved understanding of group-to-group and community-level microbial interactions influencing soil nutrient cycling. We also put forth simple experimental designs utilizing -omics techniques that can reveal important changes in the rhizosphere impacting the plant host. A greater focus on the components of complexity of the microbiome and how these impact plant host biology could yield more insight into previously unexplored aspects of host-microbe biology relevant to crop production and protection.

RevDate: 2018-07-26

Klassen JL (2018)

Defining microbiome function.

Nature microbiology, 3(8):864-869.

Why does a microorganism associate with a host? What function does it perform? Such questions are difficult to unequivocally address and remain hotly debated. This is partially because scientists often use different philosophical definitions of 'function' ambiguously and interchangeably, as exemplified by the controversy surrounding the Encyclopedia of DNA Elements (ENCODE) project. Here, I argue that research studying host-associated microbial communities and their genomes (that is, microbiomes) faces similar pitfalls and that unclear or misapplied conceptions of function underpin many controversies in this field. In particular, experiments that support phenomenological models of function can inappropriately be used to support functional models that instead require specific measurements of evolutionary selection. Microbiome research also requires uniquely clear definitions of 'who the function is for', in contrast to most single-organism systems where this is implicit. I illustrate how obscuring either of these issues can lead to substantial confusion and misinterpretation of microbiome function, using the varied conceptions of the holobiont as a current and cogent example. Using clear functional definitions and appropriate types of evidence are essential to effectively communicate microbiome research and foster host health.

RevDate: 2018-11-14

Karimi K, Wuitchik DM, Oldach MJ, et al (2018)

Distinguishing Species Using GC Contents in Mixed DNA or RNA Sequences.

Evolutionary bioinformatics online, 14:1176934318788866.

With the advent of whole transcriptome and genome analysis methods, classifying samples containing multiple origins has become a significant task. Nucleotide sequences can be allocated to a genome or transcriptome by aligning sequences to multiple target sequence sets, but this approach requires extensive computational resources and also depends on target sequence sets lacking contaminants, which is often not the case. Here, we demonstrate that raw sequences can be rapidly sorted into groups, in practice corresponding to genera, by exploiting differences in nucleotide GC content. To do so, we introduce GCSpeciesSorter, which uses classification, specifically Support Vector Machines (SVM) and the C4.5 decision tree generator, to differentiate sequences. It also implements a secondary BLAST feature to identify known outliers. In the test case presented, a hermatypic coral holobiont, the cnidarian host includes various endosymbionts. The best characterized and most common of these symbionts are zooxanthellae of the genus Symbiodinium. GCSpeciesSorter separates cnidarian from Symbiodinium sequences with a high degree of accuracy. We show that if the GC contents of the species differ enough, this method can be used to accurately distinguish the sequences of different species when using high-throughput sequencing technologies.

RevDate: 2018-11-14

Li Y, Liles MR, KM Halanych (2018)

Endosymbiont genomes yield clues of tubeworm success.

The ISME journal, 12(11):2785-2795.

Forty years after discovery of chemosynthetic symbiosis in the tubeworm Riftia pachyptila, how organisms maintain their unique host-symbiont associations at the cellular level is still largely unknown. Previous studies primarily focus on symbionts associated with host lineages living in hydrothermal vents. To understand physiological adaptations and evolution in these holobiont systems in markedly different habitats, we characterized four novel siboglinid-symbiont genomes spanning deep-sea seep and sedimented environments. Our comparative analyses suggest that all sampled siboglinid chemoautotrophic symbionts, except for frenulate symbionts, can use both rTCA and Calvin cycle for carbon fixation. We hypothesize that over evolutionary time siboglinids have been able to utilize different bacterial lineages allowing greater metabolic flexibility of carbon fixation (e.g., rTCA) enabling tubeworms to thrive in more reducing habitats, such as vents and seeps. Moreover, we show that sulfur metabolism and molecular mechanisms related to initial infection are remarkably conserved across chemoautotrophic symbionts in different habitats. Unexpectedly, we find that the ability to use hydrogen, as an additional energy source, is potentially more widespread than previously recognized. Our comparative genomic results help elucidate potential mechanisms used to allow chemosynthetically dependent holobionts adapt to, and evolve in, different environments.

