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Bibliography on: Symbiosis

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ESP: PubMed Auto Bibliography 13 Nov 2018 at 01:42 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: 2018-11-12

Kalita M, W Małek (2018)

The ftsA gene as a molecular marker for phylogenetic studies in Bradyrhizobium and identification of Bradyrhizobium japonicum.

Journal of applied genetics pii:10.1007/s13353-018-0479-9 [Epub ahead of print].

The use of ftsA gene sequences for taxonomic studies of the genus Bradyrhizobium bacteria was assessed. The ftsA gene codes for an actin-like protein involved in prokaryotic cell division. Up to now, this gene has not been used as a phylogenetic marker for analysis of bacteria establishing root nodule symbiosis with Fabaceae plants. In this study, the ftsA gene sequences obtained for bradyrhizobia forming N2 fixing symbiosis with four Genisteae tribe plants growing in Poland and most of the type strains of the genus Bradyrhizobium species were analyzed and evaluated as molecular markers for phylogenetic studies of these bacteria for the first time. The ftsA gene sequences of all bradyrhizobial strains with completely or partially sequenced genomes, available in the GenBank database, were also included into the analysis. The phylogeny of the ftsA gene was compared to the phylogenies of other chromosomal genes commonly used in the studies of Bradyrhizobium bacteria. The results showed that the phylogenies of ftsA and the core genes recA and glnII were congruent, making the ftsA gene useful as a phylogenetic marker. Analysis of the ftsA gene sequences revealed a single-nucleotide polymorphism unique to Bradyrhizobium japonicum strains, and the potential use of this SNP for identification of this species was discussed.

RevDate: 2018-11-12

Treanor D, Pamminger T, WOH Hughes (2018)

The evolution of caste-biasing symbionts in the social hymenoptera.

Insectes sociaux, 65(4):513-519.

The separation of individuals into reproductive and worker castes is the defining feature of insect societies. However, caste determination is itself a complex phenomenon, dependent on interacting genetic and environmental factors. It has been suggested by some authors that widespread maternally transmitted symbionts such as Wolbachia may be selected to interfere with caste determination, whilst others have discounted this possibility on theoretical grounds. We argue that there are in fact three distinct evolutionary scenarios in which maternally transmitted symbionts might be selected to influence the process of caste determination in a social hymenopteran host. Each of these scenarios generate testable predictions which we outline here. Given the increasing recognition of the complexity and multi-faceted nature of caste determination in social insects, we argue that maternally transmitted symbionts should also be considered as possible factors influencing the development of social hymenopterans.

RevDate: 2018-11-12

Gaudioso-Pedraza R, Beck M, Frances L, et al (2018)

Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development.

Current biology : CB pii:S0960-9822(18)31226-0 [Epub ahead of print].

The formation of nitrogen-fixing nodules in legumes involves the initiation of synchronized programs in the root epidermis and cortex to allow rhizobial infection and nodule development. In this study, we provide evidence that symplastic communication, regulated by callose turnover at plasmodesmata (PD), is important for coordinating nodule development and infection in Medicago truncatula. Here, we show that rhizobia promote a reduction in callose levels in inner tissues where nodules initiate. This downregulation coincides with the localized expression of M. truncatula β-1,3-glucanase 2 (MtBG2), encoding a novel PD-associated callose-degrading enzyme. Spatiotemporal analyses revealed that MtBG2 expression expands from dividing nodule initials to rhizobia-colonized cortical and epidermal tissues. As shown by the transport of fluorescent molecules in vivo, symplastic-connected domains are created in rhizobia-colonized tissues and enhanced in roots constitutively expressing MtBG2. MtBG2-overexpressing roots additionally displayed reduced levels of PD-associated callose. Together, these findings suggest an active role for MtBG2 in callose degradation and in the formation of symplastic domains during sequential nodule developmental stages. Interfering with symplastic connectivity led to drastic nodulation phenotypes. Roots ectopically expressing β-1,3-glucanases (including MtBG2) exhibited increased nodule number, and those expressing MtBG2 RNAi constructs or a hyperactive callose synthase (under symbiotic promoters) showed defective nodulation phenotypes. Obstructing symplastic connectivity appears to block a signaling pathway required for the expression of NODULE INCEPTION (NIN) and its target NUCLEAR FACTOR-YA1 (NF-YA1) in the cortex. We conclude that symplastic intercellular communication is proactively enhanced by rhizobia, and this is necessary for appropriate coordination of bacterial infection and nodule development.

RevDate: 2018-11-12

Decelle J, Carradec Q, Pochon X, et al (2018)

Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean.

Current biology : CB pii:S0960-9822(18)31219-3 [Epub ahead of print].

The dinoflagellate microalga Symbiodinium sustains coral reefs, one of the most diverse ecosystems of the biosphere, through mutualistic endosymbioses with a wide diversity of benthic hosts [1]. Despite its ecological and economic importance, the presence of Symbiodinium in open oceanic waters remains unknown, which represents a significant knowledge gap to fully understand the eco-evolutionary trajectory and resilience of endangered Symbiodinium-based symbioses. Here, we document the existence of Symbiodinium (i.e., now the family Symbiodiniaceae [2]) in tropical- and temperate-surface oceans using DNA and RNA metabarcoding of size-fractionated plankton samples collected at 109 stations across the globe. Symbiodinium from clades A and C were, by far, the most prevalent and widely distributed lineages (representing 0.1% of phytoplankton reads), while other lineages (clades B, D, E, F, and G) were present but rare. Concurrent metatranscriptomics analyses using the Tara Oceans gene catalog [3] revealed that Symbiodinium clades A and C were transcriptionally active in the open ocean and expressed core metabolic pathways (e.g., photosynthesis, carbon fixation, glycolysis, and ammonium uptake). Metabarcodes and expressed genes of clades A and C were detected in small and large plankton size fractions, suggesting the existence of a free-living population and a symbiotic lifestyle within planktonic hosts, respectively. However, high-resolution genetic markers and microscopy are required to confirm the life history of oceanic Symbiodinium. Overall, the previously unknown, metabolically active presence of Symbiodinium in oceanic waters opens up new avenues for investigating the potential of this oceanic reservoir to repopulate coral reefs following stress-induced bleaching.

