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31 Jul 2021 at 01:51
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Bibliography on: Symbiosis


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RJR: Recommended Bibliography 31 Jul 2021 at 01:51 Created: 


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

Created with PubMed® Query: symbiosis NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2021-07-30

Sharma R, Shahbaz M, Sinha A, et al (2021)

Examining the temporal impact of stock market development on carbon intensity: Evidence from South Asian countries.

Journal of environmental management, 297:113248 pii:S0301-4797(21)01310-4 [Epub ahead of print].

The growing size of stock market in the South Asian countries might have contributed to raising the level of industrial production and energy consumption. This upturned energy usage might have widened the scope for carbon emissions because these nations heavily rely on fossil fuels. In this milieu, therefore, in the present study, we assessed the impacts of stock market development, per capita income, trade expansion, renewable energy solutions, and technological innovations on carbon intensity in the four South Asia countries from 1990 to 2016. The empirical results based on the CS-ARDL approach revealed that stock market development, per capita income, and trade expansion invigorated carbon intensity in the South Asian countries. On the contrary, the increased usage of renewable energy solutions and technological advancement helped in reducing the energy-led carbon intensity. Further, the interaction of stock market with renewable energy, and subsequently with technological advancement delivered insignificant coefficients, which indicates the inefficacy of renewable energy and technological advancement in regulating stock market-led carbon intensity during the study period. Therefore, by considering the need for complementarity between economic growth and environmental targets, we proposed a multipronged policy framework, which may help the selected countries to attain the Sustainable Development Goals, with a special focus on SDG 7, 8, 9, and 13.

RevDate: 2021-07-30

Boco SR, Pitt KA, SD Melvin (2021)

Ocean acidification impairs the physiology of symbiotic phyllosoma larvae of the lobster Thenus australiensis and their ability to detect cues from jellyfish.

The Science of the total environment, 793:148679 pii:S0048-9697(21)03751-7 [Epub ahead of print].

Ocean acidification (OA) can alter the behaviour and physiology of marine fauna and impair their ability to interact with other species, including those in symbiotic and predatory relationships. Phyllosoma larvae of lobsters are symbionts to many invertebrates and often ride and feed on jellyfish, however OA may threaten interactions between phyllosomas and jellyfish. Here, we tested whether OA predicted for surface mid-shelf waters of Great Barrier Reef, Australia, under ∆ pH = -0.1 (pH ~7.9) and ∆pH = -0.3 (pH ~7.7) relative to the present pH (~8.0) (P) impaired the survival, moulting, respiration, and metabolite profiles of phyllosoma larvae of the slipper lobster Thenus australiensis, and the ability of phyllosomas to detect chemical cues of fresh jellyfish tissue. We discovered that OA was detrimental to survival of phyllosomas with only 20% survival under ∆pH = -0.3 compared to 49.2% and 45.3% in the P and ∆pH = -0.1 treatments, respectively. The numbers of phyllosomas that moulted in the P and ∆pH = -0.1 treatments were 40% and 34% higher, respectively, than those in the ∆pH = -0.3 treatment. Respiration rates varied between pH treatments, but were not consistent through time. Respiration rates in the ∆pH = -0.3 and ∆pH = -0.1 treatments were initially 40% and 22% higher, respectively, than in the P treatment on Day 2 and then rates varied to become 26% lower (∆pH = -0.3) and 17% (∆pH = -0.1) higher towards the end of the experiment. Larvae were attracted to jellyfish tissue in treatments P and ∆pH = -0.1 but avoided jellyfish at ∆pH = -0.3. Moreover, OA conditions under ∆pH = -0.1 and ∆pH = -0.3 levels reduced the relative abundances of 22 of the 34 metabolites detected in phyllosomas via Nuclear Magnetic Resonance (NMR) spectroscopy. Our study demonstrates that the physiology and ability to detect jellyfish tissue by phyllosomas of the lobster T. australiensis may be impaired under ∆pH = -0.3 relative to the present conditions, with potential negative consequences for adult populations of this commercially important species.

RevDate: 2021-07-30

Palazzo Q, Prada F, Steffens T, et al (2021)

The skeleton of Balanophyllia coral species suggests adaptive traits linked to the onset of mixotrophy.

The Science of the total environment, 795:148778 pii:S0048-9697(21)03850-X [Epub ahead of print].

The diversity in the skeletal features of coral species is an outcome of their evolution, distribution and habitat. Here, we explored, from macro- to nano-scale, the skeletal structural and compositional characteristics of three coral species belonging to the genus Balanophyllia having different trophic strategies. The goal is to address whether the onset of mixotrophy influenced the skeletal features of B. elegans, B. regia, and B. europaea. The macroscale data suggest that the presence of symbiotic algae in B. europaea can lead to a surplus of energy input that increases its growth rate and skeletal bulk density, leading to larger and denser corals compared to the azooxanthellate ones, B. regia and B. elegans. The symbiosis would also explain the higher intra-skeletal organic matrix (OM) content, which is constituted by macromolecules promoting the calcification, in B. europaea compared to the azooxanthellate species. The characterization of the soluble OM also revealed differences between B. europaea and the azooxanthellate species, which may be linked to diverse macromolecular machineries responsible for skeletal biosynthesis and final morphology. Differently, the crystallographic features were homogenous among species, suggesting that the basic building blocks of skeletons remained a conserved trait in these related species, regardless of the trophic strategy. These results show changes in skeletal phenotype that could be triggered by the onset of mixotrophy, as a consequence of the symbiotic association, displaying remarkable plasticity of coral skeletons which repeatedly allowed this coral group to adapt to a range of changing environments throughout its geological history.

RevDate: 2021-07-30

Koskimäki JJ, Pohjanen J, Kvist J, et al (2021)

The meristem-associated endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of pine seedlings.

Tree physiology pii:6330022 [Epub ahead of print].

Microbes living in plant tissues, endophytes, are mainly studied in crop plants where they typically colonize the root apoplast. Trees, a large carbon source with a high capacity for photosynthesis, provide a variety of niches for endophytic colonization. We have earlier identified a new type of plant-endophyte interaction in buds of adult Scots pine, where Methylorubrum species live inside the meristematic cells. The endosymbiont M. extorquens DSM13060 significantly increases needle and root growth of pine seedlings without producing plant hormones, but by aggregating around host nuclei. Here we studied gene expression and metabolites of the pine host induced by M. extorquens DSM13060 infection. Malic acid was produced by pine to potentially boost M. extorquens colonization and interaction. Based on gene expression, the endosymbiont activated the auxin- and ethylene (ET)-associated hormonal pathways through induction of CUL1 and HYL1, and suppressed salicylic and abscisic acid signaling of pine. Infection by the endosymbiont had an effect on pine meristem and leaf development through activation of GLP1-7 and ALE2, and suppressed flowering, root hair and lateral root formation by down-regulation of AGL8, plantacyanin, GASA7, COW1 and RALFL34. Despite of systemic infection of pine seedlings by the endosymbiont, the pine genes CUL1, ETR2, ERF3, HYL, GLP1-7, and CYP71 were highly expressed in the shoot apical meristem, rarely in needles, and not in stem or root tissues. Low expression of MERI5, CLH2, EULS3, and high quantities of ononitol suggest that endosymbiont promotes viability and protects pine seedlings against abiotic stress. Our results indicate that the endosymbiont positively affects host development and stress tolerance through mechanisms previously unknown for endophytic bacteria, manipulation of plant hormone signaling pathways, down-regulation of senescence and cell death-associated genes, and induction of ononitol biosynthesis.

RevDate: 2021-07-30

Kotova TP, AI Lesnikov (2021)


Problemy sotsial'noi gigieny, zdravookhraneniia i istorii meditsiny, 29(Special Issue):684-688.

The article discusses the possibilities and prospects of using apitherapy in health tourism in Bashkortostan. The features of the development of beekeeping in the republic and the prospects for the use of beekeeping products in the restoration of the immune system, improvement of the psychological state of the consequences of covid in the conditions of tourist and recreational centers of the region are considered. A health-improving tourist product with the use of apitherapy has been developed. The Bashkirsky Med brand is widely known not only in Russia, but also abroad. The list of measures for the development of beekeeping in the republic includes support for scientific developments in the field of apitherapy. The article examines apitourism as a promising type of tourism in Bashkortostan. It can become one of the most popular types of health tourism and attract not only Russian, but also foreign tourists.

RevDate: 2021-07-30

Säle V, Palenzuela J, Azcón-Aguilar C, et al (2021)

Ancient lineages of arbuscular mycorrhizal fungi provide little plant benefit.

Mycorrhiza [Epub ahead of print].

Almost all land plants form symbiotic associations with arbuscular mycorrhizal fungi (AMF). Individual plants usually are colonized by a wide range of phylogenetically diverse AMF species. The impact that different AMF taxa have on plant growth is only partly understood. We screened 44 AMF isolates for their effect on growth promotion and nutrient uptake of leek plants (Allium porrum), including isolates that have not been tested previously. In particular, we aimed to test weather AMF lineages with an ancient evolutionary age differ from relatively recent lineages in their effects on leek plants. The AMF isolates that were tested covered 18 species from all five AMF orders, eight families, and 13 genera. The experiment was conducted in a greenhouse. A soil-sand mixture was used as substrate for the leek plants. Plant growth response to inoculation with AMF varied from - 19 to 232% and depended on isolate, species, and family identity. Species from the ancient families Archaeosporaceae and Paraglomeraceae tended to be less beneficial, in terms of stimulation plant growth and nutrient uptake, than species of Glomeraceae, Entrophosporaceae, and Diversisporaceae, which are considered phylogenetically more recent than those ancient families. Root colonization levels also depended on AMF family. This study indicates that plant benefit in the symbiosis between plants and AMF is linked to fungal identity and phylogeny and it shows that there are large differences in effectiveness of different AMF.

RevDate: 2021-07-30

Xiao Y, Li W, Yang X, et al (2021)

Rapid spread of a densovirus in a major crop pest following wide-scale adoption of Bt-cotton in China.

eLife, 10: pii:66913.

Bacillus thuringiensis (Bt) crops have been widely planted and the effects of Bt-crops on populations of the target and non-target insect pests have been well studied. However, the effects of Bt-crops exposure on microorganisms that interact with crop pests have not previously been quantified. Here, we use laboratory and field data to show that infection of Helicoverpa armigera with a densovirus (HaDV2) is associated with its enhanced growth and tolerance to Bt-cotton. Moreover, field monitoring showed a much higher incidence of cotton bollworm infection with HaDV2 in regions cultivated with Bt-cotton than in regions without it, with the rate of densovirus infection increasing with increasing use of Bt-cotton. RNA-seq suggested tolerance to both baculovirus and Cry1Ac were enhanced via the immune-related pathways. These findings suggest that exposure to Bt-crops has selected for beneficial interactions between the target pest and a mutualistic microorganism that enhances its performance on Bt-crops under field conditions.

RevDate: 2021-07-30
CmpDate: 2021-07-30

Van Goor J, Piatscheck F, Houston DD, et al (2021)

Differential effects of nematode infection on pollinating and non-pollinating fig wasps: Can shared antagonism provide net benefits to a mutualism?.

The Journal of animal ecology, 90(7):1764-1775.

Species pairs that form mutualistic associations are also components of broader organismal community networks. These interaction networks have shaped the evolution of individual mutualisms through interspecific interactions ranging from secondarily mutualistic to intensely antagonistic. Our understanding of this complex context remains limited because characterizing the impacts of species interacting with focal mutualists is often difficult. How is the fitness of mutualists impacted by the co-occurring interactive network of community associates? We investigated this context using a model interaction network comprised of a fig and fig wasp mutualist, eight non-pollinating fig wasp (NPFW) antagonists/commensals and a nematode previously believed to be associated only with the pollinator wasp mutualist. Through repeated sampling and field observations, we characterized the ecological roles of these mutualist-associated organisms to identify key antagonists. We then investigated how potential nematode infection of NPFWs could impact wasp survival across key life stages and, in turn, inferred how this influences the fitness of the fig-pollinator mutualists. Unexpectedly, we found all Ficus petiolaris-associated NPFWs to be the targets for nematode infection, with infection levels sometimes exceeding that of pollinators. Experimental data collected for the most abundant NPFW species suggest that nematode infection significantly reduces their longevity. Further, comparisons of nematode loads for emerging and successfully arriving NPFWs suggest that infection severely limits their dispersal ability. Through these observations, we conclude that this infection could impact NPFWs more severely than either mutualistic partner, suggesting a novel role of density-dependent facultative mutualism between figs, pollinator wasps and the nematode. This antagonist-mediated suppression of other network antagonists may present an ecologically common mechanism through which antagonists can present net benefits for mutualists' fitness.

RevDate: 2021-07-30
CmpDate: 2021-07-30

Deng X, Chen L, Tian E, et al (2021)

Low host specificity and broad geographical ranges in a community of parasitic non-pollinating fig wasps (Sycoryctinae; Chalcidoidea).

The Journal of animal ecology, 90(7):1678-1690.

Plants, phytophagous insects and their parasitoids form the most diverse assemblages of macroscopic organisms on earth. Enclosed assemblages in particular represent a tractable system for studying community assembly and diversification. Communities associated with widespread plant species are especially suitable as they facilitate a comparative approach. Pantropical fig-wasp communities represent a remarkably well-replicated system, ideal for studying these historical processes. We expect high dispersal ability in non-pollinating fig wasps to result in lower geographical turnover in comparison to pollinating fig wasps. The ability of non-pollinating wasps to utilise a number of hosts (low host specificity) is a key determinant of overall geographical range, with intraspecific competition becoming a constraining factor should diet breadth overlap among species. Finally, we expect conserved community structure throughout the host range. We aim to test these expectations, derived from population genetic and community studies, using the multi-trophic insect community associated with Ficus hirta throughout its 3,500 km range across continental and insular Asia. We collect molecular evidence from one coding mitochondrial gene, one non-coding nuclear gene and multiple microsatellites across 25 geographical sites. Using these data, we establish species boundaries, determine levels of host specificity among non-pollinating fig wasps and quantify geographical variation in community composition. We find low host specificity in two genera of non-pollinating fig wasps. Functional community structure is largely conserved across the range of the host fig, despite limited correspondence between the ranges of non-pollinator and pollinator species. While nine pollinators are associated with Ficus hirta, the two non-pollinator tribes developing in its figs each contained only four species. Contrary to predictions, we find stronger isolation by distance in non-pollinators than pollinators. Long-lived non-pollinators may disperse more gradually and be less reliant on infrequent long-distance dispersal by wind currents. Segregation among non-pollinating species across their range is suggestive of competitive exclusion and we propose that this may be a result of increased levels of local adaptation and moderate, but regular, rates of dispersal. Our findings provide one more example of lack of strict codiversification in the geographical diversification of plant-associated insect communities.

RevDate: 2021-07-30
CmpDate: 2021-07-30

Pizo MA, Morales JM, Ovaskainen O, et al (2021)

Frugivory Specialization in Birds and Fruit Chemistry Structure Mutualistic Networks across the Neotropics.

The American naturalist, 197(2):236-249.

AbstractThe interaction between fruit chemistry and the physiological traits of frugivores is expected to shape the structure of mutualistic seed dispersal networks, but it has been understudied compared with the role of morphological trait matching in structuring interaction patterns. For instance, highly frugivorous birds (i.e., birds that have fruits as the main component of their diets), which characteristically have fast gut passage times, are expected to avoid feeding on lipid-rich fruits because of the long gut retention times associated with lipid digestion. Here, we compiled data from 84 studies conducted in the Neotropics that used focal plant methods to record 35,815 feeding visits made by 317 bird species (155 genera in 28 families) to 165 plant species (82 genera in 48 families). We investigated the relationship between the degree of frugivory of birds (i.e., how much of their diet is composed of fruit) at the genus level and their visits to plant genera that vary in fruit lipid content. We used a hierarchical modeling of species communities approach that accounted for the effects of differences in body size, bird and plant phylogeny, and spatial location of study sites. We found that birds with a low degree of frugivory (e.g., predominantly insectivores) tend to have the highest increase in visitation rates as fruits become more lipid rich, while birds that are more frugivorous tend to increase visits at a lower rate or even decrease visitation rates as lipids increase in fruits. This balance between degree of frugivory and visitation rates to lipid-poor and lipid-rich fruits provides a mechanism to explain specialized dispersal systems and the occurrence of certain physiological nutritional filters, ultimately helping us to understand community-wide interaction patterns between birds and plants.

RevDate: 2021-07-30
CmpDate: 2021-07-30

Darriba S, Lee RS, C López (2020)

Mikrocytos mytilicoli n.sp. (Cercozoa, Mikrocytida, Mikrocytiidae) infecting the copepod Mytilicola intestinalis (Arthropoda, Cyclopoida, Mytilicolidae), a symbiont of Mytilus galloprovincialis in Galicia (NW Spain).

Journal of invertebrate pathology, 176:107460.