RevDate: 2018-07-13

Lorimer J (2018)

Hookworms Make Us Human: The Microbiome, Eco-immunology, and a Probiotic Turn in Western Health Care.

Medical anthropology quarterly [Epub ahead of print].

Historians of science have identified an ecological turn underway in immunology, driven by the mapping of the human microbiome and wider environmentalist anxieties. A figure is emerging of the human as a holobiont, composed of microbes and threatened by both microbial excess and microbial absence. Antimicrobial approaches to germ warfare are being supplemented by probiotic approaches to restoring microbial life. This article examines the political ecology of this probiotic turn in Western health care. It focuses on Necator americanus-a species of human hookworm-and its relations with immunologists. The analysis moves from a history of human disentanglement from hookworm, to contemporary anxieties about their absence. It examines the reintroduction of worms for helminthic therapy and explores emerging trajectories for probiotic health care involving the synthesis, modification, and/or restoration of worms and their salutary ecologies. The conclusion differentiates these trajectories and identifies an emerging model of "post-paleo" microbiopolitics. This article is protected by copyright. All rights reserved.

RevDate: 2018-08-22

Klimovich AV, TCG Bosch (2018)

Rethinking the Role of the Nervous System: Lessons From the Hydra Holobiont.

BioEssays : news and reviews in molecular, cellular and developmental biology, 40(9):e1800060.

Here we evaluate our current understanding of the function of the nervous system in Hydra, a non-bilaterian animal which is among the first metazoans that contain neurons. We highlight growing evidence that the nervous system, with its rich repertoire of neuropeptides, is involved in controlling resident beneficial microbes. We also review observations that indicate that microbes affect the animal's behavior by directly interfering with neuronal receptors. These findings provide new insight into the original role of the nervous system, and suggest that it emerged to orchestrate multiple functions including host-microbiome interactions. The excitement of future research in the Hydra model now relies on uncovering the common rules and principles that govern the interaction between neurons and microbes and the extent to which such laws might apply to other and more complex organisms.

RevDate: 2019-02-04

Lian J, Wijffels RH, Smidt H, et al (2018)

The effect of the algal microbiome on industrial production of microalgae.

Microbial biotechnology, 11(5):806-818.

Microbes are ubiquitously distributed, and they are also present in algae production systems. The algal microbiome is a pivotal part of the alga holobiont and has a key role in modulating algal populations in nature. However, there is a lack of knowledge on the role of bacteria in artificial systems ranging from laboratory flasks to industrial ponds. Coexisting microorganisms, and predominantly bacteria, are often regarded as contaminants in algal research, but recent studies manifested that many algal symbionts not only promote algal growth but also offer advantages in downstream processing. Because of the high expectations for microalgae in a bio-based economy, better understanding of benefits and risks of algal-microbial associations is important for the algae industry. Reducing production cost may be through applying specific bacteria to enhance algae growth at large scale as well as through preventing the growth of a broad spectrum of algal pathogens. In this review, we highlight the latest studies of algae-microbial interactions and their underlying mechanisms, discuss advantages of large-scale algal-bacterial cocultivation and extend such knowledge to a broad range of biotechnological applications.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Kutschera U (2018)

Systems biology of eukaryotic superorganisms and the holobiont concept.

Theory in biosciences = Theorie in den Biowissenschaften, 137(2):117-131.