RevDate: 2018-11-12

Flores-Félix JD, Sánchez-Juanes F, García-Fraile P, et al (2018)

Phaseolus vulgaris is nodulated by the symbiovar viciae of several genospecies of Rhizobium laguerreae complex in a Spanish region where Lens culinaris is the traditionally cultivated legume.

Systematic and applied microbiology pii:S0723-2020(18)30367-9 [Epub ahead of print].

Phaseolus vulgaris and Lens culinaris are two legumes with different distribution centers that were introduced in Spain at different times, but in some regions L. culinaris has been traditionally cultivated and P. vulgaris did not. Here we analysed the rhizobia isolated from nodules of these two legumes in one of these regions. MALDI-TOF MS analysis showed that all isolated strains matched with Rhizobium laguerreae and the phylogenetic analysis of rrs, atpD and recA genes confirmed these results. The phylogenetic analysis of these core genes allowed the differentiation of several groups within R. laguerreae and unexpectedly, strains with housekeeping genes identical to that of the type strain of R. laguerreae presented some differences in the rrs gene. In some strains this gene contains an intervening sequence (IVS) identical to that found in Rhizobium strains nodulating several legumes in different geographical locations. The atpD, recA and nodC genes of all isolated strains clustered with those of strains nodulating L. culinaris in its distribution centers, but not with those nodulating P. vulgaris in theirs. Therefore, all these strains belong to the symbiovar viciae, including those isolated from P. vulgaris, which in the studied region established effective symbiosis with the common endosymbiont of L. culinaris, instead to with its common endosymbiont, the symbiovar phaseoli. These results are particularly interesting for biogeography studies, because they showed that, due its high promiscuity degree, P. vulgaris is able to establish symbiosis with local symbiovars well established in the soil after centuries of cultivation with other legumes.

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

Biondi N, Cheloni G, Rodolfi L, et al (2018)

Tetraselmis suecica F&M-M33 growth is influenced by its associated bacteria.

Microbial biotechnology, 11(1):211-223.

Algal cultures are usually co-cultures of algae and bacteria, especially when considering outdoor mass cultivation. The influence of associated bacteria on algal culture performance has been poorly investigated, although bacteria may strongly affect biomass (or derived product) yield and quality. In this work, the influence on growth and productivity of Tetraselmis suecica F&M-M33 of bacterial communities and single bacterial isolates from the algal phycosphere was investigated. Xenic laboratory and outdoor cultures were compared with an axenic culture in batch. The presence of the bacterial community significantly promoted culture growth. Single bacterial isolates previously found to be strictly associated with T. suecica F&M-M33 also increased growth compared with the axenic culture, whereas loosely associated and common seawater bacteria induced variable growth responses, from positive to detrimental. The increased growth was mainly evidenced as increased algal biomass production and cell size, and occurred after exhaustion of nutrients. This finding is of interest for biofuel production from microalgae, often attained through nutrient starvation processes leading to oil or carbohydrate accumulation. As axenic T. suecica F&M-M33 showed a similar growth with or without vitamins, the most probable mechanism behind bacterial positive influence on algal growth seems nutrient recycling.

RevDate: 2018-11-10

Fagorzi C, Checcucci A, diCenzo GC, et al (2018)

Harnessing Rhizobia to Improve Heavy-Metal Phytoremediation by Legumes.

Genes, 9(11): pii:genes9110542.

Rhizobia are bacteria that can form symbiotic associations with plants of the Fabaceae family, during which they reduce atmospheric di-nitrogen to ammonia. The symbiosis between rhizobia and leguminous plants is a fundamental contributor to nitrogen cycling in natural and agricultural ecosystems. Rhizobial microsymbionts are a major reason why legumes can colonize marginal lands and nitrogen-deficient soils. Several leguminous species have been found in metal-contaminated areas, and they often harbor metal-tolerant rhizobia. In recent years, there have been numerous efforts and discoveries related to the genetic determinants of metal resistance by rhizobia, and on the effectiveness of such rhizobia to increase the metal tolerance of host plants. Here, we review the main findings on the metal resistance of rhizobia: the physiological role, evolution, and genetic determinants, and the potential to use native and genetically-manipulated rhizobia as inoculants for legumes in phytoremediation practices.

RevDate: 2018-11-09

Rossi A, Bellone A, Fokin SI, et al (2018)

Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study.

Microbial ecology pii:10.1007/s00248-018-1279-9 [Epub ahead of print].

Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.

RevDate: 2018-11-09

Morris JJ (2018)

What is the hologenome concept of evolution?.

F1000Research, 7:.

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

RevDate: 2018-11-09

Colella S, Parisot N, Simonet P, et al (2018)

Bacteriocyte Reprogramming to Cope With Nutritional Stress in a Phloem Sap Feeding Hemipteran, the Pea Aphid Acyrthosiphon pisum.

Frontiers in physiology, 9:1498.