During a histopathological survey of Mytilus galloprovincialis in Galicia (NW Spain), microcells were observed infecting several organs of the symbiont copepod Mytilicola intestinalis. Positive results of PCR assay with specific primers for genus Mikrocytos and a clear signal of in situ hybridization with MACKINI-1 digoxigenin- labelled DNA probe (DIG-ISH) indicated a protozoan parasite of Mikrocytos genus. The ultrastructural study revealed intra and extracellular locations, polymorphic nuclei, intracellular round vesicles in the cytoplasm and absence of mitochondria. The present paper reports the characterization of the Mikrocytos sp. infecting M. intestinalis and proposes a novel species in the genus: Mikrocytos mytilicoli n. sp. A sequence of 18S-28S rDNA was obtained with 95.6% maximum identity (query cover 100%) with Mikrocytos mackini. Phylogenetic analysis showed that M. mytilicoli n. sp. and M. mackini share a common ancestor. However, comparison of the ITS1 rDNA region showed low similarity (75.8%) with M. mackini, which, combined with differences in ultrastructural details, host and geographic location, support the designation of a new species. This is the first description of a microcytid parasite of the genus Mikrocytos from a non-bivalve host.

RevDate: 2021-07-30
CmpDate: 2021-07-30

Samson JE, Ray DD, Porfiri M, et al (2020)

Collective Pulsing in Xeniid Corals: Part I-Using Computer Vision and Information Theory to Search for Coordination.

Bulletin of mathematical biology, 82(7):90 pii:10.1007/s11538-020-00759-2.

Xeniid corals (Cnidaria: Alcyonacea), a family of soft corals, include species displaying a characteristic pulsing behavior. This behavior has been shown to increase oxygen diffusion away from the coral tissue, resulting in higher photosynthetic rates from mutualistic symbionts. Maintaining such a pulsing behavior comes at a high energetic cost, and it has been proposed that coordinating the pulse of individual polyps within a colony might enhance the efficiency of fluid transport. In this paper, we test whether patterns of collective pulsing emerge in coral colonies and investigate possible interactions between polyps within a colony. We video recorded different colonies of Heteroxenia sp. in a laboratory environment. Our methodology is based on the systematic integration of a computer vision algorithm (ISOMAP) and an information-theoretic approach (transfer entropy), offering a vantage point to assess coordination in collective pulsing. Perhaps surprisingly, we did not detect any form of collective pulsing behavior in the colonies. Using artificial data sets, however, we do demonstrate that our methodology is capable of detecting even weak information transfer. The lack of a coordination is consistent with previous work on many cnidarians where coordination between actively pulsing polyps and medusa has not been observed. In our companion paper, we show that there is no fluid dynamic benefit of coordinated pulsing, supporting this result. The lack of coordination coupled with no obvious fluid dynamic benefit to grouping suggests that there may be non-fluid mechanical advantages to forming colonies, such as predator avoidance and defense.

RevDate: 2021-07-29

Ueno AC, Gundel PE, Ghersa CM, et al (2021)

Seed-borne fungal endophytes constrain reproductive success of host plants under ozone pollution.

Environmental research pii:S0013-9351(21)01067-7 [Epub ahead of print].

Tropospheric ozone is among the global change factors that pose a threat to plants and microorganisms. Symbiotic microorganisms can assist plants to cope with stress, but their role in the tolerance of plants to ozone is poorly understood. Here, we subjected endophyte-symbiotic and non-symbiotic plants of Lolium multiflorum, an annual species widely distributed in temperate grasslands, to high and low (i.e., charcoal-filtered air) ozone levels at vegetative and reproductive phases. Exposure to high ozone reduced leaf photochemical efficiency and greenness in both symbiotic and non-symbiotic plants. However, ozone-induced oxidative damage at biochemical level (i.e., lipid peroxidation) was mostly detected in symbiotic plants. Ozone exposure at the vegetative phase did not affect the reproductive investment in seeds, indicating full recovery from stress. Ozone exposure at the reproductive phase reduced biomass and seed production only in symbiotic plants indicating a symbiont-associated cost. At low ozone, endophyte-symbiotic plants showed a steeper slope in the relationship between seed number and seed weight (i.e., a number-weight trade-off) compared to non-symbiotic plants. However, when plants were treated at the reproductive phase, ozone increased the imbalance between seed number and seed weight in both endophyte-symbiotic and non-symbiotic plants. Plants with endophytes at the reproductive stage produced fewer seeds, which were not compensated by increased seed weight. Thus, fungal mycelium growing within ovaries or ozone-induced antioxidant systems may result in costs that finally depress the fitness of plants. Despite ozone pollution could destabilize plant-endophyte mutualisms and render them dysfunctional, other endophyte-mediated benefits (e.g., resistance to herbivory, tolerance to drought) could over-compensate these losses and explain the high incidence of the symbiosis in nature.

RevDate: 2021-07-29

Su ZZ, Dai MD, Zhu JN, et al (2021)

Dark septate endophyte Falciphora oryzae-assisted alleviation of cadmium in rice.

Journal of hazardous materials, 419:126435 pii:S0304-3894(21)01400-X [Epub ahead of print].

Dark septate endophytes (DSEs) are the typical representatives of root endophytic fungi in heavy metal (HM)-contaminated environments. However, little is known about their roles in the HMs tolerance of hosts and the underlying mechanism. Here, we investigated the biological roles and molecular mechanisms of a DSE strain Falciphora oryzae in alleviating cadmium (Cd) toxicities in rice. It was found that F. oryzae possessed a capacity of accumulating Cd in its vacuoles and chlamydospores. During symbiosis, F. oryzae conferred improved Cd tolerance to rice, decreasing Cd accumulation in roots and translocation to shoots. F. oryzae alleviated Cd toxicity to rice by sequestering Cd in its vacuoles. Further application of F. oryzae as fertilizer in the field could reduce Cd content in rice grains. We identified a SNARE Syntaxin 1 gene through proteomics, which participated in Cd tolerance of F. oryzae by regulating chlamydospore formation and vacuole enlargement. This study provided novel insights into how the DSEs and their host plants combat Cd stress.

RevDate: 2021-07-29

Shinde S, Tupe-Waghmare P, Chougule T, et al (2021)

Predictive and discriminative localization of pathology using high resolution class activation maps with CNNs.

PeerJ. Computer science, 7:e622 pii:cs-622.

Purpose: Existing class activation mapping (CAM) techniques extract the feature maps only from a single layer of the convolutional neural net (CNN), generally from the final layer and then interpolate to upsample to the original image resolution to locate the discriminative regions. Consequently these provide a coarse localization that may not be able to capture subtle abnormalities in medical images. To alleviate this, our work proposes a technique called high resolution class activation mapping (HR-CAMs) that can provide enhanced visual explainability to the CNN models.

Methods: HR-CAMs fuse feature maps by training a network using the input from multiple layers of a trained CNN, thus gaining information from every layer that can localize abnormalities with greater details in original image resolution. The technique is validated qualitatively and quantitatively on a simulated dataset of 8,000 images followed by applications on multiple image analysis tasks that include (1) skin lesion classification (ISIC open dataset-25,331 cases) and (2) predicting bone fractures (MURA open dataset-40,561 images) (3) predicting Parkinson's disease (PD) from neuromelanin sensitive MRI (small cohort-80 subjects).

Results: We demonstrate that our model creates clinically interpretable subject specific high resolution discriminative localizations when compared to widely used CAMs and Gradient-CAMs.

Conclusion: HR-CAMs provide finer delineation of abnormalities thus facilitating superior explainability to CNNs as has been demonstrated from its rigorous validation.

RevDate: 2021-07-28
CmpDate: 2021-07-28

Thierry M, Pardikes NA, Lue CH, et al (2021)

Experimental warming influences species abundances in a Drosophila host community through direct effects on species performance rather than altered competition and parasitism.

PloS one, 16(2):e0245029.

Global warming is expected to have direct effects on species through their sensitivity to temperature, and also via their biotic interactions, with cascading indirect effects on species, communities, and entire ecosystems. To predict the community-level consequences of global climate change we need to understand the relative roles of both the direct and indirect effects of warming. We used a laboratory experiment to investigate how warming affects a tropical community of three species of Drosophila hosts interacting with two species of parasitoids over a single generation. Our experimental design allowed us to distinguish between the direct effects of temperature on host species performance, and indirect effects through altered biotic interactions (competition among hosts and parasitism by parasitoid wasps). Although experimental warming significantly decreased parasitism for all host-parasitoid pairs, the effects of parasitism and competition on host abundances and host frequencies did not vary across temperatures. Instead, effects on host relative abundances were species-specific, with one host species dominating the community at warmer temperatures, irrespective of parasitism and competition treatments. Our results show that temperature shaped a Drosophila host community directly through differences in species' thermal performance, and not via its influences on biotic interactions.

RevDate: 2021-07-29
CmpDate: 2021-07-29

Joseph A, J Roper (2021)

Genetic Evidence That a Gut Commensal Bacterium Can Cause Colorectal Cancer.

Gastroenterology, 160(4):1424-1426.

RevDate: 2021-07-28
CmpDate: 2021-07-28

Daillère R, Routy B, Goubet AG, et al (2020)

Elucidating the gut microbiota composition and the bioactivity of immunostimulatory commensals for the optimization of immune checkpoint inhibitors.

Oncoimmunology, 9(1):1794423.

Accumulating evidence from preclinical studies and human trials demonstrated the crucial role of the gut microbiota in determining the effectiveness of anticancer therapeutics such as immunogenic chemotherapy or immune checkpoint blockade. In summary, it appears that a diverse intestinal microbiota supports therapeutic anticancer responses, while a dysbiotic microbiota composition that lacks immunostimulatory bacteria or contains overabundant immunosuppressive species causes treatment failure. In this review, we explore preclinical and translational studies highlighting how eubiotic and dysbiotic microbiota composition can affect progression-free survival in cancer patients.

RevDate: 2021-07-27

Fraccascia L, Spagnoli M, Riccini L, et al (2021)

Designing the biomethane production chain from urban wastes at the regional level: An application to the Rome Metropolitan Area.

Journal of environmental management, 297:113328 pii:S0301-4797(21)01390-6 [Epub ahead of print].

This paper proposes a methodology to design the biomethane production chain from MSW at the regional level and to assess the environmental and economic performance of the chain. In the design phase, the following parameters are considered: number and production capacity of biomethane plants, localization of plants, waste flows among municipalities and plants. The model is adopted to design the biomethane chain in the Rome Metropolitan Area (Italy). Several structures of production chain are designed and their performances are assessed. The economic factors mostly able to affect the performance of the chain are waste disposal tariff, biomethane selling price, and the economic incentive provided to biomethane producers. Their impacts are discussed through sensitivity analyses. Results show that the structure maximizing the economic performance has the worst environmental performance and vice versa. Hence, a new structure of the economic incentive is proposed, aimed at re-aligning economic and environmental performance.

RevDate: 2021-07-27

Feng Y, Wu P, Liu C, et al (2021)

Suppression of LjBAK1-mediated immunity by SymRK promotes rhizobial infection in Lotus japonicus.

Molecular plant pii:S1674-2052(21)00304-X [Epub ahead of print].

An important question in biology is how organisms can associate with different microbes that pose no threat (commensals), pose a severe threat (pathogens) and those that are beneficial (symbionts). The root nodule symbiosis serves as important model system to address such questions in the context of plant-microbe interactions. It is now generally accepted that rhizobia have the abilities to actively suppress host immune responses during the infection process, analogous to the way in which plant pathogens can evade immune recognition. However, much remains to be elucidated with regard to the mechanisms by which the host recognizes the rhizobia as pathogens and how, subsequently, these pathways are suppressed to allow establishment of the nitrogen fixing symbiosis. In this study, we found that SymRK (Symbiosis Receptor-like Kinase) is required for rhizobial suppression of plant innate immunity in Lotus japonicus. SymRK associates with LjBAK1 (BRASSINOSTEROID INSENSITIVE 1-Associated receptor Kinase 1), a well characterized, positive regulator of plant innate immunity, and directly inhibits LjBAK1 kinase activity. Rhizobial inoculation enhances the association between SymRK and LjBAK1 in planta. LjBAK1 is required to regulate plant innate immunity and plays a negative role in mediating rhizobial infection in L. japonicus. The data indicate that the protein complex of SymRK-LjBAK1 serves as an intersection point between rhizobial symbiotic signaling pathways and innate immunity pathways, which provides an evidence that rhizobia might actively suppress the host's ability to mount a defense response in the legume-rhizobium symbiosis.

RevDate: 2021-07-27

Bellabarba A, Bacci G, Decorosi F, et al (2021)

Competitiveness for Nodule Colonization in Sinorhizobium meliloti: Combined In Vitro-Tagged Strain Competition and Genome-Wide Association Analysis.

mSystems [Epub ahead of print].

Associations between leguminous plants and symbiotic nitrogen-fixing rhizobia are a classic example of mutualism between a eukaryotic host and a specific group of prokaryotic microbes. Although this symbiosis is in part species specific, different rhizobial strains may colonize the same nodule. Some rhizobial strains are commonly known as better competitors than others, but detailed analyses that aim to predict rhizobial competitive abilities based on genomes are still scarce. Here, we performed a bacterial genome-wide association (GWAS) analysis to define the genomic determinants related to the competitive capabilities in the model rhizobial species Sinorhizobium meliloti. For this, 13 tester strains were green fluorescent protein (GFP) tagged and assayed versus 3 red fluorescent protein (RFP)-tagged reference competitor strains (Rm1021, AK83, and BL225C) in a Medicago sativa nodule occupancy test. Competition data and strain genomic sequences were employed to build a model for GWAS based on k-mers. Among the k-mers with the highest scores, 51 k-mers mapped on the genomes of four strains showing the highest competition phenotypes (>60% single strain nodule occupancy; GR4, KH35c, KH46, and SM11) versus BL225C. These k-mers were mainly located on the symbiosis-related megaplasmid pSymA, specifically on genes coding for transporters, proteins involved in the biosynthesis of cofactors, and proteins related to metabolism (e.g., fatty acids). The same analysis was performed considering the sum of single and mixed nodules obtained in the competition assays versus BL225C, retrieving k-mers mapped on the genes previously found and on vir genes. Therefore, the competition abilities seem to be linked to multiple genetic determinants and comprise several cellular components. IMPORTANCE Decoding the competitive pattern that occurs in the rhizosphere is challenging in the study of bacterial social interaction strategies. To date, the single-gene approach has mainly been used to uncover the bases of nodulation, but there is still a knowledge gap regarding the main features that a priori characterize rhizobial strains able to outcompete indigenous rhizobia. Therefore, tracking down which traits make different rhizobial strains able to win the competition for plant infection over other indigenous rhizobia will improve the strain selection process and, consequently, plant yield in sustainable agricultural production systems. We proved that a k-mer-based GWAS approach can efficiently identify the competition determinants of a panel of strains previously analyzed for their plant tissue occupancy using double fluorescent labeling. The reported strategy will be useful for detailed studies on the genomic aspects of the evolution of bacterial symbiosis and for an extensive evaluation of rhizobial inoculants.

RevDate: 2021-07-27

Nicoud Q, Barrière Q, Busset N, et al (2021)

Sinorhizobium meliloti Functions Required for Resistance to Antimicrobial NCR Peptides and Bacteroid Differentiation.

mBio [Epub ahead of print].

Legumes of the Medicago genus have a symbiotic relationship with the bacterium Sinorhizobium meliloti and develop root nodules housing large numbers of intracellular symbionts. Members of the nodule-specific cysteine-rich peptide (NCR) family induce the endosymbionts into a terminal differentiated state. Individual cationic NCRs are antimicrobial peptides that have the capacity to kill the symbiont, but the nodule cell environment prevents killing. Moreover, the bacterial broad-specificity peptide uptake transporter BacA and exopolysaccharides contribute to protect the endosymbionts against the toxic activity of NCRs. Here, we show that other S. meliloti functions participate in the protection of the endosymbionts; these include an additional broad-specificity peptide uptake transporter encoded by the yejABEF genes and lipopolysaccharide modifications mediated by lpsB and lpxXL, as well as rpoH1, encoding a stress sigma factor. Strains with mutations in these genes show a strain-specific increased sensitivity profile against a panel of NCRs and form nodules in which bacteroid differentiation is affected. The lpsB mutant nodule bacteria do not differentiate, the lpxXL and rpoH1 mutants form some seemingly fully differentiated bacteroids, although most of the nodule bacteria are undifferentiated, while the yejABEF mutants form hypertrophied but nitrogen-fixing bacteroids. The nodule bacteria of all the mutants have a strongly enhanced membrane permeability, which is dependent on the transport of NCRs to the endosymbionts. Our results suggest that S. meliloti relies on a suite of functions, including peptide transporters, the bacterial envelope structures, and stress response regulators, to resist the aggressive assault of NCR peptides in the nodule cells. IMPORTANCE The nitrogen-fixing symbiosis of legumes with rhizobium bacteria has a predominant ecological role in the nitrogen cycle and has the potential to provide the nitrogen required for plant growth in agriculture. The host plants allow the rhizobia to colonize specific symbiotic organs, the nodules, in large numbers in order to produce sufficient reduced nitrogen for the plants' needs. Some legumes, including Medicago spp., produce massively antimicrobial peptides to keep this large bacterial population in check. These peptides, known as NCRs, have the potential to kill the rhizobia, but in nodules, they rather inhibit the division of the bacteria, which maintain a high nitrogen-fixing activity. In this study, we show that the tempering of the antimicrobial activity of the NCR peptides in the Medicago symbiont Sinorhizobium meliloti is multifactorial and requires the YejABEF peptide transporter, the lipopolysaccharide outer membrane, and the stress response regulator RpoH1.