The founders of modern biology (Jean Lamarck, Charles Darwin, August Weismann etc.) were organismic life scientists who attempted to understand the morphology and evolution of living beings as a whole (i.e., the phenotype). However, with the emergence of the study of animal and plant physiology in the nineteenth century, this "holistic view" of the living world changed and was ultimately replaced by a reductionistic perspective. Here, I summarize the history of systems biology, i.e., the modern approach to understand living beings as integrative organisms, from genotype to phenotype. It is documented that the physiologists Claude Bernard and Julius Sachs, who studied humans and plants, respectively, were early pioneers of this discipline, which was formally founded 50 years ago. In 1968, two influential monographs, authored by Ludwig von Bertalanffy and Mihajlo D. Mesarović, were published, wherein a "systems theory of biology" was outlined. Definitions of systems biology are presented with reference to metabolic or cell signaling networks, analyzed via genomics, proteomics, and other methods, combined with computer simulations/mathematical modeling. Then, key insights of this discipline with respect to epiphytic microbes (Methylobacterium sp.) and simple bacteria (Mycoplasma sp.) are described. The principles of homeostasis, molecular systems energetics, gnotobiology, and holobionts (i.e., complexities of host-microbiota interactions) are outlined, and the significance of systems biology for evolutionary theories is addressed. Based on the microbe-Homo sapiens-symbiosis, it is concluded that human biology and health should be interpreted in light of a view of the biomedical sciences that is based on the holobiont concept.

RevDate: 2018-11-14

Münger E, Montiel-Castro AJ, Langhans W, et al (2018)

Reciprocal Interactions Between Gut Microbiota and Host Social Behavior.

Frontiers in integrative neuroscience, 12:21.

Animals harbor an extensive, dynamic microbial ecosystem in their gut. Gut microbiota (GM) supposedly modulate various host functions including fecundity, metabolism, immunity, cognition and behavior. Starting by analyzing the concept of the holobiont as a unit of selection, we highlight recent findings suggesting an intimate link between GM and animal social behavior. We consider two reciprocal emerging themes: (i) that GM influence host social behavior; and (ii) that social behavior and social structure shape the composition of the GM across individuals. We propose that, throughout a long history of coevolution, GM may have become involved in the modulation of their host's sociality to foster their own transmission, while in turn social organization may have fine-tuned the transmission of beneficial endosymbionts and prevented pathogen infection. We suggest that investigating these reciprocal interactions can advance our understanding of sociality, from healthy and impaired social cognition to the evolution of specific social behaviors and societal structure.

RevDate: 2018-11-14

Marchesi JR (2018)

Advancing microbiome research.

RevDate: 2018-08-01

Marchesi JR (2018)

Advancing microbiome research.

Microbiology (Reading, England), 164(8):1005-1006.

RevDate: 2018-11-14

Yurgel SN, Douglas GM, Dusault A, et al (2018)

Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome.

Frontiers in microbiology, 9:1187.

A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host-microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a foundation for root microbiome, plant-influenced species sorting had stronger effect on eukaryotes than on bacteria. Our study identified several fungal and protist taxa, which are correlated with decreased fruit production in wild blueberry agricultural ecosystems. The specific effect of species sorting in root microbiome resulted in an increase in relative abundance of fungi adapted to plant-associated life-style, while the relative abundance of non-fungal eukaryotes was decreased along the soil-endosphere continuum in the root, probably because of low adaptation of these microorganisms to host-plant defense responses. Analysis of community correlation networks indicated that bacterial and eukaryotic interactions became more complex along the soil-endosphere continuum and, in addition to extensive mutualistic interactions, co-exclusion also played an important role in shaping wild blueberry associated microbiome. Our study identified several potential hub taxa with important roles in soil fertility and/or plant-microbe interaction, suggesting the key role of these taxa in the interconnection between soils and plant health and overall microbial community structure. This study also provides a comprehensive view of the role of non-fungal eukaryotes in soil ecosystem.

RevDate: 2018-11-27
CmpDate: 2018-11-27

Celis JS, Wibberg D, Ramírez-Portilla C, et al (2018)

Binning enables efficient host genome reconstruction in cnidarian holobionts.