Nutritional symbioses play a central role in the ability of insects to thrive on unbalanced diets and in ensuring their evolutionary success. A genomic model for nutritional symbiosis comprises the hemipteran Acyrthosiphon pisum, and the gamma-3-proteobacterium, Buchnera aphidicola, with genomes encoding highly integrated metabolic pathways. A. pisum feeds exclusively on plant phloem sap, a nutritionally unbalanced diet highly variable in composition, thus raising the question of how this symbiotic system responds to nutritional stress. We addressed this by combining transcriptomic, phenotypic and life history trait analyses to determine the organismal impact of deprivation of tyrosine and phenylalanine. These two aromatic amino acids are essential for aphid development, are synthesized in a metabolic pathway for which the aphid host and the endosymbiont are interdependent, and their concentration can be highly variable in plant phloem sap. We found that this nutritional challenge does not have major phenotypic effects on the pea aphid, except for a limited weight reduction and a 2-day delay in onset of nymph laying. Transcriptomic analyses through aphid development showed a prominent response in bacteriocytes (the core symbiotic tissue which houses the symbionts), but not in gut, thus highlighting the role of bacteriocytes as major modulators of this homeostasis. This response does not involve a direct regulation of tyrosine and phenylalanine biosynthetic pathway and transporter genes. Instead, we observed an extensive transcriptional reprogramming of the bacteriocyte with a rapid down-regulation of genes encoding sugar transporters and genes required for sugar metabolism. Consistently, we observed continued overexpression of the A. pisum homolog of RRAD, a small GTPase implicated in repressing aerobic glycolysis. In addition, we found increased transcription of genes involved in proliferation, cell size control and signaling. We experimentally confirmed the significance of these gene expression changes detecting an increase in bacteriocyte number and cell size in vivo under tyrosine and phenylalanine depletion. Our results support a central role of bacteriocytes in the aphid response to amino acid deprivation: their transcriptional and cellular responses fine-tune host physiology providing the host insect with an effective way to cope with the challenges posed by the variability in composition of phloem sap.

RevDate: 2018-11-09

Roth R, Chiapello M, Montero H, et al (2018)

A rice Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal symbiosis at the peri-arbuscular membrane.

Nature communications, 9(1):4677 pii:10.1038/s41467-018-06865-z.

In terrestrial ecosystems most plant species live in mutualistic symbioses with nutrient-delivering arbuscular mycorrhizal (AM) fungi. Establishment of AM symbioses includes transient, intracellular formation of fungal feeding structures, the arbuscules. A plant-derived peri-arbuscular membrane (PAM) surrounds the arbuscules, mediating reciprocal nutrient exchange. Signaling at the PAM must be well coordinated to achieve this dynamic cellular intimacy. Here, we identify the PAM-specific Arbuscular Receptor-like Kinase 1 (ARK1) from maize and rice to condition sustained AM symbiosis. Mutation of rice ARK1 causes a significant reduction in vesicles, the fungal storage structures, and a concomitant reduction in overall root colonization by the AM fungus Rhizophagus irregularis. Arbuscules, although less frequent in the ark1 mutant, are morphologically normal. Co-cultivation with wild-type plants restores vesicle and spore formation, suggesting ARK1 function is required for the completion of the fungal life-cycle, thereby defining a functional stage, post arbuscule development.

RevDate: 2018-11-09

Parakh SK, Praveen P, Loh KC, et al (2019)

Wastewater treatment and microbial community dynamics in a sequencing batch reactor operating under photosynthetic aeration.

Chemosphere, 215:893-903.

A sequencing batch bioreactor (SBR) treating municipal wastewater was photosynthetically aerated using microalgae cultivated in a photobioreactor (PBR). Symbiotic interactions and CO2/O2 exchange were established between activated sludge in the SBR and microalgae in the PBR through hydrophobic hollow fiber membranes. Photosynthetic aeration enhanced COD removal in the SBR from 52.2% (without external aeration) to 90.3%, whereas N-NH4+ and P-PO43- removal increased by 63.5% and 90.4%, respectively. The SBR performance under photosynthetic aeration was comparable to that under mechanical aeration. However, no nitrification was observed in the SBR, indicating oxygen limitation and poor growth condition for nitrifiers. In the PBR, there was a rapid increase in biomass concentration and it stabilized at 3.0 g/L after 22 days of operation. High nitrogen demand in the PBR indicated the steady flow of inorganic carbon from the SBR through the membranes. Prolonged oxygen limitation and massive sludge attachment on the membranes resulted in low suspended sludge concentration in the SBR. Microbial community analysis indicated gradual enrichment of facultative and strictly anaerobic microorganisms in the SBR. These results highlight the potential of microalgae in lowering the cost of wastewater aeration and underline the challenges in sustaining symbiotic gas exchange during long-term.

RevDate: 2018-11-09
CmpDate: 2018-11-09

Sandaa RA, G Bratbak (2018)

Is the Virus Important? And Some Other Questions.

Viruses, 10(8): pii:v10080442.

The motivation for focusing on a specific virus is often its importance in terms of impact on human interests. The chlorella viruses are a notable exception and 40 years of research has made them the undisputed model system for large icosahedral dsDNA viruses infecting eukaryotes. Their status has changed from inconspicuous and rather odd with no ecological relevance to being the Phycodnaviridae type strain possibly affecting humans and human cognitive functioning in ways that remain to be understood. The Van Etten legacy is the backbone for research on Phycodnaviridae. After highlighting some of the peculiarities of chlorella viruses, we point to some issues and questions related to the viruses we choose for our research, our prejudices, what we are still missing, and what we should be looking for.

RevDate: 2018-11-09
CmpDate: 2018-11-09

Shi C, An S, Yao Z, et al (2017)

Toxin-producing Epichloë bromicola strains symbiotic with the forage grass Elymus dahuricus in China.