RevDate: 2021-07-23

Szabó G, Schulz F, Manzano-Marín A, et al (2021)

Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles.

The ISME journal [Epub ahead of print].

Adelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelges tardus species complex containing betaproteobacterial ("Candidatus Vallotia tarda") and gammaproteobacterial ("Candidatus Profftia tarda") symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other's role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

RevDate: 2021-07-23

Chaturvedi A, Cruz Corella J, Robbins C, et al (2021)

The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya.

Communications biology, 4(1):901.

Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). As plants transitioned to land the EDF sub-phylum, arbuscular mycorrhizal fungi (AMF; Glomeromycotina) evolved a symbiotic lifestyle with 80% of plant species worldwide. Here we show that these fungi exhibit 5mC and 6mA methylation characteristics that jointly set them apart from other fungi. The model AMF, R. irregularis, evolved very high levels of 5mC and greatly reduced levels of 6mA. However, unlike the Dikarya, 6mA in AMF occurs at symmetrical ApT motifs in genes and is associated with their transcription. 6mA is heterogeneously distributed among nuclei in these coenocytic fungi suggesting functional differences among nuclei. While far fewer genes are regulated by 6mA in the AMF genome than in EDF, most strikingly, 6mA methylation has been specifically retained in genes implicated in components of phosphate regulation; the quintessential hallmark defining this globally important symbiosis.

RevDate: 2021-07-27
CmpDate: 2021-07-27

Hardy BL, DS Merrell (2021)

Friend or Foe: Interbacterial Competition in the Nasal Cavity.

Journal of bacteriology, 203(5):.

Like other microbes that live on or in the human body, the bacteria that inhabit the upper respiratory tract, in particular the nasal cavity, have evolved to survive in an environment that presents a number of physical and chemical challenges; these microbes are constantly bombarded with nutritional fluctuations, changes in humidity, the presence of inhaled particulate matter (odorants and allergens), and competition with other microbes. Indeed, only a specialized set of species is able to colonize this niche and successfully contend with the host's immune system and the constant threat from competitors. To this end, bacteria that live in the nasal cavity have evolved a variety of approaches to outcompete contenders for the limited nutrients and space; broadly speaking, these strategies may be considered a type of "bacterial warfare." A greater molecular understanding of bacterial warfare has the potential to reveal new approaches or molecules that can be developed as novel therapeutics. As such, there are many studies within the last decade that have sought to understand the complex polymicrobial interactions that occur in various environments. Here, we review what is currently known about the age-dependent structure and interbacterial relationships within the nasal microbiota and summarize the molecular mechanisms that are predicted to dictate bacterial warfare in this niche. Although the currently described interactions are complex, in reality, we have likely only scratched the surface in terms of a true understanding of the types of interbacterial competition and cooperation that are thought to take place in and on the human body.

RevDate: 2021-07-26

Kaup M, Trull S, EFY Hom (2021)

On the move: sloths and their epibionts as model mobile ecosystems.

Biological reviews of the Cambridge Philosophical Society [Epub ahead of print].

Sloths are unusual mobile ecosystems, containing a high diversity of epibionts living and growing in their fur as they climb slowly through the canopies of tropical forests. These epibionts include poorly studied algae, arthropods, fungi, and bacteria, making sloths likely reservoirs of unexplored biodiversity. This review aims to identify gaps and eliminate misconceptions in our knowledge of sloths and their epibionts, and to identify key questions to stimulate future research into the functions and roles of sloths within a broader ecological and evolutionary context. This review also seeks to position the sloth fur ecosystem as a model for addressing fundamental questions in metacommunity and movement ecology. The conceptual and evidence-based foundation of this review aims to serve as a guide for future hypothesis-driven research into sloths, their microbiota, sloth health and conservation, and the coevolution of symbioses in general.

RevDate: 2021-07-27

Zou K, Liu X, Hu Q, et al (2021)

Root Endophytes and Ginkgo biloba Are Likely to Share and Compensate Secondary Metabolic Processes, and Potentially Exchange Genetic Information by LTR-RTs.

Frontiers in plant science, 12:704985.

Ginkgo biloba is a pharmaceutical resource for terpenes and flavonoids. However, few insights discussed endophytes' role in Ginkgo, and whether genetic exchange happens between Ginkgo and endophytes remains unclear. Herein, functional gene profiles and repetitive sequences were analyzed to focus on these issues. A total of 25 endophyte strains were isolated from the Ginkgo root and distributed in 16 genera of 6 phyla. Significant morphological diversities lead to the diversity in the COG functional classification. KEGG mapping revealed that endophytic bacteria and fungi potentially synthesize chalcone, while endophytic fungi might also promote flavonoid derivatization. Both bacteria and fungi may facilitate the lignin synthesis. Aspergillus sp. Gbtc_1 exhibited the feasibility of regulating alcohols to lignans. Although Ginkgo and the endophytes have not observed the critical levopimaradiene synthase in ginkgolides synthesis, the upstream pathways of terpenoid precursors are likely intact. The MVK genes in Ginkgo may have alternative non-homologous copies or be compensated by endophytes in long-term symbiosis. Cellulomonas sp. Gbtc_1 became the only bacteria to harbor both MEP and MVA pathways. Endophytes may perform the mutual transformation of IPP and DMAPP in the root. Ginkgo and bacteria may lead to the synthesis and derivatization of the carotenoid pathway. The isoquinoline alkaloid biosynthesis seemed lost in the Ginkgo root community, but L-dopa is more probably converted into dopamine as an essential signal-transduction substance. So, endophytes may participate in the secondary metabolism of the Ginkgo in a shared or complementary manner. Moreover, a few endophytic sequences predicted as Ty3/Gypsy and Ty1/Copia superfamilies exhibited extremely high similarity to those of Ginkgo. CDSs in such endophytic LTR-RT sequences were also highly homologous to one Ginkgo CDS. Therefore, LTR-RTs may be a rare unit flowing between the Ginkgo host and endophytes to exchange genetic information. Collectively, this research effectively expanded the insight on the symbiotic relationship between the Ginkgo host and the endophytes in the root.

RevDate: 2021-07-27

Pereira EC, Vazquez de Aldana BR, Arellano JB, et al (2021)

The Role of Fungal Microbiome Components on the Adaptation to Salinity of Festuca rubra subsp. pruinosa.

Frontiers in plant science, 12:695717.

Festuca rubra subsp. pruinosa is a perennial grass that inhabits sea cliffs, a habitat where salinity and low nutrient availability occur. These plants have a rich fungal microbiome, and particularly common are their associations with Epichloë festucae in aboveground tissues and with Fusarium oxysporum and Periconia macrospinosa in roots. In this study, we hypothesized that these fungi could affect the performance of F. rubra plants under salinity, being important complements for plant habitat adaptation. Two lines of F. rubra, each one consisting of Epichloë-infected and Epichloë-free clones, were inoculated with the root endophytes (F. oxysporum and P. macrospinosa) and subjected to a salinity treatment. Under salinity, plants symbiotic with Epichloë had lower Na+ content than non-symbiotic plants, but this effect was not translated into plant growth. P. macrospinosa promoted leaf and root growth in the presence and absence of salinity, and F. oxysporum promoted leaf and root growth in the presence and absence of salinity, plus a decrease in leaf Na+ content under salinity. The growth responses could be due to functions related to improved nutrient acquisition, while the reduction of Na+ content might be associated with salinity tolerance and plant survival in the long term. Each of these three components of the F. rubra core mycobiome contributed with different functions, which are beneficial and complementary for plant adaptation to its habitat in sea cliffs. Although our results do not support an obvious role of Epichloë itself in FRP salt tolerance, there is evidence that Epichloë can interact with root endophytes, affecting host plant performance.

RevDate: 2021-07-27

Wang JT, Shen JP, Zhang LM, et al (2021)

Generalist Taxa Shape Fungal Community Structure in Cropping Ecosystems.

Frontiers in microbiology, 12:678290.

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5-17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.

RevDate: 2021-07-27

Green DW, Watson JA, Ben-Nissan B, et al (2021)

Synthetic tissue engineering with smart, cytomimetic protocells.

Biomaterials, 276:120941 pii:S0142-9612(21)00297-0 [Epub ahead of print].

Synthetic protocells are rudimentary origin-of-life versions of natural cell counterparts. Protocells are widely engineered to advance efforts and useful accepted outcomes in synthetic biology, soft matter chemistry and bioinspired materials chemistry. Protocells in collective symbiosis generate synthetic proto-tissues that display unprecedented autonomy and yield advanced materials with desirable life-like features for smart multi-drug delivery, micro bioreactors, renewable fuel production, environmental clean-up, and medicine. Current levels of protocell and proto-tissue functionality and adaptivity are just sufficient to apply them in tissue engineering and regenerative medicine, where they animate biomaterials and increase therapeutic cell productivity. As of now, structural biomaterials for tissue engineering lack the properties of living biomaterials such as self-repair, stochasticity, cell synergy and the sequencing of molecular and cellular events. Future protocell-based biomaterials provide these core properties of living organisms, but excluding evolution. Most importantly, protocells are programmable for a broad array of cell functions and behaviors and collectively in consortia are tunable for multivariate functions. Inspired by upcoming designs of smart protocells, we review their developmental background and cover the most recently reported developments in this promising field of synthetic proto-biology. Our emphasis is on manufacturing proto-tissues for tissue engineering of organoids, stem cell niches and reprogramming and tissue formation through stages of embryonic development. We also highlight the exciting reported developments arising from fusing living cells and tissues, in a valuable hybrid symbiosis, with synthetic counterparts to bring about novel functions, and living tissue products for a new synthetic tissue engineering discipline.

RevDate: 2021-07-26

Traubenik S, Ferrari M, Blanco FA, et al (2021)

Translational regulation in pathogenic and beneficial plant-microbe interactions.

The Biochemical journal, 478(14):2775-2788.

Plants are surrounded by a vast diversity of microorganisms. Limiting pathogenic microorganisms is crucial for plant survival. On the other hand, the interaction of plants with beneficial microorganisms promotes their growth or allows them to overcome nutrient deficiencies. Balancing the number and nature of these interactions is crucial for plant growth and development, and thus, for crop productivity in agriculture. Plants use sophisticated mechanisms to recognize pathogenic and beneficial microorganisms and genetic programs related to immunity or symbiosis. Although most research has focused on characterizing changes in the transcriptome during plant-microbe interactions, the application of techniques such as Translating Ribosome Affinity Purification (TRAP) and Ribosome profiling allowed examining the dynamic association of RNAs to the translational machinery, highlighting the importance of the translational level of control of gene expression in both pathogenic and beneficial interactions. These studies revealed that the transcriptional and the translational responses are not always correlated, and that translational control operates at cell-specific level. In addition, translational control is governed by cis-elements present in the 5'mRNA leader of regulated mRNAs, e.g. upstream open reading frames (uORFs) and sequence-specific motifs. In this review, we summarize and discuss the recent advances made in the field of translational control during pathogenic and beneficial plant-microbe interactions.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Palomares-Rius JE, Gutiérrez-Gutiérrez C, Mota M, et al (2021)

'Candidatus Xiphinematincola pachtaicus' gen. nov., sp. nov., an endosymbiotic bacterium associated with nematode species of the genus Xiphinema (Nematoda, Longidoridae).

International journal of systematic and evolutionary microbiology, 71(7):.

An intracellular bacterium, strain IAST, was observed to infect several species of the plant-parasitic nematode genus Xiphinema (Xiphinema astaregiense, Xiphinema incertum, Xiphinema madeirense, Xiphinema pachtaicum, Xiphinema parapachydermum and Xiphinema vallense). The bacterium could not be recovered on axenic medium. The 16S rRNA gene sequence of IAST was found to be new, being related to the family Burkholderiaceae, class Betaproteobacteria. Fungal endosymbionts Mycoavidus cysteinexigens B1-EBT (92.9 % sequence identity) and 'Candidatus Glomeribacter gigasporarum' BEG34 (89.8 % identity) are the closest taxa and form a separate phylogenetic clade inside Burkholderiaceae. Other genes (atpD, lepA and recA) also separated this species from its closest relatives using a multilocus sequence analysis approach. These genes were obtained using a partial genome of this bacterium. The localization of the bacterium (via light and fluorescence in situ hybridization microscopy) is in the X. pachtaicum females clustered around the developing oocytes, primarily found embedded inside the epithelial wall cells of the ovaries, from where they are dispersed in the intestine. Transmission electron microscopy (TEM) observations supported the presence of bacteria inside the nematode body, where they occupy ovaries and occur inside the intestinal epithelium. Ultrastructural analysis of the bacterium showed cells that appear as mostly irregular, slightly curved rods with rounded ends, 0.8-1.2 µm wide and 2.5-6.0 µm long, possessing a typical Gram-negative cell wall. The peptidoglycan layer is, however, evident only occasionally and not detectable by TEM in most cells. Another irregularly occurring shell surrounding the endosymbiont cells or the cell clusters was also revealed, probably originating from the host cell membrane. Flagella or spore-like cells do not occur and the nucleoid is diffusely distributed throughout the cell. This endosymbiont is transmitted vertically through nematode generations. These results support the proposal of IAST as a new species, although its obligate intracellular and obligate endosymbiont nature prevented isolation of a definitive type strain. Strain IAST is therefore proposed as representing 'Candidatus Xiphinematincola pachtaicus' gen. nov., sp. nov.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Pierella Karlusich JJ, Pelletier E, Lombard F, et al (2021)

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods.

Nature communications, 12(1):4160.

Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2-2000 μm). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 μm) to mesoplankton (180-2000 μm) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.

RevDate: 2021-07-26
CmpDate: 2021-07-26

González-López MDC, Jijón-Moreno S, Dautt-Castro M, et al (2021)

Secretome Analysis of Arabidopsis-Trichoderma atroviride Interaction Unveils New Roles for the Plant Glutamate:Glyoxylate Aminotransferase GGAT1 in Plant Growth Induced by the Fungus and Resistance against Botrytis cinerea.

International journal of molecular sciences, 22(13):.

The establishment of plant-fungus mutualistic interaction requires bidirectional molecular crosstalk. Therefore, the analysis of the interacting organisms secretomes would help to understand how such relationships are established. Here, a gel-free shotgun proteomics approach was used to identify the secreted proteins of the plant Arabidopsis thaliana and the mutualistic fungus Trichoderma atroviride during their interaction. A total of 126 proteins of Arabidopsis and 1027 of T. atroviride were identified. Among them, 118 and 780 were differentially modulated, respectively. Bioinformatic analysis unveiled that both organisms' secretomes were enriched with enzymes. In T. atroviride, glycosidases, aspartic endopeptidases, and dehydrogenases increased in response to Arabidopsis. Additionally, amidases, protein-serine/threonine kinases, and hydro-lyases showed decreased levels. Furthermore, peroxidases, cysteine endopeptidases, and enzymes related to the catabolism of secondary metabolites increased in the plant secretome. In contrast, pathogenesis-related proteins and protease inhibitors decreased in response to the fungus. Notably, the glutamate:glyoxylate aminotransferase GGAT1 was secreted by Arabidopsis during its interaction with T. atroviride. Our study showed that GGAT1 is partially required for plant growth stimulation and on the induction of the plant systemic resistance by T. atroviride. Additionally, GGAT1 seems to participate in the negative regulation of the plant systemic resistance against B. cinerea through a mechanism involving H2O2 production.

RevDate: 2021-07-23
CmpDate: 2021-07-23

Dângelo RAC, Michereff-Filho M, Inoue-Nagata AK, et al (2021)

Area-wide insecticide resistance and endosymbiont incidence in the whitefly Bemisia tabaci MEAM1 (B biotype): A Neotropical context.

Ecotoxicology (London, England), 30(6):1056-1070.

Agriculture insecticides are used against insect pest species, but are able to change community structure in contaminated habitats, and also the genetic pool of exposed individuals. In fact, the latter effect is a relevant tool to in situ biomonitoring of pollutant contamination and impact, besides its practical economic and management concerns. This takes place because the emergence of individuals with resistance to insecticides is particularly frequent among insect pest species and usually enhances insecticide overuse and crop losses. Pest insects of global prominence such as whiteflies are a focus of attention due to problems with insecticide resistance and association with endosymbionts, as the case of the invasive putative species Bemisia tabaci MEAM1. The scenario is particularly complex in the Neotropics, where insecticide use is ubiquitous, but whose spatial scale of occurrence is usually neglected. Here we explored the spatial-dependence of both phenomena in MEAM1 whiteflies recording resistance to two widely used insecticides, lambda-cyhalothrin and spiromesifen, and endosymbiont co-occurrence. Resistance to both insecticides was frequent exhibiting low to moderate frequency of lambda-cyhalothrin resistance and moderate to high frequency of spiromesifen resistance. Among the prevailing whitefly endosymbionts, Wolbachia, Cardinium and Arsenophonus were markedly absent. In contrast, Hamiltonella and Rickettsia prevailed and their incidence was correlated. Furthermore, Rickettsia endosymbionts were particularly associated with lambda-cyhalothrin susceptibility. These traits were spatially dependent with significant variation taking place within an area of about 700 Km2. Such findings reinforce the notion of endosymbiont-associated resistance to insecticides, and also of their local incidence allowing spatial mapping and locally-targeted mitigation.