GigaScience, 7(7):.

Background: Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities-together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.

Results: Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.

Conclusions: Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.

RevDate: 2018-07-12

van Oppen MJH, Bongaerts P, Frade P, et al (2018)

Adaptation to reef habitats through selection on the coral animal and its associated microbiome.

Molecular ecology, 27(14):2956-2971.

Spatially adjacent habitats on coral reefs can represent highly distinct environments, often harbouring different coral communities. Yet, certain coral species thrive across divergent environments. It is unknown whether the forces of selection are sufficiently strong to overcome the counteracting effects of the typically high gene flow over short distances, and for local adaptation to occur. We screened the coral genome (using restriction site-associated sequencing) and characterized both the dinoflagellate photosymbiont- and tissue-associated prokaryote microbiomes (using metabarcoding) of a reef flat and slope population of the reef-building coral, Pocillopora damicornis, at two locations on Heron Island in the southern Great Barrier Reef. Reef flat and slope populations were separated by <100 m horizontally and ~5 m vertically, and the two study locations were separated by ~1 km. For the coral host, genetic divergence between habitats was much greater than between locations, suggesting limited gene flow between the flat and slope populations. Consistent with environmental selection, outlier loci primarily belonged to the conserved, minimal cellular stress response, likely reflecting adaptation to the different temperature and irradiance regimes on the reef flat and slope. The prokaryote community differed across both habitat and, to a lesser extent, location, whereas the dinoflagellate photosymbionts differed by habitat but not location. The observed intraspecific diversity associated with divergent habitats supports that environmental adaptation involves multiple members of the coral holobiont. Adaptive alleles or microbial associations present in coral populations from the environmentally variable reef flat may provide a source of adaptive variation for assisted evolution approaches, through assisted gene flow, artificial cross-breeding or probiotic inoculations, with the aim to increase climate resilience in the slope populations.

RevDate: 2018-07-12

Vančurová L, Muggia L, Peksa O, et al (2018)

The complexity of symbiotic interactions influences the ecological amplitude of the host: A case study in Stereocaulon (lichenized Ascomycota).

Molecular ecology, 27(14):3016-3033.

Symbiosis plays a fundamental role in nature. Lichens are among the best known, globally distributed symbiotic systems whose ecology is shaped by the requirements of all symbionts forming the holobiont. The widespread lichen-forming fungal genus Stereocaulon provides a suitable model to study the ecology of microscopic green algal symbionts (i.e., phycobionts) within the lichen symbiosis. We analysed 282 Stereocaulon specimens, collected in diverse habitats worldwide, using the algal ITS rDNA and actin gene sequences and fungal ITS rDNA sequences. Phylogenetic analyses revealed a great diversity among the predominant phycobionts. The algal genus Asterochloris (Trebouxiophyceae) was recovered in most sampled thalli, but two additional genera, Vulcanochloris and Chloroidium, were also found. We used variation-partitioning analyses to investigate the effects of climatic conditions, substrate/habitat characteristic, spatial distribution and mycobionts on phycobiont distribution. Based on an analogy, we examined the effects of climate, substrate/habitat, spatial distribution and phycobionts on mycobiont distribution. According to our analyses, the distribution of phycobionts is primarily driven by mycobionts and vice versa. Specificity and selectivity of both partners, as well as their ecological requirements and the width of their niches, vary significantly among the species-level lineages. We demonstrated that species-level lineages, which accept more symbiotic partners, have wider climatic niches, overlapping with the niches of their partners. Furthermore, the survival of lichens on substrates with high concentrations of heavy metals appears to be supported by their association with toxicity-tolerant phycobionts. In general, low specificity towards phycobionts allows the host to associate with ecologically diversified algae, thereby broadening its ecological amplitude.