Mycologia, 109(6):847-859.

Cool-season grasses (Poaceae subfamily Poöideae) are an important forage component for livestock in western China, and many have seed-transmitted symbionts of the genus Epichloë, fungal endophytes that are broadly distributed geographically and in many tribes of the Poöideae. Epichloë strains can produce any of several classes of alkaloids, of which ergot alkaloids and indole-diterpenes can be toxic to mammalian and invertebrate herbivores, whereas lolines and peramine are more selective against invertebrates. The authors characterized genotypes and alkaloid profiles of Epichloë bromicola isolates symbiotic with Elymus dahuricus, an important forage grass in rangelands of China. The endophyte was seed-transmitted and occasionally produced fruiting bodies (stromata), but its sexual state was not observed on this host. The genome sequence of E. bromicola isolate E7626 from El. dahuricus in Xinjiang Province revealed gene sets for peramine, ergot alkaloids, and indole-diterpenes. In multiplex polymerase chain reaction (PCR) screens of El. dahuricus-endophyte isolates from Beijing and two locations in Shanxi Province, most were also positive for these genes. Ergovaline and other ergot alkaloids, terpendoles and other indole-diterpenes, and peramine were confirmed in El. dahuricus plants with E. bromicola. The presence of ergot alkaloids and indole-diterpenes in this grass is a potential concern for managers of grazing livestock.

RevDate: 2018-11-09
CmpDate: 2018-11-09

Carlson AL, Ishak HD, Kurian J, et al (2017)

Nuclear populations of the multinucleate fungus of leafcutter ants can be dekaryotized and recombined to manipulate growth of nutritive hyphal nodules harvested by the ants.

Mycologia, 109(5):832-846.

We dekaryotized the multinucleate fungus Leucocoprinus gongylophorus, a symbiotic fungus cultivated vegetatively by leafcutter ants as their food. To track genetic changes resulting from dekaryotization (elimination of some nuclei from the multinuclear population), we developed two multiplex microsatellite fingerprinting panels (15 loci total), then characterized the allele profiles of 129 accessions generated by dekaryotization treatment. Genotype profiles of the 129 accessions confirmed allele loss expected by dekaryotization of the multinucleate fungus. We found no evidence for haploid and single-nucleus strains among the 129 accessions. Microscopy of fluorescently stained dekaryotized accessions revealed great variation in nuclei number between cells of the same vegetative mycelium, with cells containing typically between 3 and 15 nuclei/cell (average = 9.4 nuclei/cell; mode = 8). We distinguish four mycelial morphotypes among the dekaryotized accessions; some of these morphotypes had lost the full competence to produce gongylidia (nutritive hyphal-tip swellings consumed by leafcutter ants as food). In mycelial growth confrontations between different gongylidia-incompetent accessions, allele profiles suggest exchange of nuclei between dekaryotized accessions, restoring full gongylidia competence in some of these strains. The restoration of gongylidia competence after genetic exchange between dekaryotized strains suggests the hypothesis that complementary nuclei interact, or nuclear and cytoplasmic factors interact, to promote or enable gongylidia competence.

RevDate: 2018-11-09
CmpDate: 2018-11-09

Corcione S, Curtoni A, Paolucci IA, et al (2018)

Neurological disease may precede lymphadenopathies in Actinomyces europaeus infection.

Journal of infection and public health, 11(4):592-593.

Actinomyces species are part of the commensal flora of the mucous membranes of the oropharynx, gastrointestinal tract and female genital tract. Actinomyces europaeus is a short, nonmotile, facultative anaerobic rod first described in 1997, susceptible in vitro to a wide range of b-lactam antibiotics which are regarded as first choice. In this report we described the case of A. europaeus infection in a young female patient admitted to Intensive Care Unit and the possible damage of vascular endothelium due to a chronic progressive actinomycosis that at first involved neck soft tissue, then cervical lymphnodes, and finally extended to the vascular structure.

RevDate: 2018-11-09
CmpDate: 2018-11-09

Chen JE, Cui G, Wang X, et al (2018)

Recent expansion of heat-activated retrotransposons in the coral symbiont Symbiodinium microadriaticum.

The ISME journal, 12(2):639-643.

Rising sea surface temperature is the main cause of global coral reef decline. Abnormally high temperatures trigger the breakdown of the symbiotic association between corals and their photosynthetic symbionts in the genus Symbiodinium. Higher genetic variation resulting from shorter generation times has previously been proposed to provide increased adaptability to Symbiodinium compared to the host. Retrotransposition is a significant source of genetic variation in eukaryotes and some transposable elements are specifically expressed under adverse environmental conditions. We present transcriptomic and phylogenetic evidence for the existence of heat stress-activated Ty1-copia-type LTR retrotransposons in the coral symbiont Symbiodinium microadriaticum. Genome-wide analyses of emergence patterns of these elements further indicate recent expansion events in the genome of S. microadriaticum. Our findings suggest that acute temperature increases can activate specific retrotransposons in the Symbiodinium genome with potential impacts on the rate of retrotransposition and the generation of genetic variation under heat stress.

RevDate: 2018-11-09
CmpDate: 2018-11-09

Tout J, Astudillo-García C, Taylor MW, et al (2017)

Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds.

Environmental microbiology reports, 9(6):750-755.