RevDate: 2021-07-23
CmpDate: 2021-07-23

Liu Y, Palaniveloo K, Alias SA, et al (2021)

Species Diversity and Secondary Metabolites of Sarcophyton-Associated Marine Fungi.

Molecules (Basel, Switzerland), 26(11):.

Soft corals are widely distributed across the globe, especially in the Indo-Pacific region, with Sarcophyton being one of the most abundant genera. To date, there have been 50 species of identified Sarcophyton. These soft corals host a diverse range of marine fungi, which produce chemically diverse, bioactive secondary metabolites as part of their symbiotic nature with the soft coral hosts. The most prolific groups of compounds are terpenoids and indole alkaloids. Annually, there are more bio-active compounds being isolated and characterised. Thus, the importance of the metabolite compilation is very much important for future reference. This paper compiles the diversity of Sarcophyton species and metabolites produced by their associated marine fungi, as well as the bioactivity of these identified compounds. A total of 88 metabolites of structural diversity are highlighted, indicating the huge potential these symbiotic relationships hold for future research.

RevDate: 2021-07-23
CmpDate: 2021-07-23

Flores P, Alvarado A, Lankin G, et al (2021)

Morphological, molecular and ecological characterization of a native isolate of Steinernema feltiae (Rhabditida: Steinernematidae) from southern Chile.

Parasites & vectors, 14(1):45.

BACKGROUND: Steinernema feltiae is an entomopathogenic nematode used in biological control programs with a global distribution. Populations of this species show phenotypic plasticity derived from local adaptation and vary in different traits, such as location and host penetration. The aim of this work was to describe a Chilean isolate of this nematode species, using integrative approaches.

METHODS: Nematode morphological and morphometric studies were conducted along with molecular analysis of nuclear genes. The symbiotic bacterium was also identified by sequencing the 16S rRNA gene. Some ecological characteristics were described, including the temperature requirements for the nematode life cycle and the effect of soil water content for optimal reproduction.

RESULTS: Morphometric characterization revealed a large intra-specific variability. The isolate identity was also corroborated with the analysis of nuclear genes. Based on the 16S gene, its symbiont bacteria, Xenorhabdus bovienii, was identified. The lowest, optimal and highest temperatures found to limit the infestation and reproduction on Galleria mellonella were 10, 20 and 30 °C, respectively; the emergence from the host larvae occurred approximately 10 days after inoculation. Differences were observed in offspring, and 120 infective juveniles (IJ)/larva was the most prolific dose at 20 °C. The soil water content did not affect the number of IJ invaders, penetration efficacy and IJ emergence time or offspring per larva, but it caused a delay in achieving full mortality at the permanent wilting point with respect to saturation and field capacity.

CONCLUSIONS: For the first time, a Chilean isolate of S. feltiae is described in detail considering morphological, molecular and ecological aspects. The isolate was shown to be efficient in soil containing water, with optimal temperatures ranging from 15 to 25 °C for host infestation and production of an abundant offspring; these characteristics would allow its potential use as control agents in a wide geographical area of the country.

RevDate: 2021-07-23
CmpDate: 2021-07-23

Bojar D, Powers RK, Camacho DM, et al (2021)

Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions.

Cell host & microbe, 29(1):132-144.e3.

Glycans, the most diverse biopolymer, are shaped by evolutionary pressures stemming from host-microbe interactions. Here, we present machine learning and bioinformatics methods to leverage the evolutionary information present in glycans to gain insights into how pathogens and commensals interact with hosts. By using techniques from natural language processing, we develop deep-learning models for glycans that are trained on a curated dataset of 19,299 unique glycans and can be used to study and predict glycan functions. We show that these models can be utilized to predict glycan immunogenicity and the pathogenicity of bacterial strains, as well as investigate glycan-mediated immune evasion via molecular mimicry. We also develop glycan-alignment methods and use these to analyze virulence-determining glycan motifs in the capsular polysaccharides of bacterial pathogens. These resources enable one to identify and study glycan motifs involved in immunogenicity, pathogenicity, molecular mimicry, and immune evasion, expanding our understanding of host-microbe interactions.

RevDate: 2021-07-22

Ficano N, Porder S, LA McCulloch (2021)

Tripartite legume-rhizobia-mycorrhizae relationship is influenced by light and soil nitrogen in Neotropical canopy gaps.

Ecology [Epub ahead of print].

Plants and their soil microbial symbionts influence ecosystem productivity and nutrient cycling, but the controls on these symbioses remain poorly understood. This is particularly true for plants in the Fabaceae family (hereafter legumes), which can associate with both arbuscular mycorrhizal fungi (AMF) and nitrogen (N)-fixing bacteria. Here we report results of the first manipulated field experiment to explore the abiotic and biotic controls of this tripartite symbiosis in Neotropical canopy gaps (hereafter gaps). We grew three species of Neotropical N-fixing legume seedlings under different light (gap-full light, gap-shadecloth, and understory) and soil nitrogen (20 g N m-2 yr-1 versus 0 g N m-2 yr-1) conditions across a lowland tropical forest at La Selva Biological Station, Costa Rica. We harvested the seedlings after four months growth in the field and measured percent AMF root colonization (%AMF), nodule and seeding biomass, and seedling above:below-ground biomass ratios. Our expectation was that seedlings in gaps would grow larger and, as a result of higher light, invest more carbon in both AMF and N-fixing bacteria. Indeed, seedlings in gaps had higher total biomass, nodule biomass (a proxy for N-fixing bacteria investment) and rates of AMF root colonization, and the three were significantly positively correlated. However, we only found a significant positive effect of light availability on %AMF when seedlings were fertilized with N. Furthermore, when we statistically controlled for treatment, species, and site effects, we found %AMF and seedling biomass had a negative relationship. This was likely driven by the fact that seedlings invested relatively less in AMF as they increased in biomass (lower %AMF per gram of seedling). Taken together, these results challenge the long-held assumption that high light conditions universally increase carbon investment in AMF and demonstrate that this tripartite symbiosis is influenced by soil nutrient and light conditions.

RevDate: 2021-07-22

Suárez LJ, Arboleda S, Angelov N, et al (2021)

Oral Versus Gastrointestinal Mucosal Immune Niches in Homeostasis and Allostasis.

Frontiers in immunology, 12:705206.

Different body systems (epidermis, respiratory tract, cornea, oral cavity, and gastrointestinal tract) are in continuous direct contact with innocuous and/or potentially harmful external agents, exhibiting dynamic and highly selective interaction throughout the epithelia, which function as both a physical and chemical protective barrier. Resident immune cells in the epithelia are constantly challenged and must distinguish among antigens that must be either tolerated or those to which a response must be mounted for. When such a decision begins to take place in lymphoid foci and/or mucosa-associated lymphoid tissues, the epithelia network of immune surveillance actively dominates both oral and gastrointestinal compartments, which are thought to operate in the same immune continuum. However, anatomical variations clearly differentiate immune processes in both the mouth and gastrointestinal tract that demonstrate a wide array of independent immune responses. From single vs. multiple epithelia cell layers, widespread cell-to-cell junction types, microbial-associated recognition receptors, dendritic cell function as well as related signaling, the objective of this review is to specifically contrast the current knowledge of oral versus gut immune niches in the context of epithelia/lymphoid foci/MALT local immunity and systemic output. Related differences in 1) anatomy 2) cell-to-cell communication 3) antigen capture/processing/presentation 4) signaling in regulatory vs. proinflammatory responses and 5) systemic output consequences and its relations to disease pathogenesis are discussed.

RevDate: 2021-07-22

Cai Z, Li H, Pu S, et al (2021)

Development of autotrophic and heterotrophic consortia via immobilized microbial beads for chemical wastewater treatment, using PTA wastewater as an approach.

Chemosphere, 281:131001.

Studies on the symbiosis of microalgae-bacteria have been accelerating as a mean for wastewater remediation. However, there were few reports about the microalgae-bacteria consortia for chemical wastewater treatment. The aim of the present study is to develop an autotrophic and heterotrophic consortium for chemical wastewater treatment and probe whether and how bacteria could benefit from the microalgae during the treatment process, using PTA wastewater as an approach. A process-dependent strategy was applied. First of all, the results showed that the sludge beads with the sludge concentration of 30 g/L were the optimal one with the COD removal rate at 84.8% but the ceiling effect occurred (COD removal rate < 90%) even several common reinforcement methods were applied. Additionally, by adding the microalgae Chlorella vulgaris, a microalgae-activated sludge consortium was formed inside the immobilized beads, which provided better performance to shatter the ceiling effect. The COD remove rate was higher than 90%, regardless of the activated sludge was pre-culture or not. COD removal capacity could also be improved (COD removal rate > 92%) when LEDs light belt was offered as an advanced light condition. Biochemical assay and DNA analysis indicated that the microalgae could form an internal circulation of substances within the activated sludge and drove the microbial community to success and the corresponding gene functions, like metabolism and.

RevDate: 2021-07-22
CmpDate: 2021-07-22

Devegili AM, Lescano MN, Gianoli E, et al (2021)

Evidence of indirect biotic resistance: native ants decrease invasive plant fitness by enhancing aphid infestation.

Oecologia, 196(3):607-618.

The biotic resistance hypothesis asserts that native species may hinder the invasion of exotic species, which can occur either directly or indirectly by influencing interactions between exotic and local species. Aphid-tending ants may play a key role in the indirect biotic resistance to plant invasion. Ants may protect aphids, thus increasing their negative effect on exotic plants, but may also deter chewing herbivores, thus benefiting exotic plants. We studied native aphid-tending ants (Dorymyrmex tener, Camponotus distinguendus, and Dorymyrmex richteri) on exotic nodding thistles (Carduus thoermeri), which are attacked by thistle aphids (Brachycaudus cardui) and thistle-head weevils (Rhinocyllus conicus). We evaluated the impact of ants, aphids, and weevils on thistle seed set. We compared ant species aggressiveness towards aphid predators and weevils and performed ant-exclusion experiments to determine the effects of ants on aphid predators and weevils. We analysed whether ant species affected thistle seed set through their effects on aphids and/or weevils. The ant D. tener showed the most aggressive behaviour towards aphid predators and weevils. Further, D. tener successfully removed aphid predators from thistles but did not affect weevils. Excluding D. tener from thistles increased seed set. Analyses supported a negative indirect pathway between the aggressive D. tener and thistle seed set through aphid populations, while the other ant species showed no indirect effects on thistle reproduction. Therefore, aggressive aphid-tending ants may enhance biotic resistance by increasing aphid infestation on exotic invasive plants. This study highlights the importance of indirect biotic resistance in modulating the success of invasive species.

RevDate: 2021-07-22
CmpDate: 2021-07-22

Eleftherianos I, C Heryanto (2021)

Transcriptomic Insights into the Insect Immune Response to Nematode Infection.

Genes, 12(2):.

Insects in nature interact with a wide variety of microbial enemies including nematodes. These include entomopathogenic nematodes that contain mutualistic bacteria and together are able to infect a broad range of insects in order to complete their life cycle and multiply, filarial nematodes which are vectored by mosquitoes, and other parasitic nematodes. Entomopathogenic nematodes are commonly used in biological control practices and they form excellent research tools for understanding the genetic and functional bases of nematode pathogenicity and insect anti-nematode immunity. In addition, clarifying the mechanism of transmission of filarial nematodes by mosquitoes is critical for devising strategies to reduce disease transmission in humans. In all cases and in order to achieve these goals, it is vital to determine the number and type of insect host genes which are differentially regulated during infection and encode factors with anti-nematode properties. In this respect, the use of transcriptomic approaches has proven a key step for the identification of insect molecules with anti-nematode activity. Here, we review the progress in the field of transcriptomics that deals with the insect response to nematode infection. This information is important because it will expose conserved pathways of anti-nematode immunity in humans.

RevDate: 2021-07-22
CmpDate: 2021-07-22

Vishnyakov AE, Karagodina NP, Lim-Fong G, et al (2021)

First evidence of virus-like particles in the bacterial symbionts of Bryozoa.

Scientific reports, 11(1):4.

Bacteriophage communities associated with humans and vertebrate animals have been extensively studied, but the data on phages living in invertebrates remain scarce. In fact, they have never been reported for most animal phyla. Our ultrastructural study showed for the first time a variety of virus-like particles (VLPs) and supposed virus-related structures inside symbiotic bacteria in two marine species from the phylum Bryozoa, the cheilostomes Bugula neritina and Paralicornia sinuosa. We also documented the effect of VLPs on bacterial hosts: we explain different bacterial 'ultrastructural types' detected in bryozoan tissues as stages in the gradual destruction of prokaryotic cells caused by viral multiplication during the lytic cycle. We speculate that viruses destroying bacteria regulate symbiont numbers in the bryozoan hosts, a phenomenon known in some insects. We develop two hypotheses explaining exo- and endogenous circulation of the viruses during the life-cycle of B. neritina. Finally, we compare unusual 'sea-urchin'-like structures found in the collapsed bacteria in P. sinuosa with so-called metamorphosis associated contractile structures (MACs) formed in the cells of the marine bacterium Pseudoalteromonas luteoviolacea which are known to trigger larval metamorphosis in a polychaete worm.

RevDate: 2021-07-22
CmpDate: 2021-07-22

Tariq S, AH Clifford (2021)

An update on the microbiome in vasculitis.

Current opinion in rheumatology, 33(1):15-23.

PURPOSE OF REVIEW: To summarize recent evidence regarding the presence and potential role of the microbiome in systemic vasculitides.

RECENT FINDINGS: Microbiomic descriptions are now available in patients with small, medium and large vessel vasculitis. The majority of studies have evaluated gastrointestinal inhabitants, with a smaller number of studies describing the nasal, pulmonary or vascular microbiomes. Most published studies are observational and cross-sectional. Dysbiosis is seen frequently in vasculitis patients with reduced microbial diversity observed in nasal, fecal and vascular samples compared with disease and/or healthy controls. Predominant bacteria vary, but overall, patients with vasculitis tend to have more pathogenic and less commensal bacteria in active disease. In the few longitudinal studies available, improvement or resolution of dysbiosis has been observed following vasculitis treatment and improved disease activity.

SUMMARY: Dysbiosis and reduced microbial diversity has been identified in patients with small, medium and large vessel vasculitis. Although limited data suggests microbiomes may 'normalize' following immunosuppression, cause or effect cannot be determined. It is hypothesized that microbial disruption in a genetically susceptible individual may trigger excessive host immune activation and vasculitis; however, larger studies with longitudinal and translational design are needed to further our current understanding.

RevDate: 2021-07-22
CmpDate: 2021-07-22

Laventie BJ, U Jenal (2020)

Surface Sensing and Adaptation in Bacteria.

Annual review of microbiology, 74:735-760.

Bacteria thrive both in liquids and attached to surfaces. The concentration of bacteria on surfaces is generally much higher than in the surrounding environment, offering bacteria ample opportunity for mutualistic, symbiotic, and pathogenic interactions. To efficiently populate surfaces, they have evolved mechanisms to sense mechanical or chemical cues upon contact with solid substrata. This is of particular importance for pathogens that interact with host tissue surfaces. In this review we discuss how bacteria are able to sense surfaces and how they use this information to adapt their physiology and behavior to this new environment. We first survey mechanosensing and chemosensing mechanisms and outline how specific macromolecular structures can inform bacteria about surfaces. We then discuss how mechanical cues are converted to biochemical signals to activate specific cellular processes in a defined chronological order and describe the role of two key second messengers, c-di-GMP and cAMP, in this process.

RevDate: 2021-07-21

Davila-Lara A, Reichelt M, Wang D, et al (2021)

Proof of anthocyanins in the carnivorous plant genus Nepenthes.

FEBS open bio [Epub ahead of print].

Yellow to red colored betalains are a chemotaxonomic feature of Caryophyllales, while in most other plant taxa, anthocyanins are responsible for these colors. The carnivorous plant family Nepenthaceae belongs to Caryophyllales; here, red-pigmented tissues seem to attract insect prey. Strikingly, the chemical nature of red color in Nepenthes has never been elucidated. Although belonging to Caryophyllales, in Nepenthes, some molecular evidence supports the presence of anthocyanins rather than betalains. However, there was previously no direct chemical proof of this. Using UHPLC-ESI-HRMS, we identified cyanidin glycosides in Nepenthes species and tissues. Further, we reveal the existence of a complete set of constitutively expressed anthocyanin biosynthetic genes in Nepenthes. Thus, here we finally conclude the long-term open question regarding red pigmentation in Nepenthaceae.