RevDate: 2018-11-14
CmpDate: 2018-11-05

R L Morlighem JÉ, Huang C, Liao Q, et al (2018)

The Holo-Transcriptome of the Zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa): A Plentiful Source of Enzymes for Potential Application in Green Chemistry, Industrial and Pharmaceutical Biotechnology.

Marine drugs, 16(6):.

Marine invertebrates, such as sponges, tunicates and cnidarians (zoantharians and scleractinian corals), form functional assemblages, known as holobionts, with numerous microbes. This type of species-specific symbiotic association can be a repository of myriad valuable low molecular weight organic compounds, bioactive peptides and enzymes. The zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa) is one such example of a marine holobiont that inhabits the coastal reefs of the tropical Atlantic coast and is an interesting source of secondary metabolites and biologically active polypeptides. In the present study, we analyzed the entire holo-transcriptome of P. variabilis, looking for enzyme precursors expressed in the zoantharian-microbiota assemblage that are potentially useful as industrial biocatalysts and biopharmaceuticals. In addition to hundreds of predicted enzymes that fit into the classes of hydrolases, oxidoreductases and transferases that were found, novel enzyme precursors with multiple activities in single structures and enzymes with incomplete Enzyme Commission numbers were revealed. Our results indicated the predictive expression of thirteen multifunctional enzymes and 694 enzyme sequences with partially characterized activities, distributed in 23 sub-subclasses. These predicted enzyme structures and activities can prospectively be harnessed for applications in diverse areas of industrial and pharmaceutical biotechnology.

RevDate: 2018-11-14

Nguyen MTHD, T Thomas (2018)

Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges.

PeerJ, 6:e4965.

Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few "variable/core" fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.

RevDate: 2018-12-24
CmpDate: 2018-12-24

Hall ER, Muller EM, Goulet T, et al (2018)

Eutrophication may compromise the resilience of the Red Sea coral Stylophora pistillata to global change.

Marine pollution bulletin, 131(Pt A):701-711.

Environmental stressors are adversely affecting coral reef ecosystems. There is ample evidence that scleractinian coral growth and physiology may be compromised by reduced pH, and elevated temperature, and that this is exacerbated by local environmental stressors. The Gulf of Aqaba is considered a coral reef refuge from acidification and warming but coastal development and nutrient effluent may pose a local threat. This study examined the effects of select forecasted environmental changes (acidification, warming, and increased nutrients) individually and in combination on the coral holobiont Stylophora pistillata from the Gulf of Aqaba to understand how corals in a potential global climate change refugia may fare in the face of local eutrophication. The results indicate interactions between all stressors, with elevated nutrient concentrations having the broadest individual and additive impacts upon the performance of S. pistillata. These findings highlight the importance of maintaining oligotrophic conditions to secure these reefs as potential refugia.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Meng A, Marchet C, Corre E, et al (2018)

A de novo approach to disentangle partner identity and function in holobiont systems.

Microbiome, 6(1):105.

BACKGROUND: Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept.

RESULTS: We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner's transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited.

CONCLUSIONS: In contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages and ultimately expand our knowledge about these associations.

RevDate: 2018-05-25

Rädecker N, Raina JB, Pernice M, et al (2018)

Corrigendum: Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses.

Frontiers in physiology, 9:449.

[This corrects the article on p. 214 in vol. 9, PMID: 29615919.].

RevDate: 2019-01-22
CmpDate: 2019-01-22

García-Bonilla E, Brandão PFB, Pérez T, et al (2019)

Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida).

Microbial ecology, 77(1):25-36.

Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.

RevDate: 2018-11-14

Houdek P (2018)

Economic Holobiont: Influence of Parasites, Microbiota and Chemosignals on Economic Behavior.

Frontiers in behavioral neuroscience, 12:77.