Marine sponges host stable and species-specific microbial symbionts that are thought to be acquired and maintained by the host through a combination of vertical transmission and filtration from the surrounding seawater. To assess whether the microbial symbionts also actively contribute to the establishment of these symbioses, we performed in situ experiments on Orpheus Island, Great Barrier Reef, to quantify the chemotactic responses of natural populations of seawater microorganisms towards cellular extracts of the reef sponge Rhopaloeides odorabile. Flow cytometry analysis revealed significant levels of microbial chemotaxis towards R. odorabile extracts and 16S rRNA gene amplicon sequencing showed enrichment of 'sponge-specific' microbial phylotypes, including a cluster within the Gemmatimonadetes and another within the Actinobacteria. These findings infer a potential mechanism for how sponges can acquire bacterial symbionts from the surrounding environment and suggest an active role of the symbionts in finding their host.

RevDate: 2018-11-09
CmpDate: 2018-11-09

Keren R, Mayzel B, Lavy A, et al (2017)

Sponge-associated bacteria mineralize arsenic and barium on intracellular vesicles.

Nature communications, 8:14393 pii:ncomms14393.

Arsenic and barium are ubiquitous environmental toxins that accumulate in higher trophic-level organisms. Whereas metazoans have detoxifying organs to cope with toxic metals, sponges lack organs but harbour a symbiotic microbiome performing various functions. Here we examine the potential roles of microorganisms in arsenic and barium cycles in the sponge Theonella swinhoei, known to accumulate high levels of these metals. We show that a single sponge symbiotic bacterium, Entotheonella sp., constitutes the arsenic- and barium-accumulating entity within the host. These bacteria mineralize both arsenic and barium on intracellular vesicles. Our results indicate that Entotheonella sp. may act as a detoxifying organ for its host.

RevDate: 2018-11-09
CmpDate: 2018-11-09

Pascual-García A, U Bastolla (2017)

Mutualism supports biodiversity when the direct competition is weak.

Nature communications, 8:14326 pii:ncomms14326.

A key question of theoretical ecology is which properties of ecosystems favour their stability and help maintaining biodiversity. This question recently reconsidered mutualistic systems, generating intense controversy about the role of mutualistic interactions and their network architecture. Here we show analytically and verify with simulations that reducing the effective interspecific competition and the propagation of perturbations positively influences structural stability against environmental perturbations, enhancing persistence. Noteworthy, mutualism reduces the effective interspecific competition only when the direct interspecific competition is weaker than a critical value. This critical competition is in almost all cases larger in pollinator networks than in random networks with the same connectance. Highly connected mutualistic networks reduce the propagation of environmental perturbations, a mechanism reminiscent of MacArthur's proposal that ecosystem complexity enhances stability. Our analytic framework rationalizes previous contradictory results, and it gives valuable insight on the complex relationship between mutualism and biodiversity.

RevDate: 2018-11-09
CmpDate: 2018-11-09

Groussin M, Mazel F, Sanders JG, et al (2017)

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time.

Nature communications, 8:14319 pii:ncomms14319.

Whether mammal-microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution. Considering microbiomes at appropriate phylogenetic scales allows us to model their evolution along the mammalian tree and to infer ancient diets from the predicted microbiomes of mammalian ancestors. Phylogenetic analyses support co-speciation as having a significant role in the evolution of mammalian gut microbiome compositions. Highly co-speciating bacterial genera are also associated with immune diseases in humans, laying a path for future studies that probe these co-speciating bacteria for signs of co-evolution.

RevDate: 2018-11-08

Buendia L, Girardin A, Wang T, et al (2018)

LysM Receptor-Like Kinase and LysM Receptor-Like Protein Families: An Update on Phylogeny and Functional Characterization.

Frontiers in plant science, 9:1531.

Members of plant specific families of receptor-like kinases (RLKs) and receptor-like proteins (RLPs), containing 3 extracellular LysMs have been shown to directly bind and/or to be involved in perception of lipo-chitooligosaccharides (LCO), chitooligosaccharides (CO), and peptidoglycan (PGN), three types of GlcNAc-containing molecules produced by microorganisms. These receptors are involved in microorganism perception by plants and can activate different plant responses leading either to symbiosis establishment or to defense responses against pathogens. LysM-RLK/Ps belong to multigenic families. Here, we provide a phylogeny of these families in eight plant species, including dicotyledons and monocotyledons, and we discuss known or putative biological roles of the members in each of the identified phylogenetic groups. We also report and discuss known biochemical properties of the LysM-RLK/Ps.

RevDate: 2018-11-08

Hujber Z, Horváth G, Petővári G, et al (2018)

GABA, glutamine, glutamate oxidation and succinic semialdehyde dehydrogenase expression in human gliomas.

Journal of experimental & clinical cancer research : CR, 37(1):271 pii:10.1186/s13046-018-0946-5.

BACKGROUND: Bioenergetic characterisation of malignant tissues revealed that different tumour cells can catabolise multiple substrates as salvage pathways, in response to metabolic stress. Altered metabolism in gliomas has received a lot of attention, especially in relation to IDH mutations, and the associated oncometabolite D-2-hydroxyglutarate (2-HG) that impact on metabolism, epigenetics and redox status. Astrocytomas and oligodendrogliomas, collectively called diffuse gliomas, are derived from astrocytes and oligodendrocytes that are in metabolic symbiosis with neurons; astrocytes can catabolise neuron-derived glutamate and gamma-aminobutyric acid (GABA) for supporting and regulating neuronal functions.

METHODS: Metabolic characteristics of human glioma cell models - including mitochondrial function, glycolytic pathway and energy substrate oxidation - in relation to IDH mutation status and after 2-HG incubation were studied to understand the Janus-faced role of IDH1 mutations in the progression of gliomas/astrocytomas. The metabolic and bioenergetic features were identified in glioma cells using wild-type and genetically engineered IDH1-mutant glioblastoma cell lines by metabolic analyses with Seahorse, protein expression studies and liquid chromatography-mass spectrometry.