RevDate: 2021-07-21

Wagner MR (2021)

Prioritizing host phenotype to understand microbiome heritability in plants.

The New phytologist [Epub ahead of print].

Breeders and evolutionary geneticists have grappled with the complexity of the "genotype-to-phenotype map" for decades. Now, recent studies highlight the relevance of this concept for understanding heritability of plant microbiomes. Because host phenotype is a more proximate cause of microbiome variation than host genotype, microbiome heritability varies across plant anatomy and development. Fine-scale variation of plant traits within organs suggests that the well-established concept of "microbiome compartment" should be refined. Additionally, recent work shows that the balance of deterministic processes (including host genetic effects) vs. stochastic processes also varies over time and space. Together, these findings suggest that re-centering plant phenotype-both as a predictor and a readout of microbiome function-will accelerate new insights into microbiome heritability.

RevDate: 2021-07-21

Speare L, Woo M, Bultman KM, et al (2021)

Host-Like Conditions Are Required for T6SS-Mediated Competition among Vibrio fischeri Light Organ Symbionts.

mSphere [Epub ahead of print].

Bacteria employ diverse competitive strategies to enhance fitness and promote their own propagation. However, little is known about how symbiotic bacteria modulate competitive mechanisms as they compete for a host niche. The bacterium Vibrio fischeri forms a symbiotic relationship with marine animals and encodes a type VI secretion system (T6SS), which is a contact-dependent killing mechanism used to eliminate competitors during colonization of the Euprymna scolopes squid light organ. Like other horizontally acquired symbionts, V. fischeri experiences changes in its physical and chemical environment during symbiosis establishment. Therefore, we probed both environmental and host-like conditions to identify ecologically relevant cues that control T6SS-dependent competition during habitat transition. Although the T6SS did not confer a competitive advantage for V. fischeri strain ES401 under planktonic conditions, a combination of both host-like pH and viscosity was necessary for T6SS competition. For ES401, high viscosity activates T6SS expression and neutral/acidic pH promotes cell-cell contact for killing, and this pH-dependent phenotype was conserved in the majority of T6SS-encoding strains examined. We also identified a subset of V. fischeri isolates that engaged in T6SS-mediated competition at high viscosity under both planktonic and host-like pH conditions. T6SS phylogeny revealed that strains with pH-dependent phenotypes cluster together to form a subclade within the pH-independent strains, suggesting that V. fischeri may have recently evolved to limit competition to the host niche. IMPORTANCE Bacteria have evolved diverse strategies to compete for limited space and resources. Because these mechanisms can be costly to use, their expression and function are often restricted to specific environments where the benefits outweigh the costs. However, little is known about the specific cues that modulate competitive mechanisms as bacterial symbionts transition between free-living and host habitats. Here, we used the bioluminescent squid and fish symbiont Vibrio fischeri to probe for host and environmental conditions that control interbacterial competition via the type VI secretion system. Our findings identify a new host-specific cue that promotes competition among many but not all V. fischeri isolates, underscoring the utility of studying multiple strains to reveal how competitive mechanisms may be differentially regulated among closely related populations as they evolve to fill distinct niches.

RevDate: 2021-07-21

Di Lorenzo F, Duda KA, Lanzetta R, et al (2021)

A Journey from Structure to Function of Bacterial Lipopolysaccharides.

Chemical reviews [Epub ahead of print].

Lipopolysaccharide (LPS) is a crucial constituent of the outer membrane of most Gram-negative bacteria, playing a fundamental role in the protection of bacteria from environmental stress factors, in drug resistance, in pathogenesis, and in symbiosis. During the last decades, LPS has been thoroughly dissected, and massive information on this fascinating biomolecule is now available. In this Review, we will give the reader a third millennium update of the current knowledge of LPS with key information on the inherent peculiar carbohydrate chemistry due to often puzzling sugar residues that are uniquely found on it. Then, we will drive the reader through the complex and multifarious immunological outcomes that any given LPS can raise, which is strictly dependent on its chemical structure. Further, we will argue about issues that still remain unresolved and that would represent the immediate future of LPS research. It is critical to address these points to complete our notions on LPS chemistry, functions, and roles, in turn leading to innovative ways to manipulate the processes involving such a still controversial and intriguing biomolecule.

RevDate: 2021-07-21

Dessì A, Bosco A, Pintus R, et al (2021)

Fusobacterium nucleatum and alteration of the oral microbiome: from pregnancy to SARS-COV-2 infection.

European review for medical and pharmacological sciences, 25(13):4579-4596.

OBJECTIVE: The human being has evolved in close symbiosis with its own ecological community of commensal, symbiotic and pathogenic bacteria. After the intestinal microbiome, that of the oral cavity is the largest and most diversified. Its importance is reflected not only in local and systemic diseases, but also in pregnancy since it would seem to influence the placental microbiome.

MATERIALS AND METHODS: This is a literature review of articles published in PubMed about Fusobacterium Nucleatum and both its implications with systemic and oral health, adverse pregnancy outcomes, flavors perception and its interference in the oral-nasal mucosal immunity.

RESULTS: It is in maintaining the microbiome's homeostasis that the Fusobacterium nucleatum, an opportunistic periodontal pathogen of the oral cavity, plays a crucial role both as a bridge microorganism of the tongue biofilm, and in maintaining the balance between the different species in the oral-nasal mucosal immunity also by taste receptors interaction. It is also involved in the flavor perception and its detection in the oral microbiome of children from the first days of life suggests a possible physiological role. However, the dysbiosis can determine its pathogenicity with local and systemic consequences, including the pathogenesis of respiratory infections.

CONCLUSIONS: It is interesting to evaluate its possible correlation with Sars-CoV-2 and the consequences on the microflora of the oral cavity, both to promote a possible broad-spectrum preventive action, in favor of all subjects for whom, by promoting the eubiosis of the oral microbiome, a defensive action could be envisaged by the commensals themselves but, above all, for patients with specific comorbidities and therefore already prone to oral dysbiosis.

RevDate: 2021-07-21

Reuter C, TA Oelschlaeger (2018)

Enhancement of Mucus Production in Eukaryotic Cells and Quantification of Adherent Mucus by ELISA.

Bio-protocol, 8(12):e2879 pii:2879.

The mucosal surfaces of the gastrointestinal, respiratory, reproductive, and urinary tracts, and the surface of the eye harbor a resident microflora that lives in symbiosis with their host and forms a complex ecosystem. The protection of the vulnerable epithelium is primarily achieved by mucins that form a gel-like structure adherent to the apical cell surface. This mucus layer constitutes a physical and chemical barrier between the microbial flora and the underlying epithelium. Mucus is critical to the maintenance of a homeostatic relationship between the microbiota and its host. Subtle deviations from this dynamic interaction may result in major implications for health. The protocol in this article describes the procedures to grow low mucus-producing HT29 and high mucus-producing HT29-MTX-E12 cells, maintain cells and use them for mucus quantification by ELISA. Additionally, it is described how to assess the amount of secreted adherent mucus. This system can be used to study the protective effect of mucus, e.g., against bacterial toxins, to test the effect of different culture conditions on mucus production or to analyze diffusion of molecules through the mucus layer. Since the ELISA used in this protocol is available for different species and mucus proteins, also other cell types can be used.

RevDate: 2021-07-21

Tortorelli G, Rautengarten C, Bacic A, et al (2021)

Cell surface carbohydrates of symbiotic dinoflagellates and their role in the establishment of cnidarian-dinoflagellate symbiosis.

The ISME journal [Epub ahead of print].

Symbiodiniaceae algae are often photosymbionts of reef-building corals. The establishment of their symbiosis resembles a microbial infection where eukaryotic pattern recognition receptors (e.g. lectins) are thought to recognize a specific range of taxon-specific microbial-associated molecular patterns (e.g. glycans). The present study used the sea anemone, Exaiptasia diaphana and three species of Symbiodiniaceae (the homologous Breviolum minutum, the heterologous-compatible Cladocopium goreaui and the heterologous-incompatible Fugacium kawagutii) to compare the surface glycomes of three symbionts and explore the role of glycan-lectin interactions in host-symbiont recognition and establishment of symbiosis. We identified the nucleotide sugars of the algal cells, then examined glycans on the cell wall of the three symbiont species with monosaccharide analysis, lectin array technology and fluorescence microscopy of the algal cell decorated with fluorescently tagged lectins. Armed with this inventory of possible glycan moieties, we then assayed the ability of the three Symbiodiniaceae to colonize aposymbiotic E. diaphana after modifying the surface of one of the two partners. The Symbiodiniaceae cell-surface glycome varies among algal species. Trypsin treatment of the alga changed the rate of B. minutum and C. goreaui uptake, suggesting that a protein-based moiety is an essential part of compatible symbiont recognition. Our data strongly support the importance of D-galactose (in particular β-D-galactose) residues in the establishment of the cnidarian-dinoflagellate symbiosis, and we propose a potential involvement of L-fucose, D-xylose and D-galacturonic acid in the early steps of this mutualism.

RevDate: 2021-07-21
CmpDate: 2021-07-21

Jönsson H, Michaud M, N Neuman (2021)

What Is Commensality? A Critical Discussion of an Expanding Research Field.

International journal of environmental research and public health, 18(12): pii:ijerph18126235.

Commensality (the act of eating together) is studied in a range of disciplines and often considered important for social communion, order, health and well-being, while simultaneously being understood as in decline (especially the family meal). However, such claims are also contested in various ways. In this paper, we discuss the expanding field of commensality research and critically reflect on the debates surrounding its social functions, including its role in public health. We illuminate the deep social and cultural significance of commensality, through time and space, and conclude that whether or not commensality is the preferred social form of eating for any given individual, it is difficult to escape its sociocultural desirability and idealization. As a cross-cultural phenomenon in both past, present, and future, we suggest that commensality deserves further research. This includes commensality as a research topic in itself and as an entry point to unveil different dimensions of social relations between people, as well as interactions between humans and material objects.

RevDate: 2021-07-21
CmpDate: 2021-07-21

Copeland C (2021)

Same but different: examining the molecular mechanisms of intercellular rhizobial infection.

Plant physiology, 185(3):754-756.

RevDate: 2021-07-21
CmpDate: 2021-07-21

Zhan M, Tian M, Wang W, et al (2020)

Draft genomic sequence of Armillaria gallica 012m: insights into its symbiotic relationship with Gastrodia elata.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology], 51(4):1539-1552.

Armillaria species (Basidiomycota, Physalacriaceae) are well known as plant pathogens related to serious root rot disease on various trees in forests and plantations. Interestingly, some Armillaria species are essential symbionts of the rare Chinese medicinal herb Gastrodia elata, a rootless and leafless orchid used for over 2000 years. In this work, an 87.3-M draft genome of Armillaria gallica 012m strain, which was symbiotic with G. elata, was assembled. The genome includes approximately 23.6% repetitive sequences and encodes 26,261 predicted genes. In comparison with other four genomes of Armillaria, the following gene families related to pathogenicity/saprophytic phase, including cytochrome P450 monooxygenases, carbohydrate-active enzyme AA3, and hydrophobins, were significantly contracted in A. gallica 012m. These characteristics may be beneficial for G. elata to get less injuries. The genome-guided analysis of differential expression between rhizomorph (RH) and vegetative mycelium (VM) showed that a total of 2549 genes were differentially expressed, including 632 downregulated genes and 1917 upregulated genes. In the RH, most differentially expressed genes (DEGs) related to pathogenicity were significantly upregulated. To further elucidate gene function, Gene Ontology enrichment analysis showed that the upregulated DEGs significantly grouped into monooxygenase activity, hydrolase activity, glucosidase activity, extracellular region, fungal cell wall, response to xenobiotic stimulus, response to toxic substance, etc. These phenomena indicate that RH had better infection ability than VM. The infection ability of RH may be beneficial for G. elata to obtain nutrition, because the rhizomorph constantly infected the nutritional stems of G. elata and formed the hyphae that can be digested by G. elata. These results clarified the characteristics of A. gallica 012m and the reason why the strain 012m can establish a symbiotic relationship with G. elata in some extent from the perspective of genomics.

RevDate: 2021-07-20

Xie X, Li X, Fan H, et al (2021)

Spatial analysis of production-living-ecological functions and zoning method under symbiosis theory of Henan, China.

Environmental science and pollution research international [Epub ahead of print].

Land space is the carrier of human production, living activities, and ecological civilization construction. How to promote the orderly, moderate, and sustainable development and utilization of land space is a scientific problem to be solved. As a key element in China's spatial planning, the quantitative analysis of spatial pattern and functional zoning has become a focus of China's current development. Based on the analysis of land space symbiosis development, this study takes Henan province as the case study; appropriate indicators were selected from the perspective of "production-living-ecological" functions (PLEFs) index that was developed including three subsystems of the production function, living function, and ecological function. The entropy weight method and geographic information system (GIS) spatial method were used to analyze the PLEF status and spatial pattern in Henan province. The PLEF score showed a certain geographical pattern, where in the southwestern areas of Henan province have higher PLEFs than that in the northeastern areas. The PLEFs have an obvious positive correlation in the spatial distribution by spatial correlation analysis. In addition, this study designs a three-dimensional magic cube evaluation model to analyze the symbiotic function type of land space. The results indicated that the PLEFs of Henan province were classified into 13 symbiotic function types of areas, which can better reflect the spatial differentiation characteristics. Moreover, we proposed paths to promote the development and management of each type function area.

RevDate: 2021-07-20
CmpDate: 2021-07-20

Alves MF, Pinheiro F, Nunes CEP, et al (2021)

Reproductive development and genetic structure of the mycoheterotrophic orchid Pogoniopsis schenckii Cogn.

BMC plant biology, 21(1):332.

BACKGROUND: Pogoniopsis schenckii Cogn. is a mycoheterotrophic orchid that can be used as a model to understand the influence of mycoheterotrophy at different stages of the reproductive cycle. We aimed to verify the presence of endophytic and epiphytic fungi at each stage of the reproductive process and investigated how the breeding system may relate to genetic structure and diversity of populations. In this study we performed anatomical and ultrastructural analyses of the reproductive organs, field tests to confirm the breeding system, and molecular analysis to assess genetic diversity and structure of populations.

RESULTS: During the development of the pollen grain, embryo sac and embryogenesis, no fungal infestation was observed. The presence of endophytic fungal hyphae was observed just within floral stems and indehiscent fruit. Beyond assuring the presence of fungus that promote seed germination, specific fungi hyphae in the fruit may affect other process, such as fruit ripening. As other mycoheterotrophic orchids, P. schenckii is autogamous, which may explain the low genetic diversity and high genetic structure in populations.

CONCLUSIONS: We discuss an interesting interaction: fungal hyphae in the indehiscent fruit. These fungal hyphae seem to play different roles inside fruit tissues, such as acting in the fruit maturation process and increasing the proximity between fungi and plant seeds even before dispersion occurs. As other mycoheterotrophic orchids, P. schenckii is autogamous, which may explain the low genetic diversity and high genetic structure in populations. Altogether, our findings provide important novel information about the mechanisms shaping ecology and evolution of fragmented populations of mycoheterotrophic plant.

RevDate: 2021-07-20
CmpDate: 2021-07-20

Cimen H, Touray M, Gulsen SH, et al (2021)

Antifungal activity of different Xenorhabdus and Photorhabdus species against various fungal phytopathogens and identification of the antifungal compounds from X. szentirmaii.

Applied microbiology and biotechnology, 105(13):5517-5528.

Xenorhabdus and Photorhabdus spp. are enteric bacterial symbionts of Steinernema and Heterorhabditis nematodes, respectively. These bacteria produce an extensive set of natural products (NPs) with antibacterial, antifungal, antiprotozoal, insecticidal, or other bioactivities when vectored into insect hemocoel by nematodes. We assessed the in vitro activity of different Xenorhabdus and Photorhabdus cell-free supernatants against important fungal phytopathogens, viz., Cryphonectria parasitica, Fusarium oxysporum, Rhizoctonia solani, and Sclerotinia sclerotiorum and identified the bioactive antifungal compound/s present in the most effective bacterial supernatant using the easyPACId (easy promoter-activated compound identification) approach against chestnut blight C. parasitica. Our data showed that supernatants from Xenorhabdus species were comparatively more effective than extracts from Photorhabdus in suppressing the fungal pathogens; among the bacteria assessed, Xenorhabdus szentirmaii was the most effective species against all tested phytopathogens especially against C. parasitica. Subsequent analysis revealed fabclavines as antifungal bioactive compounds in X. szentirmaii, generated by a polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) hybrid system. Fabclavines are broad-spectrum, heat-stable NPs that have great potential as biological control compounds against fungal plant pathogens. More studies are needed to assess the potential phytotoxicity of these compounds and their effects on non-target organisms before commercialization. KEY POINTS: • Chemical fungicides have toxic effects on humans and other non-target organisms. • Alternatives with novel modes of action to supplant current fungicide are needed. • A novel bioactive antifungal compound from Xenorhabdus szentirmaii was identified.