The article is a perspective on utilization of microorganisms and chemosignals in studying human economic behavior. Research in biological roots of economic development has already confirmed that parasitic pressure influenced the creation and development of cultural norms and institutions. However, other effects of microorganisms on human groups and individual decision-making and behavior are heavily understudied. The perspective discusses how parasitic infections, sexually transmitted organisms and microbiota (i.e., "human holobiont") could causally influence risk-seeking behavior, impulsivity, social dominance, empathy, political views and gender differences. As a case study, the parasite Toxoplasma gondii and its influence on economic preferences, personal characteristics and human appearance are examined. I also briefly review how chemosignals influence decision-making, particularly in the social preferences domain. I mention some predictions that arise from the paradigm of economic holobiont for the economic science. The conclusion summarizes limitations of the discussed findings and the stated speculations.

RevDate: 2018-05-15

Bourrat P, PE Griffiths (2018)

Multispecies individuals.

History and philosophy of the life sciences, 40(2):33 pii:10.1007/s40656-018-0194-1.

We assess the arguments for recognising functionally integrated multispecies consortia as genuine biological individuals, including cases of so-called 'holobionts'. We provide two examples in which the same core biochemical processes that sustain life are distributed across a consortium of individuals of different species. Although the same chemistry features in both examples, proponents of the holobiont as unit of evolution would recognize one of the two cases as a multispecies individual whilst they would consider the other as a compelling case of ecological dependence between separate individuals. Some widely used arguments in support of the 'holobiont' concept apply equally to both cases, suggesting that those arguments have misidentified what is at stake when seeking to identify a new level of biological individuality. One important aspect of biological individuality is evolutionary individuality. In line with other work on the evolution of individuality, we show that our cases can be distinguished by focusing on the fitness alignment between the partners of the consortia. We conclude that much of the evidence currently presented for the ubiquity and importance of multi-species individuals is simply not to the point, at least unless the issue of biological individuality is firmly divorced from the question of evolutionary individuality.

RevDate: 2018-11-14
CmpDate: 2018-08-01

León-Palmero E, Joglar V, Álvarez PA, et al (2018)

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes.

PloS one, 13(5):e0196178.

Marine invertebrates, as holobionts, contain symbiotic bacteria that coevolve and develop antimicrobial substances. These symbiotic bacteria are an underexplored source of new bioactive molecules to face the emerging antibiotic resistance in pathogens. Here, we explored the antimicrobial activity of bacteria retrieved from the microbiota of two sea anemones (Anemonia sulcata, Actinia equina) and two holothurians (Holothuria tubulosa, Holothuria forskali). We tested the antimicrobial activity of the isolated bacteria against pathogens with interest for human health, agriculture and aquaculture. We isolated 27 strains with antibacterial activity and 12 of these isolates also showed antifungal activity. We taxonomically identified these strains being Bacillus and Vibrio species the most representative producers of antimicrobial substances. Microbiome species composition of the two sea anemones was similar between them but differed substantially of seawater bacteria. In contrast, microbiome species composition of the two holothurian species was different between them and in comparison with the bacteria in holothurian feces and seawater. In all the holobiont microbiomes Bacteroidetes was the predominant phylum. For each microbiome, we determined diversity and the rank-abundance dominance using five fitted models (null, pre-emption, log-Normal, Zipf and Zipf-Mandelbrot). The models with less evenness (i.e. Zipf and Zipf-Mandelblot) showed the best fits in all the microbiomes. Finally, we tracked (using the V4 hypervariable region of 16S rRNA gene) the relative abundance of these 27 isolates with antibacterial activity in the total pool of sequences obtained for the microbiome of each holobiont. Coincidences, although with extremely low frequencies, were detected only in the microbiome of H. forskali. This fact suggests that these isolated bacteria belong to the long tail of rare symbiotic bacteria. Therefore, more and more sophisticated culture techniques are necessary to explore this apparently vast pool of rare symbiontic bacteria and to determine their biotechnological potentiality.

RevDate: 2019-01-24

Domin H, Zurita-Gutiérrez YH, Scotti M, et al (2018)

Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella.

Frontiers in microbiology, 9:728.