RESULTS: U251 glioma cells were characterised by high levels of glutamine, glutamate and GABA oxidation. Succinic semialdehyde dehydrogenase (SSADH) expression was correlated to GABA oxidation. GABA addition to glioma cells increased proliferation rates. Expression of mutated IDH1 and treatment with 2-HG reduced glutamine and GABA oxidation, diminished the pro-proliferative effect of GABA in SSADH expressing cells. SSADH protein overexpression was found in almost all studied human cases with no significant association between SSADH expression and clinicopathological parameters (e.g. IDH mutation).

CONCLUSIONS: Our findings demonstrate that SSADH expression may participate in the oxidation and/or consumption of GABA in gliomas, furthermore, GABA oxidation capacity may contribute to proliferation and worse prognosis of gliomas. Moreover, IDH mutation and 2-HG production inhibit GABA oxidation in glioma cells. Based on these data, GABA oxidation and SSADH activity could be additional therapeutic targets in gliomas/glioblastomas.

RevDate: 2018-11-08

Wang T, Song Z, Wang X, et al (2018)

Functional Insights into the Roles of Hormones in the Dendrobium officinale-Tulasnella sp. Germinated Seed Symbiotic Association.

International journal of molecular sciences, 19(11): pii:ijms19113484.

Dendrobium is one of the largest genera in the Orchidaceae, and D. officinale is used in traditional medicine, particularly in China. D. officinale seeds are minute and contain limited energy reserves, and colonization by a compatible fungus is essential for germination under natural conditions. When the orchid mycorrhizal fungi (OMF) initiates symbiotic interactions with germination-driven orchid seeds, phytohormones from the orchid or the fungus play key roles, but the details of the possible biochemical pathways are still poorly understood. In the present study, we established a symbiotic system between D. officinale and Tulasnella sp. for seed germination. RNA-Seq was used to construct libraries of symbiotic-germinated seeds (DoTc), asymbiotic-germinated seeds (Do), and free-living OMF (Tc) to investigate the expression profiles of biosynthesis and metabolism pathway genes for three classes of endogenous hormones: JA (jasmonic acid), ABA (abscisic acid) and SLs (strigolactones), in D. officinale seeds and OMF under symbiotic and asymbiotic conditions. Low concentrations of endogenous JA, ABA, or SLs were detected in the D. officinale-Tulasnella symbiont compared with the asymbiotic tissues. Gene annotation results suggest that the expression of DEGs (differentially expressed genes) related to JA and ABA biosynthesis from D. officinale were down-regulated, while most of the key DEGs related to SL biosynthesis from D. officinale were up-regulated in the symbiotic germinated seeds compared with the asymbiotic germinated seeds. Moreover, in the OMF, we found a significantly up-regulated differential expression of the JA and ABA biosynthesis-related genes in the symbiotic interaction, with the opposite expression trends to those found in Dendrobium. This indicates that Dendrobium seed symbiotic germination may be stimulated by the apparent involvement of the OMF in the production of hormones, and relatively low concentrations of endogenous JA, ABA, or SLs might be maintained to promote the growth of the D. officinale-Tulasnella symbiotic protocorm-like body. These results will increase our understanding of the possible roles played by endogenous hormones in the regulation of the orchid-fungus symbiosis.

RevDate: 2018-11-08
CmpDate: 2018-11-08

Zouari S, Ben Halima MK, Reyes-Prieto M, et al (2018)

Natural Occurrence of Secondary Bacterial Symbionts in Aphids from Tunisia, with a Focus on Genus Hyalopterus.

Environmental entomology, 47(2):325-333.

Aphids (Hemiptera: Aphididae) can harbor two types of bacterial symbionts. In addition to the obligate endosymbiont Buchnera aphidicola Munson, Baumann and Kinsey 1991 (Enterobacteriales: Enterobacteriaceae), several facultative symbiotic bacteria, called secondary (S) symbionts, have been identified among many important pest aphid species. To determine interpopulational diversity of S-symbionts, we carried out a survey in a total of 18 populations of six aphid species collected from six localities in Tunisia, by performing a diagnostic polymerase chain reaction analysis of partial 16S-23S rRNA operon sequences. While 61.7% of individuals contained only Buchnera, three S-symbionts were found at different frequencies. Arsenophonus sp. Gherna et al. 1991 (Enterobacteriales: Enterobacteriaceae) was found in all species under study except for Acyrtosiphon pisum (Harris 1776) (Aphidinae: Macrosiphini); Serratia symbiotica Moran et al. 2005 (Enterobacteriales: Enterobacteriaceae) was present in all analyzed individuals of A. pisum but only sporadically in Aphis spiraecola (Patch 1914) (Aphidinae: Aphidini) and Hyalopterus amygdali (Blanchard 1840) (Aphidinae: Aphidini), while Hamiltonella defensa Moran et al. 2005 (Enterobacteriales: Enterobacteriaceae) was found in all analyzed individuals of one population of Aphis gossypii (Glover 1877) (Aphidinae: Aphidini) and sporadically in two populations of Hyalopterus. The lysogenic bacteriophage APSE-1 (A. pisum secondary endosymbiont, type 1) was detected in the three populations infected with H. defensa. This bacteriophage has been associated with moderate protection against braconid parasitoids in pea aphids. The high prevalence of Arsenophonus sp. in our samples is in accordance with previous studies indicating that, among gammaproteobacteria, this genus is one of the most widespread insect facultative symbionts.

RevDate: 2018-11-08
CmpDate: 2018-11-08

Lee ST, Davy SK, Tang SL, et al (2017)

Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata.

Scientific reports, 7:43600 pii:srep43600.