RevDate: 2021-07-20
CmpDate: 2021-07-20

Sundarraman D, Hay EA, Martins DM, et al (2020)

Higher-Order Interactions Dampen Pairwise Competition in the Zebrafish Gut Microbiome.

mBio, 11(5):.

The microbial communities resident in animal intestines are composed of multiple species that together play important roles in host development, health, and disease. Due to the complexity of these communities and the difficulty of characterizing them in situ, the determinants of microbial composition remain largely unknown. Further, it is unclear for many multispecies consortia whether their species-level makeup can be predicted based on an understanding of pairwise species interactions or whether higher-order interactions are needed to explain emergent compositions. To address this, we examine commensal intestinal microbes in larval zebrafish, initially raised germfree, to allow the introduction of controlled combinations of bacterial species. Using a dissection and plating assay, we demonstrate the construction of communities of one to five bacterial species and show that the outcomes from the two-species competitions fail to predict species abundances in more complex communities. With multiple species present, interbacterial interactions become weaker, suggesting that higher-order interactions in the vertebrate gut stabilize complex communities.IMPORTANCE Understanding the rules governing the composition of the diverse microbial communities that reside in the vertebrate gut environment will enhance our ability to manipulate such communities for therapeutic ends. Synthetic microbial communities, assembled from specific combinations of microbial species in germfree animals, allow investigation of the fundamental question of whether multispecies community composition can be predicted solely based on the combined effects of interactions between pairs of species. If so, such predictability would enable the construction of communities with desired species from the bottom up. If not, the apparent higher-order interactions imply that emergent community-level characteristics are crucial. Our findings using up to five coexisting native bacterial species in larval zebrafish, a model vertebrate, provide experimental evidence for higher-order interactions and, moreover, show that these interactions promote the coexistence of microbial species in the gut.

RevDate: 2021-07-20
CmpDate: 2021-07-20

Cerezini P, Kuwano BH, Grunvald AK, et al (2020)

Soybean tolerance to drought depends on the associated Bradyrhizobium strain.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology], 51(4):1977-1986.

We evaluated the effect of three different Bradyrhizobium strains inoculated in two soybean genotypes (R01-581F, drought-tolerant, and NA5858RR, drought-sensitive) submitted to drought in two trials conducted simultaneously under greenhouse. The strains (SEMIA 587, SEMIA 5019 (both B. elkanii), and SEMIA 5080 (B. diazoefficiens)) were inoculated individually in each genotype and then submitted to water restriction (or kept well-watered, control) between 45 and 62 days after emergence. No deep changes in plant physiological variables were observed under the moderate water restriction imposed during the first 10 days. Nevertheless, photosynthesis and transpiration decreased after the severe water restriction imposed for further 7 days. Water restriction reduced growth (- 30%) and the number of nodules (- 47% and - 58% for R01-581F and NA5858RR, respectively) of both genotypes, with a negative effect on N-metabolism. The genotype R01-581F inoculated with SEMIA 5019 strain had higher photosynthetic rates compared with NA5858RR, regardless of the Bradyrhizobium strain. On average, R01-581F showed better performance under drought than NA5858RR, with higher number of nodules (51 vs. 38 nodules per plant, respectively) and less accumulation of ureides in petioles (15 μmol g-1 vs. 34 μmol g-1, respectively). Moreover, plants inoculated with SEMIA 5080 had higher glutamine synthetase activity under severe water restriction, especially in the drought-tolerant R01-518F, suggesting maintenance of N metabolism under drought. The Bradyrhizobium strain affects the host plant responses to drought in which the strain SEMIA 5080 improves the drought tolerance of R01-518F genotype.

RevDate: 2021-07-19

Sharma R, Shahbaz M, Kautish P, et al (2021)

Does energy consumption reinforce environmental pollution? Evidence from emerging Asian economies.

Journal of environmental management, 297:113272 pii:S0301-4797(21)01334-7 [Epub ahead of print].

Steadily improving per capita income level, energy consumption, and delivery of financial services in South and Southeast Asian countries has remained a subject of discussion among policymakers. Because these endeavors have not only elevated their growth trajectory but also widened the scope for carbon emissions, especially in the preceding two decades. In order to confirm this argument, therefore, in the present study, we intended to examine their dynamic impacts on carbon emissions. In this pursuit, by using the second-generation unit-root test, cointegration test, and panel regression procedures, we investigated the moderating impact of energy solutions on the association between per capita income and CO2 emissions and financial development and CO2 emissions from 1976 to 2015. The computed results revealed that the energy's interaction with the linear per capita income significantly escalated carbon emissions in the long run. However, the impact of energy's interaction with the squared per capita income on carbon emissions is found insignificant but positive in the long run. On the other hand, the interaction of energy with financial development provided a negative but insignificant coefficient. Based on the outcomes, we can ascertain that, at the lower level of income, energy consumption leads to environmental pollution, whereas at the higher level of income, its harmful effect on carbon emissions becomes weak in the given regions. By taking a cue from the computed results, we proposed a policy framework that might help these regions to navigate the energy-led environmental challenges in the coming years.

RevDate: 2021-07-19

Sen A, Sharma S, Dutta S, et al (2021)

Functionalized Ionic Porous Organic Polymers Exhibiting High Iodine Uptake from Both the Vapor and Aqueous Medium.

ACS applied materials & interfaces [Epub ahead of print].

Large-scale generation of radioactive iodine (129I, 131I) in nuclear power plants pose a critical threat in the event of fallout, thus rendering the development of iodine sequestering materials (from both the vapor and aqueous medium) highly pivotal. Herein, we report two chemically stable ionic polymers containing multiple binding sites, including phenyl rings, imidazolium cations, and bromide anions, which in synergy promote adsorption of iodine/triiodide anions. In brief, exceptional iodine uptake (from the vapor phase) was observed at nuclear fuel reprocessing conditions. Furthermore, the ionic nature propelled removal of >99% of I3- from water within 30 min. Additionally, benchmark uptake capacities, as well as unprecedented selectivity, were observed for I3-anions. The excellent affinity (distribution coefficient, ∼105 mL/g) enabled iodine capture from seawater-spiked samples. Moreover, iodine-loaded compounds showed conductivity (10-4 S/cm, 10-6 S/cm), placing them among the best known conducting porous organic polymers. Lastly, DFT studies unveiled key insights in coherence with the experimental findings.

RevDate: 2021-07-19

Hao R, Huang W, B Jiu (2021)

Characteristics and the Model of Thermal Evolution and Gas Generation of Late Paleozoic Coal in the Qinshui Basin, Based on Hydrous Pyrolysis.

ACS omega, 6(27):17660-17673.

The Qinshui basin is an important coal-accumulating basin in China, and its Late Paleozoic coal is an important source rock of coalbed methane in the basin. Its thermal evolution and gas generation characteristics determined the grade of coalbed methane resources, especially the coal measure free gas resources in the basin. Late Paleozoic coal samples were collected for organic geochemical analysis, a high-volatile bituminous coal was used for hydrous pyrolysis, to propose the thermal evolution characteristics, gas generation characteristics, thermal evolution, and free gas accumulation model, and the Ordos Basin is compared. The results show that the variation trends of various geochemical parameters are different with the increase in R o. Hydrous pyrolysis shows that the gas production potential of coal is excellent. The gases produced consist mainly of CH4, C2-, CO2, and H2. C2- is produced only before the simulated temperature of 550 °C, and oil is produced only before the temperature of 500 °C. The thermal evolution stages can be divided into the immature stage, symbiosis stage, wet gas stage, and dry gas stage, and the symbiosis stage can be divided into the preliminary stage and mainly gas stage. R o, T max, (2+3)MP/(1+9)MP, saturated+arene, V daf, and H/C can be used as indicators of the thermal evolution stages. On the plane, the distribution of thermal evolution stages of the Shanxi Formation and the Taiyuan Formation is very alike. The gas generating strength of the Taiyuan Formation is higher than that of the Shanxi Formation. The gas generating strength in the north of the Taiyuan Formation is higher, while that in the south of the Shanxi Formation is higher. The second gas generation stage has a good spatio-temporal configuration relationship with accumulation factors, and the gas production is large, which is beneficial to the enrichment of the coal measure free gas resources. Relatively, the Ordos Basin has better prospects for exploration and development.

RevDate: 2021-07-19

Dang BT, Truong OT, Tran SQ, et al (2021)

Comparative population genetics of swimming crab host (Portunus pelagicus) and common symbiotic barnacle (Octolasmis angulata) in Vietnam.

PeerJ, 9:e11671 pii:11671.

Background: By comparing spatial geographical structures of host populations with that of their symbionts light can be shed on their biological interactions, and the degree of congruence between host and symbiont phylogeographies should reflect their life histories and especially dispersal mechanisms.

Methods: Here, we analyzed the genetic diversity and structure of a host, the blue swimming crab, Portunus pelagicus, and its symbiotic pedunculate barnacle Octolasmis angulata from six location sites representing three geographic regions (north, central and south) along the Vietnam coastline. High levels of congruence in their phylogeographic patterns were expected as they both undergo planktonic larval stages.

Results: Based on the COI mtDNA markers, O. angulata populations showed higher genetic diversity in comparison with their host P. pelagicus (number of haplotype/individuals, haplotype and nucleotide diversity are 119/192, 0.991 ± 0.002 and 0.02; and 89/160, 0.913 ± 0.02 and 0.015, respectively). Pairwise Fst and AMOVA analyses showed a more pronounced population structure in the symbiotic barnacle than in its crab host. The DAPC analyses identified three genetic clusters. However, both haplotype networks and scatter plots supported connectivity of the host and the symbiotic barnacle throughout their distribution range, except for low subdivision of southern population. Isolation by distance were detected only for the symbiont O. angulata (R2 = 0.332, P = 0.05), while dbMEM supported spatial structure of both partners, but only at MEM-1 (Obs. 0.2686, P < 0.01 and Obs. 0.2096, P < 0.01, respectively).

RevDate: 2021-07-19

Zhao DK, Selosse MA, Wu L, et al (2021)

Orchid Reintroduction Based on Seed Germination-Promoting Mycorrhizal Fungi Derived From Protocorms or Seedlings.

Frontiers in plant science, 12:701152.

Orchids are among the most endangered in the plant kingdom. Lack of endosperm in their seeds renders orchids to depend on nutrients provided by orchid mycorrhizal fungi (OMF) for seed germination and seedling formation in the wild. OMF that parasitize in germination seeds is an essential element for orchid seedling formation, which can also help orchid reintroduction. Considering the limitations of the previous orchid reintroduction technology based on seed germination-promoting OMF (sgOMF) sourced from orchid roots, an innovative approach is proposed here in which orchid seeds are directly co-sown with sgOMF carrying ecological specificity from protocorms/seedlings. Based on this principle, an integrative and practical procedure concerning related ecological factors is further raised for re-constructing long-term and self-sustained orchid populations. We believe that this new approach will benefit the reintroduction of endangered orchids in nature.

RevDate: 2021-07-19

Yu YC, Dickstein R, A Longo (2021)

Structural Modeling and in planta Complementation Studies Link Mutated Residues of the Medicago truncatula Nitrate Transporter NPF1.7 to Functionality in Root Nodules.

Frontiers in plant science, 12:685334.

Symbiotic nitrogen fixation is a complex and regulated process that takes place in root nodules of legumes and allows legumes to grow in soils that lack nitrogen. Nitrogen is mostly acquired from the soil as nitrate and its level in the soil affects nodulation and nitrogen fixation. The mechanism(s) by which legumes modulate nitrate uptake to regulate nodule symbiosis remain unclear. In Medicago truncatula, the MtNPF1.7 transporter has been shown to control nodulation, symbiosis, and root architecture. MtNPF1.7 belongs to the nitrate/peptide transporter family and is a symporter with nitrate transport driven by proton(s). In this study we combined in silico structural predictions with in planta complementation of the severely defective mtnip-1 mutant plants to understand the role of a series of distinct amino acids in the transporter's function. Our results support hypotheses about the functional importance of the ExxE(R/K) motif including an essential role for the first glutamic acid of the motif in proton(s) and possibly substrate transport. Results reveal that Motif A, a motif conserved among major facilitator transport (MFS) proteins, is essential for function. We hypothesize that it participates in intradomain packing of transmembrane helices and stabilizing one conformation during transport. Our results also question the existence of a putative TMH4-TMH10 salt bridge. These results are discussed in the context of potential nutrient transport functions for MtNPF1.7. Our findings add to the knowledge of the mechanism of alternative conformational changes as well as symport transport in NPFs and enhance our knowledge of the mechanisms for nitrate signaling.

RevDate: 2021-07-19

Singh J, PK Verma (2021)

NSP1 allies with GSK3 to inhibit nodule symbiosis.

Trends in plant science pii:S1360-1385(21)00174-6 [Epub ahead of print].

Salt stress reduces N2 fixation by causing a reduction in nodule number, nodule weight, and nitrogenase activity in legumes. Emerging evidence from He et al. now suggests that glycogen synthase kinase 3 (GSK3) phosphorylates nodulation signaling pathway 1 (NSP1) in response to salt stress, reducing its DNA-binding activity, and thereby causing a reduction in nodulation.

RevDate: 2021-07-18

Gottshall EY, Bryson SJ, Cogert KI, et al (2021)

Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria.

Water research, 202:117426 pii:S0043-1354(21)00624-2 [Epub ahead of print].

The discovery of anaerobic ammonia-oxidizing bacteria (Anammox) and, more recently, aerobic bacteria common in many natural and engineered systems that oxidize ammonia completely to nitrate (Comammox) have significantly altered our understanding of the global nitrogen cycle. A high affinity for ammonia (Km(app),NH3 ≈ 63nM) and oxygen place Comammox Nitrospira inopinata, the first described isolate, in the same trophic category as organisms such as some ammonia-oxidizing archaea. However, N. inopinata has a relatively low affinity for nitrite (Km,NO2 ≈ 449.2μM) suggesting it would be less competitive for nitrite than other nitrite-consuming aerobes and anaerobes. We examined the ecological relevance of the disparate substrate affinities by coupling it with the Anammox bacterium Candidatus Brocadia anammoxidans. Synthetic communities of the two were established in hydrogel granules in which Comammox grew in the aerobic outer layer to provide Anammox with nitrite in the inner anoxic core to form dinitrogen gas. This spatial organization was confirmed with FISH imaging, supporting a mutualistic or commensal relationship. The functional significance of interspecies spatial organization was informed by the hydrogel encapsulation format, broadening our limited understanding of the interplay between these two species. The resulting low nitrate formation and the competitiveness of Comammox over other aerobic ammonia- and nitrite-oxidizers sets this ecological cooperation apart and points to potential biotechnological applications. Since nitrate is an undesirable product of wastewater treatment effluents, the Comammox-Anammox symbiosis may be of economic and ecological importance to reduce nitrogen contamination of receiving waters.

RevDate: 2021-07-18

Filatov AV, Perepelov AV, Shashkov AS, et al (2021)

Structure and genetics of the O-antigen of Enterobacter cloacae K7 containing di-N-acetylpseudaminic acid.

Carbohydrate research, 508:108392 pii:S0008-6215(21)00161-0 [Epub ahead of print].

The O-antigen (O-polysaccharide) is an essential component of lipopolysaccharide on the surface of Gram-negative bacteria and plays an important role in interaction with host organisms. In this study, we investigated the chemical structure and characterized the gene cluster of Enterobacter cloacae K7 O-antigen. As judged by sugar analyses along with NMR spectroscopy data, E. cloacae K7 antigen has a tetrasaccharide O-unit with the following structure: →8)-β-Psep5Ac7Ac-(2 → 2)-β-l-Rhap-(1 → 4)-α-l-Rhap-(1 → 3)-α-d-Galp-(1→ The O-antigen gene cluster of E. cloacae K7 between conserved genes galF and gnd was sequenced. Most genes necessary for the O-antigen synthesis were found in the cluster and their functions were tentatively assigned by comparison with sequences in the available databases.

RevDate: 2021-07-19
CmpDate: 2021-07-19

Li E, de Jonge R, Liu C, et al (2021)

Rapid evolution of bacterial mutualism in the plant rhizosphere.

Nature communications, 12(1):3829.

While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.

RevDate: 2021-07-19
CmpDate: 2021-07-19

Harbort CJ, Hashimoto M, Inoue H, et al (2020)

Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis.

Cell host & microbe, 28(6):825-837.e6.

Plants benefit from associations with a diverse community of root-colonizing microbes. Deciphering the mechanisms underpinning these beneficial services are of interest for improving plant productivity. We report a plant-beneficial interaction between Arabidopsis thaliana and the root microbiota under iron deprivation that is dependent on the secretion of plant-derived coumarins. Disrupting this pathway alters the microbiota and impairs plant growth in iron-limiting soil. Furthermore, the microbiota improves iron-limiting plant performance via a mechanism dependent on plant iron import and secretion of the coumarin fraxetin. This beneficial trait is strain specific yet functionally redundant across phylogenetic lineages of the microbiota. Transcriptomic and elemental analyses revealed that this interaction between commensals and coumarins promotes growth by relieving iron starvation. These results show that coumarins improve plant performance by eliciting microbe-assisted iron nutrition. We propose that the bacterial root microbiota, stimulated by secreted coumarins, is an integral mediator of plant adaptation to iron-limiting soils.