The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria-bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria-bacteria interactions through co-occurrence networks. The analysis indicates that bacteria-bacteria interactions are dynamic during host colonization and change according to the host's developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Sorek M, Schnytzer Y, Ben-Asher HW, et al (2018)

Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasia are determined largely by Symbiodinium.

Microbiome, 6(1):83.

BACKGROUND: All organisms employ biological clocks to anticipate physical changes in the environment; however, the integration of biological clocks in symbiotic systems has received limited attention. In corals, the interpretation of rhythmic behaviours is complicated by the daily oscillations in tissue oxygen tension resulting from the photosynthetic and respiratory activities of the associated algal endosymbiont Symbiodinium. In order to better understand the integration of biological clocks in cnidarian hosts of Symbiodinium, daily rhythms of behaviour and gene expression were studied in symbiotic and aposymbiotic morphs of the sea-anemone Aiptasia diaphana.

RESULTS: The results showed that whereas circatidal (approx. 12-h) cycles of activity and gene expression predominated in aposymbiotic morphs, circadian (approx. 24-h) patterns were the more common in symbiotic morphs, where the expression of a significant number of genes shifted from a 12- to 24-h rhythm. The behavioural experiments on symbiotic A. diaphana displayed diel (24-h) rhythmicity in body and tentacle contraction under the light/dark cycles, whereas aposymbiotic morphs showed approximately 12-h (circatidal) rhythmicity. Reinfection experiments represent an important step in understanding the hierarchy of endogenous clocks in symbiotic associations, where the aposymbiotic Aiptasia morphs returned to a 24-h behavioural rhythm after repopulation with algae.

CONCLUSION: Whilst some modification of host metabolism is to be expected, the extent to which the presence of the algae modified host endogenous behavioural and transcriptional rhythms implies that it is the symbionts that influence the pace. Our results clearly demonstrate the importance of the endosymbiotic algae in determining the timing and the duration of the extension and contraction of the body and tentacles and temporal gene expression.

RevDate: 2018-05-08

Faure D, Simon JC, T Heulin (2018)

Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems.

The New phytologist, 218(4):1321-1324.

RevDate: 2018-06-25

Nobori T, Mine A, K Tsuda (2018)

Molecular networks in plant-pathogen holobiont.

FEBS letters, 592(12):1937-1953.

Plant immune receptors enable detection of a multitude of microbes including pathogens. The recognition of microbes activates various plant signaling pathways, such as those mediated by phytohormones. Over the course of coevolution with microbes, plants have expanded their repertoire of immune receptors and signaling components, resulting in highly interconnected plant immune networks. These immune networks enable plants to appropriately respond to different types of microbes and to coordinate immune responses with developmental programs and environmental stress responses. However, the interconnectivity in plant immune networks is exploited by microbial pathogens to promote pathogen fitness in plants. Analogous to plant immune networks, virulence-related pathways in bacterial pathogens are also interconnected. Accumulating evidence implies that some plant-derived compounds target bacterial virulence networks. Thus, the plant immune and bacterial virulence networks intimately interact with each other. Here, we highlight recent insights into the structures of the plant immune and bacterial virulence networks and the interactions between them. We propose that small molecules derived from plants and/or bacterial pathogens connect the two molecular networks, forming supernetworks in the plant-bacterial pathogen holobiont.

RevDate: 2018-05-25

Karimi E, Slaby BM, Soares AR, et al (2018)

Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges.

FEMS microbiology ecology, 94(6):.

Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.


ESP Quick Facts

ESP Origins

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

ESP Support

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

ESP Rationale

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

ESP Goal

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

ESP Usage

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

ESP Content

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

ESP Help

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

ESP Plans

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

Electronic Scholarly Publishing
21454 NE 143rd Street
Woodinville, WA 98077

E-mail: RJR8222 @

Papers in Classical Genetics

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

Digital Books

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


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


Biographical information about many key scientists.

Selected Bibliographies

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

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