Deterioration of coral health and associated change in the coral holobiont's bacterial community are often a result of different environmental stressors acting synergistically. There is evidence that water flow is important for a coral's resistance to elevated seawater temperature, but there is no information on how water flow affects the coral-associated bacterial community under these conditions. In a laboratory cross-design experiment, Acropora muricata nubbins were subjected to interactive effects of seawater temperature (27 °C to 31 °C) and water flow (0.20 m s-1 and 0.03 m s-1). In an in situ experiment, water flow manipulation was conducted with three colonies of A. muricata during the winter and summer, by partially enclosing each colony in a clear plastic mesh box. 16S rRNA amplicon pyrosequencing showed an increase in the relative abundance of Flavobacteriales and Rhodobacterales in the laboratory experiment, and Vibrio spp. in the in situ experiment when corals were exposed to elevated temperature and slow water flow. In contrast, corals that were exposed to faster water flow under laboratory and in situ conditions had a stable bacterial community. These findings indicate that water flow plays an important role in the maintenance of specific coral-bacteria associations during times of elevated thermal stress.

RevDate: 2018-11-07

Somporn P, Walters L, J Ash (2018)

Expectations of rural community-based medical education: a case study from Thailand.

Rural and remote health, 18(4):4709.

INTRODUCTION: Thailand has recognised and sought to remedy rural medical workforce shortages. The Collaborative Project to Increase Production of Rural Doctors (CPIRD) has improved rural workforce recruitment through publicly funding medical school places for students with rural backgrounds. However, challenges in rural retention continue. CPIRD is seeking to develop a Thai rural community-based medical education (RCBME) program in the southern region of Thailand to improve preparation for rural practice and rural medical retention rates. Prospective stakeholder consultations will allow the understanding of expectations and concerns of stakeholders required for successful RCBME implementation. This study aims to explore stakeholders' expectations of the Southern Thai RCBME initiative.

METHODS: A qualitative case study comprised a purposive sample of students, clinical educators, policymakers, rural health professionals and local community stakeholders, all likely to be involved in a new RCBME program in Songkhla Province, Thailand. Individual semi-structured interviews were audiotaped, transcribed in Thai and coded using Worley's symbiosis framework. Following this, text and quotes used in the initial analysis were translated into English, discussed and reanalysed for emergent themes across the framework.

RESULTS: A total of 21 participants contributed RCBME stakeholder perspectives. They demonstrated expectations and concerns in each of the relationship axes of the symbiosis model including the clinical, institutional, social and personal axes. Three major themes emerged from the data that integrated stakeholder perspectives on the implication of RCBME in Thailand. These themes were a dramatic shift in Thai medical education paradigm, seeing rural practice as a future career, and collaboration to improve education and health in rural services.

CONCLUSION: This study comprehensively describes Thai stakeholder expectations of RCBME and demonstrates that, although some principles of RCBME are universal, context does influence the expectations and capacity of stakeholders to contribute to RCBME. Prospective formal stakeholder engagement is recommended to ensure successful implementation of new educational innovations.

RevDate: 2018-11-07

Sepp SK, Davison J, Jairus T, et al (2018)

Non-random association patterns in a plant-mycorrhizal fungal network reveal host-symbiont specificity.

Molecular ecology [Epub ahead of print].

Arbuscular mycorrhizal (AM) fungi are obligate plant symbionts that have important functions in most terrestrial ecosystems, but there remains an incomplete understanding of host-fungus specificity and the relationships between species or functional groups of plants and AM fungi. Here, we aimed to provide a comprehensive description of plant-AM fungal interactions in a biodiverse semi-natural grassland. We sampled all plant species in a 1000 m2 homogeneous plot of dry calcareous grassland in two seasons (summer and autumn) and identified root-colonizing AM fungi by SSU rDNA sequencing. In the network of 33 plant and 100 AM fungal species, we found a significant effect of both host plant species and host plant functional group on AM fungal richness and community composition. Comparison with network null models revealed a larger-than-random degree of partner selectivity among plants. Grasses harbored a larger number of AM fungal partners and were more generalist in partner selection, compared with forbs. More generalist partner association and lower specialization were apparent among obligately, compared with facultatively, mycorrhizal plant species and among locally more abundant plant species. This study provides the most complete dataset of co-occurring plant and AM fungal taxa to date, showing that at this particular site, the interaction network is assembled non-randomly, with moderate selectivity in associations between plant species and functional groups and their fungal symbionts. This article is protected by copyright. All rights reserved.

RevDate: 2018-11-07

Joshi S, Cook E, MS Mannoor (2018)

Bacterial Nanobionics via 3D Printing.

Nano letters [Epub ahead of print].

Investigating the multidimensional integration between different microbiological kingdoms possesses potential toward engineering next-generation bionic architectures. Bacterial and fungal kingdom exhibits mutual symbiosis that can offer advanced functionalities to these bionic architectures. Moreover, functional nanomaterials can serve as probing agents for accessing newer information from microbial organisms due to their dimensional similarities. In this article, a bionic mushroom was created by intertwining cyanobacterial cells with graphene nanoribbons (GNRs) onto the umbrella-shaped pileus of mushroom for photosynthetic bioelectricity generation. These seamlessly merged GNRs function as agents for mediating extracellular electron transport from cyanobacteria resulting in photocurrent generation. Additionally, three-dimensional (3D) printing technique was used to assemble cyanobacterial cells in anisotropic, densely packed geometry resulting in adequate cell-population density for efficient collective behavior. These 3D printed cyanobacterial colonies resulted in comparatively higher photocurrent (almost 8-fold increase) than isotropically casted cyanobacteria of similar seeding density. An insight of the proposed integration between cyanobacteria and mushroom derives remarkable advantage that arises from symbiotic relationship, termed here as engineered bionic symbiosis. Existence of this engineered bionic symbiosis was confirmed by UV-visible spectroscopy and standard plate counting method. Taken together, the present study augments scientific understanding of multidimensional integration between the living biological microworld and functional abiotic nanomaterials to establish newer dimensionalities toward advancement of bacterial nanobionics.