RevDate: 2021-07-19
CmpDate: 2021-07-19

Bobay LM, Wissel EF, K Raymann (2020)

Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome.

mSphere, 5(4):.

Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes.IMPORTANCE The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.

RevDate: 2021-07-17

Brancaccio M, Tangherlini M, Danovaro R, et al (2021)

Metabolic adaptations to marine environments: molecular diversity and evolution of ovothiol biosynthesis in Bacteria.

Genome biology and evolution pii:6323227 [Epub ahead of print].

Ovothiols are sulphur-containing amino acids synthesized by marine invertebrates, protozoans, and bacteria. They act as pleiotropic molecules in signalling and protection against oxidative stress. The discovery of ovothiol biosynthetic enzymes, sulfoxide synthase OvoA and β-lyase OvoB, paves the way for a systematic investigation of ovothiol distribution and molecular diversification in nature. In this work, we conducted genomic and metagenomics data mining to investigate the distribution and diversification of ovothiol biosynthetic enzymes in Bacteria. We identified the bacteria endowed with this secondary metabolic pathway, described their taxonomy, habitat and biotic interactions in order to provide insight into their adaptation to specific environments. We report that OvoA and OvoB are mostly encountered in marine aerobic Proteobacteria, some of them establishing symbiotic or parasitic relationships with other organisms. We identified a horizontal gene transfer event of OvoB from Bacteroidetes living in symbiosis with Hydrozoa. Our search within the Ocean Gene Atlas revealed the occurrence of ovothiol biosynthetic genes in Proteobacteria living in a wide range of pelagic and highly oxygenated environments. Finally, we tracked the evolutionary history of ovothiol biosynthesis from marine bacteria to unicellular eukaryotes and metazoans. Our analysis provides new conceptual elements to unravel the evolutionary and ecological significance of ovothiol biosynthesis.

RevDate: 2021-07-17

Qiao Z, Yates TB, Shrestha HK, et al (2021)

Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor-like kinase.

Plant biotechnology journal [Epub ahead of print].

Soil-borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole-genome resequencing studies identified a gene deletion event of a Populus trichocarpa lectin receptor-like kinase gene PtLecRLK1 in Populus deltoides that was associated with poor root colonization by the ectomycorrhizal fungus Laccaria bicolor. By introducing PtLecRLK1 into a perennial grass known to be a non-host of L. bicolor, switchgrass (Panicum virgatum L.), we found that L. bicolor colonizes ZmUbipro-PtLecRLK1 transgenic switchgrass roots, which illustrates that the introduction of PtLecRLK1 has the potential to convert a non-host to a host of L. bicolor. Furthermore, transcriptomic and proteomic analyses on inoculated transgenic switchgrass roots revealed genes/proteins overrepresented in the compatible interaction and underrepresented in the pathogenic defense pathway, consistent with the view that pathogenic defense response is downregulated during compatible interaction. Metabolomic profiling revealed that root colonization in the transgenic switchgrass was associated with an increase in N-containing metabolites and a decrease in organic acids, sugars, and aromatic hydroxycinnamate conjugates, which are often seen in the early steps of establishing compatible interactions. These studies illustrate that PtLecRLK1 is able to render a plant susceptible to colonization by the ectomycorrhizal fungus L. bicolor and shed light on engineering mycorrhizal symbiosis into a non-host to enhance plant productivity and fitness on marginal lands.

RevDate: 2021-07-17

Arashida H, Odake H, Sugawara M, et al (2021)

Evolution of rhizobial symbiosis islands through insertion sequence-mediated deletion and duplication.

The ISME journal [Epub ahead of print].

Symbiosis between organisms influences their evolution via adaptive changes in genome architectures. Immunity of soybean carrying the Rj2 allele is triggered by NopP (type III secretion system [T3SS]-dependent effector), encoded by symbiosis island A (SymA) in B. diazoefficiens USDA122. This immunity was overcome by many mutants with large SymA deletions that encompassed T3SS (rhc) and N2 fixation (nif) genes and were bounded by insertion sequence (IS) copies in direct orientation, indicating homologous recombination between ISs. Similar deletion events were observed in B. diazoefficiens USDA110 and B. japonicum J5. When we cultured a USDA122 strain with a marker gene sacB inserted into the rhc gene cluster, most sucrose-resistant mutants had deletions in nif/rhc gene clusters, similar to the mutants above. Some deletion mutants were unique to the sacB system and showed lower competitive nodulation capability, indicating that IS-mediated deletions occurred during free-living growth and the host plants selected the mutants. Among 63 natural bradyrhizobial isolates, 2 possessed long duplications (261-357 kb) harboring nif/rhc gene clusters between IS copies in direct orientation via homologous recombination. Therefore, the structures of symbiosis islands are in a state of flux via IS-mediated duplications and deletions during rhizobial saprophytic growth, and host plants select mutualistic variants from the resultant pools of rhizobial populations. Our results demonstrate that homologous recombination between direct IS copies provides a natural mechanism generating deletions and duplications on symbiosis islands.

RevDate: 2021-07-17

Osvatic JT, Wilkins LGE, Leibrecht L, et al (2021)

Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups.

Proceedings of the National Academy of Sciences of the United States of America, 118(29):.

In the ocean, most hosts acquire their symbionts from the environment. Due to the immense spatial scales involved, our understanding of the biogeography of hosts and symbionts in marine systems is patchy, although this knowledge is essential for understanding fundamental aspects of symbiosis such as host-symbiont specificity and evolution. Lucinidae is the most species-rich and widely distributed family of marine bivalves hosting autotrophic bacterial endosymbionts. Previous molecular surveys identified location-specific symbiont types that "promiscuously" form associations with multiple divergent cooccurring host species. This flexibility of host-microbe pairings is thought to underpin their global success, as it allows hosts to form associations with locally adapted symbionts. We used metagenomics to investigate the biodiversity, functional variability, and genetic exchange among the endosymbionts of 12 lucinid host species from across the globe. We report a cosmopolitan symbiont species, Candidatus Thiodiazotropha taylori, associated with multiple lucinid host species. Ca. T. taylori has achieved more success at dispersal and establishing symbioses with lucinids than any other symbiont described thus far. This discovery challenges our understanding of symbiont dispersal and location-specific colonization and suggests both symbiont and host flexibility underpin the ecological and evolutionary success of the lucinid symbiosis.

RevDate: 2021-07-17

Kanso EA, Lopes RM, Strickler JR, et al (2021)

Teamwork in the viscous oceanic microscale.

Proceedings of the National Academy of Sciences of the United States of America, 118(29):.

Nutrient acquisition is crucial for oceanic microbes, and competitive solutions to solve this challenge have evolved among a range of unicellular protists. However, solitary solutions are not the only approach found in natural populations. A diverse array of oceanic protists form temporary or even long-lasting attachments to other protists and marine aggregates. Do these planktonic consortia provide benefits to their members? Here, we use empirical and modeling approaches to evaluate whether the relationship between a large centric diatom, Coscinodiscus wailesii, and a ciliate epibiont, Pseudovorticella coscinodisci, provides nutrient flux benefits to the host diatom. We find that fluid flows generated by ciliary beating can increase nutrient flux to a diatom cell surface four to 10 times that of a still cell without ciliate epibionts. This cosmopolitan species of diatom does not form consortia in all environments but frequently joins such consortia in nutrient-depleted waters. Our results demonstrate that symbiotic consortia provide a cooperative alternative of comparable or greater magnitude to sinking for enhancement of nutrient acquisition in challenging environments.

RevDate: 2021-07-17

Xuan W, Khan F, James CD, et al (2021)

Circadian regulation of cancer cell and tumor microenvironment crosstalk.

Trends in cell biology pii:S0962-8924(21)00124-0 [Epub ahead of print].

Circadian rhythms regulate a remarkable variety of physiologic functions in living organisms. Circadian disruption is associated with tumorigenesis and tumor progression through effects on cancer cell biological properties, including proliferation, DNA repair, apoptosis, metabolism, and stemness. Emerging evidence indicates that circadian clocks also play an influential role in the tumor microenvironment (TME). This review outlines recent discoveries on how cancer cell clock components (including circadian clock and clock genes/proteins) regulate TME biology and, reciprocally, how TME clock components affect tumor growth, metastasis, and therapeutic response. An improved understanding of how clock components regulate the symbiosis between cancer cells and the TME will inform the development of novel clock-oriented therapeutic strategies, including immunotherapy.

RevDate: 2021-07-16

Renoz F, Foray V, Ambroise J, et al (2021)

At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica.

Frontiers in cellular and infection microbiology, 11:660007.

Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial associates of insects that are at the gateway to a host-dependent lifestyle.

RevDate: 2021-07-16

Kee SL, MJT Tan (2021)

Friend, Not Foe: Unveiling Vector-Bacteria Symbiosis and Its Utility as an Arboviral Intervention Strategy in the Philippines.

Frontiers in cellular and infection microbiology, 11:650277.

RevDate: 2021-07-16

Chanson A, Moreau CS, C Duplais (2021)

Assessing Biosynthetic Gene Cluster Diversity of Specialized Metabolites in the Conserved Gut Symbionts of Herbivorous Turtle Ants.

Frontiers in microbiology, 12:678100.

Cephalotes are herbivorous ants (>115 species) feeding on low-nitrogen food sources, and they rely on gut symbionts to supplement their diet by recycling nitrogen food waste into amino acids. These conserved gut symbionts, which encompass five bacterial orders, have been studied previously for their primary nitrogen metabolism; however, little is known about their ability to biosynthesize specialized metabolites which can play a role in bacterial interactions between communities living in close proximity in the gut. To evaluate the biosynthetic potential of their gut symbionts, we mine 14 cultured isolate genomes and gut metagenomes across 17 Cephalotes species to explore the biodiversity of biosynthetic gene clusters (BGCs) producing specialized metabolites. The diversity of BGCs across Cephalotes phylogeny was analyzed using sequence similarity networking and BGC phylogenetic reconstruction. Our results reveal that the conserved gut symbionts involved in the nutritional symbiosis possess 80% of all the 233 BGCs retrieved in this work. Furthermore, the phylogenetic analysis of BGCs reveals different patterns of distribution, suggesting different mechanisms of conservation. A siderophore BGC shows high similarity in a single symbiont across different ant host species, whereas a BGC encoding the production of non-ribosomal peptides (NRPs) found different symbionts within a single host species. Additionally, BGCs were abundant in four of the five bacterial orders of conserved symbionts co-occurring in the hindgut. However, one major symbiont localized alone in the midgut lack BGCs. Because the spatial isolation prevents direct interaction with other symbionts, this result supports the idea that BGCs are maintained in bacteria living in close proximity but are dispensable for an alone-living symbiont. These findings together pave the way for studying the mechanisms of BGC conservation and evolution in gut bacterial genomes associated with Cephalotes. This work also provides a genetic background for further study, aiming to characterize bacterial specialized metabolites and to understand their functional role in multipartite mutualisms between conserved gut symbionts and Cephalotes turtle ants.

RevDate: 2021-07-16
CmpDate: 2021-07-16

Zhao D, Zhang Z, Niu H, et al (2021)

Win by Quantity: a Striking Rickettsia-Bias Symbiont Community Revealed by Seasonal Tracking in the Whitefly Bemisia tabaci.

Microbial ecology, 81(2):523-534.

Maintaining an adaptive seasonality is a basic ecological requisite for cold-blooded organism insects which usually harbor various symbionts. However, how coexisting symbionts coordinate in insects during seasonal progress is still unknown. The whitefly Bemisia tabaci in China harbors the obligate symbiont Portiera that infects each individual, as well as various facultative symbionts. In this study, we investigated whitefly populations in cucumber and cotton fields from May to December 2019, aiming to reveal the fluctuations of symbiont infection frequencies, symbiont coordination in multiple infected individuals, and host plants effects on symbiont infections. The results indicated that the facultative symbionts Hamiltonella (H), Rickettsia (R), and Cardinium (C) exist in field whiteflies, with single (H) and double (HC and HR) infections occurring frequently. Infection frequencies of Hamiltonella (always 100%) and Cardinium (29.50-34.38%) remained steady during seasonal progression. Rickettsia infection frequency in the cucumber whitefly population decreased from 64.47% in summer to 35.29% in winter. Significantly lower Rickettsia infection frequency (15.55%) was identified in cotton whitefly populations and was not subject to seasonal fluctuation. Nevertheless, Rickettsia had a significantly quantitative advantage in the symbiont community of whitefly individuals and populations from both cucumber and cotton field all through the seasons. Moreover, higher Portiera and Hamiltonella densities were found in HC and HR whitefly than in H whitefly, suggesting these symbionts may contribute to producing nutrients for their symbiont partners. These results provide ample cues to further explore the interactions between coexisting symbionts, the coevolutionary relationship between symbionts and host symbiont-induced effects on host plant use.

RevDate: 2021-07-16
CmpDate: 2021-07-16

Varasteh T, Hamerski L, Tschoeke D, et al (2021)

Conserved Pigment Profiles in Phylogenetically Diverse Symbiotic Bacteria Associated with the Corals Montastraea cavernosa and Mussismilia braziliensis.

Microbial ecology, 81(1):267-277.

Pigmented bacterial symbionts play major roles in the health of coral holobionts. However, there is scarce knowledge on the diversity of these microbes for several coral species. To gain further insights into holobiont health, pigmented bacterial isolates of Fabibacter pacificus (Bacteroidetes; n = 4), Paracoccus marcusii (Alphaproteobacteria; n = 1), and Pseudoalteromonas shioyasakiensis (Gammaproteobacteria; n = 1) were obtained from the corals Mussismilia braziliensis and Montastraea cavernosa in Abrolhos Bank, Brazil. Cultures of these bacterial symbionts produced strong antioxidant activity (catalase, peroxidase, and oxidase). To explore these bacterial isolates further, we identified their major pigments by HPLC and mass spectrometry. The six phylogenetically diverse symbionts had similar pigment patterns and produced myxol and keto-carotene. In addition, similar carotenoid gene clusters were confirmed in the whole genome sequences of these symbionts, which reinforce their antioxidant potential. This study highlights the possible roles of bacterial symbionts in Montastraea and Mussismilia holobionts.

RevDate: 2021-07-15

Anonymous (2021)

Andrea Genre.

The New phytologist, 231(4):1316-1317.

RevDate: 2021-07-15

Cobos-Porras L, Rubia MI, Huertas R, et al (2021)

Increased Ascorbate Biosynthesis Does Not Improve Nitrogen Fixation Nor Alleviate the Effect of Drought Stress in Nodulated Medicago truncatula Plants.

Frontiers in plant science, 12:686075.

Legume plants are able to establish nitrogen-fixing symbiotic relations with Rhizobium bacteria. This symbiosis is, however, affected by a number of abiotic constraints, particularly drought. One of the consequences of drought stress is the overproduction of reactive oxygen (ROS) and nitrogen species (RNS), leading to cellular damage and, ultimately, cell death. Ascorbic acid (AsA), also known as vitamin C, is one of the antioxidant compounds that plants synthesize to counteract this oxidative damage. One promising strategy for the improvement of plant growth and symbiotic performance under drought stress is the overproduction of AsA via the overexpression of enzymes in the Smirnoff-Wheeler biosynthesis pathway. In the current work, we generated Medicago truncatula plants with increased AsA biosynthesis by overexpressing MtVTC2, a gene coding for GDP-L-galactose phosphorylase. We characterized the growth and physiological responses of symbiotic plants both under well-watered conditions and during a progressive water deficit. Results show that increased AsA availability did not provide an advantage in terms of plant growth or symbiotic performance either under well-watered conditions or in response to drought.

RevDate: 2021-07-15

Dial CN, Eichinger SJ, Foxall R, et al (2021)

Quorum Sensing and Cyclic di-GMP Exert Control Over Motility of Vibrio fischeri KB2B1.

Frontiers in microbiology, 12:690459.

Bacterial motility is critical for symbiotic colonization by Vibrio fischeri of its host, the squid Euprymna scolopes, facilitating movement from surface biofilms to spaces deep inside the symbiotic organ. While colonization has been studied traditionally using strain ES114, others, including KB2B1, can outcompete ES114 for colonization for a variety of reasons, including superior biofilm formation. We report here that KB2B1 also exhibits an unusual pattern of migration through a soft agar medium: whereas ES114 migrates rapidly and steadily, KB2B1 migrates slowly and then ceases migration. To better understand this phenomenon, we isolated and sequenced five motile KB2B1 suppressor mutants. One harbored a mutation in the gene for the cAMP receptor protein (crp); because this strain also exhibited a growth defect, it was not characterized further. Two other suppressors contained mutations in the quorum sensing pathway that controls bacterial bioluminescence in response to cell density, and two had mutations in the diguanylate cyclase (DGC) gene VF_1200. Subsequent analysis indicated that (1) the quorum sensing mutations shifted KB2B1 to a perceived low cell density state and (2) the high cell density state inhibited migration via the downstream regulator LitR. Similar to the initial point mutations, deletion of the VF_1200 DGC gene increased migration. Consistent with the possibility that production of the second messenger c-di-GMP inhibited the motility of KB2B1, reporter-based measurements of c-di-GMP revealed that KB2B1 produced higher levels of c-di-GMP than ES114, and overproduction of a c-di-GMP phosphodiesterase promoted migration of KB2B1. Finally, we assessed the role of viscosity in controlling the quorum sensing pathway using polyvinylpyrrolidone and found that viscosity increased light production of KB2B1 but not ES114. Together, our data indicate that while the two strains share regulators in common, they differ in the specifics of the regulatory control over downstream phenotypes such as motility.

RevDate: 2021-07-15

Vasan S, Srivastava D, Cahill D, et al (2021)

Important innate differences in determining symbiotic responsiveness in host and non-hosts of arbuscular mycorrhiza.

Scientific reports, 11(1):14444.

Genetic components that regulate arbuscular mycorrhizal (AM) interactions in hosts and non-hosts are not completely known. Comparative transcriptomic analysis was combined with phylogenetic studies to identify the factors that distinguish AM host from non-host. Mycorrhized host, non-mycorrhized host and non-host cultivars of tomato (Solanum lycopersicum) were subjected to RNA seq analysis. The top 10 differentially expressed genes were subjected to extensive in silico phylogenetic analysis along with 10 more candidate genes that have been previously reported for AM-plant interactions. Seven distantly related hosts and four non-hosts were selected to identify structural differences in selected gene/protein candidates. The screened genes/proteins were subjected to MEME, CODEML and DIVERGE analysis to identify evolutionary patterns that differentiate hosts from non-hosts. Based on the results, candidate genes were categorized as highly influenced (SYMRK and CCaMK), moderately influenced and minimally influenced by evolutionary constraints. We propose that the amino acid and nucleotide changes specific to non-hosts are likely to correspond to aberrations in functionality towards AM symbiosis. This study paves way for future research aimed at understanding innate differences in genetic make-up of AM hosts and non-hosts, in addition to the theory of gene losses from the "AM-symbiotic toolkit".

RevDate: 2021-07-14

Timoneda A, Yunusov T, Quan C, et al (2021)

MycoRed: Betalain pigments enable in vivo real-time visualisation of arbuscular mycorrhizal colonisation.

PLoS biology, 19(7):e3001326 pii:PBIOLOGY-D-20-02353 [Epub ahead of print].

Arbuscular mycorrhiza (AM) are mutualistic interactions formed between soil fungi and plant roots. AM symbiosis is a fundamental and widespread trait in plants with the potential to sustainably enhance future crop yields. However, improving AM fungal association in crop species requires a fundamental understanding of host colonisation dynamics across varying agronomic and ecological contexts. To this end, we demonstrate the use of betalain pigments as in vivo visual markers for the occurrence and distribution of AM fungal colonisation by Rhizophagus irregularis in Medicago truncatula and Nicotiana benthamiana roots. Using established and novel AM-responsive promoters, we assembled multigene reporter constructs that enable the AM-controlled expression of the core betalain synthesis genes. We show that betalain colouration is specifically induced in root tissues and cells where fungal colonisation has occurred. In a rhizotron setup, we also demonstrate that betalain staining allows for the noninvasive tracing of fungal colonisation along the root system over time. We present MycoRed, a useful innovative method that will expand and complement currently used fungal visualisation techniques to advance knowledge in the field of AM symbiosis.

RevDate: 2021-07-14

Ray P, Guo Y, Chi MH, et al (2021)

Serendipita fungi modulate the switchgrass root transcriptome to circumvent host defenses and establish a symbiotic relationship.

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

The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant response(s) to Serendipita colonization by characterizing the switchgrass root transcriptome during different stages of symbiosis in vitro. For this, we included a native switchgrass strain, Serendipita bescii, and a related strain Serendipita vermifera isolated from Australian orchids. Serendipita colonization progresses from thin hyphae that grow between root cells, and finally the production of large, bulbous hyphae that fill root cells during the later stages of colonization. We report that switchgrass seems to perceive both fungi prior to physical contact, leading to the activation of chemical and structural defense responses and putative host disease resistance genes. Subsequently, the host defense system appears to be quenched and carbohydrate metabolism adjusted, potentially to accommodate the fungal symbiont. In addition, prior to contact, switchgrass exhibited significant increases in root hair density and root surface area. Further, genes involved in phytohormone metabolism, such as gibberellin, jasmonic acid and salicylic acid were activated during different stages of colonization. Both fungal strains induced plant gene expression in a similar manner, indicating a conserved plant response to members of this fungal order. Understanding plant responsiveness to Serendipita will inform our efforts to integrate them into forages and row crops for optimal plant-microbe functioning, thus facilitating low-input, sustainable agricultural practices.

RevDate: 2021-07-14

Sen A, Dutta S, Dam G, et al (2021)

Imidazolium Functionalized Chemically Robust Ionic Porous Organic Polymers (iPOPs) toward Toxic Oxo-pollutants Capture from Water.

Chemistry (Weinheim an der Bergstrasse, Germany) [Epub ahead of print].

Fabricating new and efficient materials aimed at containment of water contamination, in particular removing toxic heavy metal based oxo-anions (for example CrO 4 2- , TcO 4 -) holds paramount importance. In this work, we report two new highly stable imidazolium based ionic porous organic polymers (i POPs) decorated with multiple interaction sites along with electrostatics driven adsorptive removal of such oxo-anions from water. Both the i POPs (namely, i POP-3 and i POP-4) exhibited rapid sieving kinetics and very high saturation uptake capacity for CrO 4 2- anions (170 and 141 mg g -1 for i POP-3 and i POP-4 respectively) and ReO 4 - (515.5 and 350.3 mg g -1 for i POP-3 and i POP-4 respectively), where ReO 4 - anions being the non-radioactive surrogative counterpart of radioactive TcO 4 - ions. Noticeably, both i POPs showed exceptional selectivity towards CrO 4 2- and ReO 4 - even in presence of several other concurrent anions such as Br - , Cl - , SO 4 2- , NO 3 - etc. The theoretical binding energy calculations via DFT method further confirmed the preferencial interaction sites as well as binding energies of both i POPs towards CrO 4 2- and ReO 4 - over all other competing anions which corroborates with the experimental high capacity and selectivity of i POPs towards such oxo-anions.

RevDate: 2021-07-14

Husnik F, Tashyreva D, Boscaro V, et al (2021)

Bacterial and archaeal symbioses with protists.

Current biology : CB, 31(13):R862-R877.

Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms - the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the origin of mitochondria. However, most of our knowledge about the evolution and functions of eukaryotic symbioses comes from the study of animal hosts, which represent only a small subset of eukaryotic diversity. Here, we take a broad view of bacterial and archaeal symbioses with protist hosts, focusing on their evolution, ecology, and cell biology, and also explore what functions (if any) the symbionts provide to their hosts. With the immense diversity of protist symbioses starting to come into focus, we can now begin to see how these systems will impact symbiosis theory more broadly.

RevDate: 2021-07-15
CmpDate: 2021-07-15

Anselmetti Y, El-Mabrouk N, Lafond M, et al (2021)

Gene tree and species tree reconciliation with endosymbiotic gene transfer.

Bioinformatics (Oxford, England), 37(Suppl_1):i120-i132.

MOTIVATION: It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α-proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree.

RESULTS: We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees.

EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.

RevDate: 2021-07-15
CmpDate: 2021-07-15

Kerwin AH, McAnulty SJ, SV Nyholm (2021)

Development of the Accessory Nidamental Gland and Associated Bacterial Community in the Hawaiian Bobtail Squid, Euprymna scolopes.

The Biological bulletin, 240(3):205-218.

AbstractThe Hawaiian bobtail squid, Euprymna scolopes, has a female reproductive organ called the accessory nidamental gland that contains a symbiotic bacterial consortium. These bacteria are deposited from the accessory nidamental gland into the squid's egg cases, where the consortium prevents microbial fouling. The symbiont community is environmentally transmitted and conserved across host populations, yet little is known about how the organ develops and is colonized by bacteria. In order to understand accessory nidamental gland development in E. scolopes, we characterized the gland during maturation by using histology and confocal and transmission electron microscopy. We found that an epithelial field formed first about four weeks after hatching, followed by the proliferation of numerous pores during what we hypothesize to be the initiation of bacterial recruitment (early development). Microscopy revealed that these pores were connected to ciliated invaginations that occasionally contained bacteria. During mid development, these epithelial fields expanded, and separate colonized tubules were observed below the epithelial layer that contained the pores and invaginations. During late development, the superficial epithelial fields appeared to regress as animals approached sexual maturity and were never observed in fully mature adults (about 2-3 months post-hatching), suggesting that they help facilitate bacterial colonization of the accessory nidamental gland. An analysis of 16S rRNA gene diversity in accessory nidamental glands from females of varying size showed that the bacterial community changed as the host approached sexual maturity, increasing in community evenness and shifting from a Verrucomicrobia-dominated to an Alphaproteobacteria-dominated consortium. Given the host's relationship with the well-characterized light organ symbiont Vibrio fischeri, our work suggests that the accessory nidamental gland of E. scolopes may have similar mechanisms to recruit bacteria from the environment. Understanding the developmental and colonization processes of the accessory nidamental gland will expand the use of E. scolopes as a model organism for studying bacterial consortia in marine symbioses.

RevDate: 2021-07-14
CmpDate: 2021-07-14

Anand S, Bose C, Kaur H, et al (2021)

'GutFeel': an in silico method for predicting gut health status based on the metabolic functional capabilities of the resident microbiome.

FEBS letters, 595(13):1825-1843.

Dysbiosis or imbalance in the gut microbiome has been correlated with the etiology of a number of diseases/disorders. Thus, gut microbial communities can potentially be utilized for assessing the health of the human gut. Although the taxonomic composition of the microbiomes is dependent on factors such as diet, lifestyle, and geography, these microbes perform a specific set of common functions in the gut. In this study, metabolic pathway-based markers (agnostic to above-mentioned factors) specific to commensals and those specific to pathogens are utilized as indicators of gut health. Furthermore, this gut health assessment requires only a small set of features rather than complete sequencing of metagenomes. The proposed scheme can also be used to design personalized biotherapeutics, depending on functional aspects observed in an individual.

RevDate: 2021-07-15
CmpDate: 2021-07-15

Murray GGR, Charlesworth J, Miller EL, et al (2021)

Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence.

Molecular biology and evolution, 38(4):1570-1579.

Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). Although genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, that is, host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of nonfunctional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a consistent correlate of pathogenicity in bacteria.

RevDate: 2021-07-15
CmpDate: 2021-07-15

Ford SA, KC King (2021)

In Vivo Microbial Coevolution Favors Host Protection and Plastic Downregulation of Immunity.

Molecular biology and evolution, 38(4):1330-1338.

Microbiota can protect their hosts from infection. The short timescales in which microbes can evolve presents the possibility that "protective microbes" can take-over from the immune system of longer-lived hosts in the coevolutionary race against pathogens. Here, we found that coevolution between a protective bacterium (Enterococcus faecalis) and a virulent pathogen (Staphylococcus aureus) within an animal population (Caenorhabditis elegans) resulted in more disease suppression than when the protective bacterium adapted to uninfected hosts. At the same time, more protective E. faecalis populations became costlier to harbor and altered the expression of 134 host genes. Many of these genes appear to be related to the mechanism of protection, reactive oxygen species production. Crucially, more protective E. faecalis populations downregulated a key immune gene, , known to be effective against S. aureus infection. These results suggest that a microbial line of defense is favored by microbial coevolution and may cause hosts to plastically divest of their own immunity.

RevDate: 2021-07-15
CmpDate: 2021-07-15

Hansen BL, Pessotti RC, Fischer MS, et al (2020)

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome.

mBio, 11(4):.

Microbiomes associated with various plant structures often contain members with the potential to make specialized metabolites, e.g., molecules with antibacterial, antifungal, or siderophore activities. However, when and where microbes associated with plants produce specialized metabolites, and the potential role of these molecules in mediating intramicrobiome interactions, is not well understood. Root nodules of legume plants are organs devoted to hosting symbiotic bacteria that fix atmospheric nitrogen and have recently been shown to harbor a relatively simple accessory microbiome containing members with the ability to produce specialized metabolites in vitro On the basis of these observations, we sought to develop a model nodule microbiome system for evaluating specialized microbial metabolism in planta Starting with an inoculum derived from field-grown Medicago sativa nodules, serial passaging through gnotobiotic nodules yielded a simplified accessory community composed of four members: Brevibacillus brevis , Paenibacillus sp., Pantoea agglomerans, and Pseudomonas sp. Some members of this community exhibited clear cooperation in planta, while others were antagonistic and capable of disrupting cooperation between other partners. Using matrix-assisted laser desorption ionization-imaging mass spectrometry, we found that metabolites associated with individual taxa had unique distributions, indicating that some members of the nodule community were spatially segregated. Finally, we identified two families of molecules produced by B. brevis in planta as the antibacterial tyrocidines and a novel set of gramicidin-type molecules, which we term the britacidins. Collectively, these results indicate that in addition to nitrogen fixation, legume root nodules are likely also sites of active antimicrobial production.

RevDate: 2021-07-15
CmpDate: 2021-07-15

Emmanuel OC, OO Babalola (2020)

Productivity and quality of horticultural crops through co-inoculation of arbuscular mycorrhizal fungi and plant growth promoting bacteria.

Microbiological research, 239:126569.

Associations between plants and microorganisms exist in nature, and they can either be beneficial or detrimental to host plants. Promoting beneficial plant-microbe interaction for increased crop yield and quality is one pathway to eco-friendly and sustainable crop production. Arbuscular mycorrhizal fungi (AMF) and plant growth promoting bacteria (PGPB) are microorganisms that are beneficial to horticultural crops. Arbuscular mycorrhizal fungi establish symbioses with plant roots which help to improve nutrient uptake by the host plant and alter its physiology to withstand external abiotic factors and pathogens. Plant growth promoting bacteria promote plant growth either directly by aiding resource acquisition and controlling the levels of plant hormones or indirectly by reducing the inhibitory effects of phytopathogens. Co-inoculation of both organisms combines the benefits of each for increased crop productivity. Even though the co-inoculation of PGPB and AMF have been shown to enhance the yield and quality of crops, its benefits have fully not been exploited for horticultural crops. In this review, the response of horticultural crops to co-inoculation with PGPB and AMF with particular interest to the impact on the yield and crop quality was discussed. We explained some of the mechanisms responsible for the synergy between AMF and PGPB in plant growth promotion. Finally, suggestions on areas that need to be researched further to exploit and improve the effects of these organisms were highlighted.

RevDate: 2021-07-15
CmpDate: 2021-07-15

Tronnet S, Floch P, Lucarelli L, et al (2020)

The Genotoxin Colibactin Shapes Gut Microbiota in Mice.

mSphere, 5(4):.

The genotoxin colibactin produced by resident bacteria of the gut microbiota may have tumorigenic effect by inducing DNA double-strand breaks in host cells. Yet, the effect of colibactin on gut microbiota composition and functions remains unknown. To address this point, we designed an experiment in which pregnant mice were colonized with the following: (i) a commensal Escherichia coli strain, (ii) a commensal E. coli strain plus a genotoxic E. coli strain, (iii) a commensal E. coli strain plus a nongenotoxic E. coli mutant strain unable to produce mature colibactin. Then, we analyzed the gut microbiota in pups at day 15 and day 35 after birth. At day 15, mice that were colonized at birth with the genotoxic strain showed lower levels of Proteobacteria and taxa belonging to the Proteobacteria, a modest effect on overall microbial diversity, and no effect on gut microbiome. At day 35, mice that received the genotoxic strain showed lower Firmicutes and taxa belonging to the Firmicutes, together with a strong effect on overall microbial diversity and higher microbial functions related to DNA repair. Moreover, the genotoxic strain strongly affected gut microbial diversity evolution of pups receiving the genotoxic strain between day 15 and day 35. Our data show that colibactin, beyond targeting the host, may also exert its genotoxic effect on the gut microbiota.IMPORTANCE Infections of genotoxic Escherichia coli spread concomitantly with urbanized progression. These bacteria may prompt cell senescence and affect DNA stability, inducing cancer via the production of colibactin, a genotoxin shown capable of affecting host DNA in eukaryotic cells. In this study, we show that the action of colibactin may also be directed against other bacteria of the gut microbiota in which genotoxic E. coli bacteria have been introduced. Indeed, the presence of genotoxic E. coli induced a change in both the structure and function of the gut microbiota. Our data indicate that genotoxic E. coli may use colibactin to compete for gut niche utilization.


RJR Experience and Expertise


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


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


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


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


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


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


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


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

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

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

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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RJR Picks from Around the Web (updated 11 MAY 2018 )