RevDate: 2018-11-07

Chashchina OE, Chibilev AA, Veselkin DV, et al (2018)

The Natural Abundance of Heavy Nitrogen Isotope (15N) in Plants Increases near a Large Copper Smelter.

Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections, 482(1):198-201.

The ratio of stable isotopes of nitrogen (15N and 14N) has been assessed in leaves of the forest plants from different functional groups (with ectomycorrhiza, ericoid, and arbuscular mycorrhiza; in a nitrogen-fixing symbiosis) under the conditions of strong transformation of ecosystems by the Karabashsky Copper-Smelting Plant effluents in the Southern Urals. The abundance of 15N in the plants generally increases in polluted habitats. The abundance of the heavy isotope 15N increases significantly with pollution in ericaceous dwarf shrubs (by 3.3‰) and herbs with arbuscular mycorrhizae (by 2.8‰). This indicates a strong alteration in conditions or modes of plant mineral nutrition under the influence of heavy metal pollution of forest ecosystems.

RevDate: 2018-11-07

Alvarado-López CJ, Dasgupta-Schubert N, Ambriz JE, et al (2018)

Lead uptake by the symbiotic Daucus carota L.-Glomus intraradices system and its effect on the morphology of extra- and intraradical fungal microstructures.

Environmental science and pollution research international pii:10.1007/s11356-018-3569-7 [Epub ahead of print].

This work examines the strategies adopted by an arbuscular mycorrhizal symbiotic system to ameliorate environmental Pb stress by examining the concentrations of P, Fe, and Pb in the fungal microstructures and the host's root. In vitro cultures of Ri-T DNA-transformed carrot (Daucus carota L.) roots were inoculated with Glomus intraradices and treated with Pb(NO3)2 solution and the extraradical spores and mycelia (S/M) and the root with the vesicles, mycelia, and root cells were subsequently analyzed by polarized energy dispersive x-ray fluorescence (PEDXRF) spectrometry. Upon Pb treatment, within the root, the percentages of mycorrhizal colonization, the vesicles, and mycelia increased as well as the areas of the vesicles and the (extraradical) spores, although the number of spores and arbuscules decreased. The S/M and the mycorrhizal root showed enhanced concentrations of Pb, Fe, and P. These were particularly marked for Fe in the Pb-treated cultures. This indicates a synergistic relationship between the arbuscular mycorrhizal fungus and the host that confers a higher Pb tolerance to the latter by the induction of higher Fe absorption in the host. The intraradical vesicle, mycelia, and arbuscule numbers are interpreted as a "tactic to divert" the intraradical Pb traffic away from the root cells to the higher affinity cell walls of the arbuscular mycorrhizal fungi (AMF) microstructures in the apoplast. The results of this work show that the symbiosis between the AMF G. intraradices and the host plant D. carota distinctly improves the latter's Pb tolerance, and imply that the appropriate metal tolerant host-AMF combinations could be employed in process designs for the phytoremediation of Pb.

RevDate: 2018-11-07

Jones VAS, Bucher M, Hambleton EA, et al (2018)

Microinjection to deliver protein, mRNA, and DNA into zygotes of the cnidarian endosymbiosis model Aiptasia sp.

Scientific reports, 8(1):16437 pii:10.1038/s41598-018-34773-1.

Reef-building corals depend on an intracellular symbiosis with photosynthetic dinoflagellates for their survival in nutrient-poor oceans. Symbionts are phagocytosed by coral larvae from the environment and transfer essential nutrients to their hosts. Aiptasia, a small tropical marine sea anemone, is emerging as a tractable model system for coral symbiosis; however, to date functional tools and genetic transformation are lacking. Here we have established an efficient workflow to collect Aiptasia eggs for in vitro fertilization and microinjection as the basis for experimental manipulations in the developing embryo and larvae. We demonstrate that protein, mRNA, and DNA can successfully be injected into live Aiptasia zygotes to label actin with recombinant Lifeact-eGFP protein; to label nuclei and cell membranes with NLS-eGFP and farnesylated mCherry translated from injected mRNA; and to transiently drive transgene expression from an Aiptasia-specific promoter, respectively, in embryos and larvae. These proof-of-concept approaches pave the way for future functional studies of development and symbiosis establishment in Aiptasia, a powerful model to unravel the molecular mechanisms underlying intracellular coral-algal symbiosis.

RevDate: 2018-11-07

Wang J, Wang J, Liu C, et al (2018)

Identification of Soybean Genes Whose Expression is Affected by the Ensifer fredii HH103 Effector Protein NopP.

International journal of molecular sciences, 19(11): pii:ijms19113438.

In some legume⁻rhizobium symbioses, host specificity is influenced by rhizobial nodulation outer proteins (Nops). However, the genes encoding host proteins that interact with Nops remain unknown. We generated an Ensifer fredii HH103 NopP mutant (HH103ΩNopP), and analyzed the nodule number (NN) and nodule dry weight (NDW) of 10 soybean germplasms inoculated with the wild-type E. fredii HH103 or the mutant strain. An analysis of recombinant inbred lines (RILs) revealed the quantitative trait loci (QTLs) associated with NopP interactions. A soybean genomic region containing two overlapping QTLs was analyzed in greater detail. A transcriptome analysis and qRT-PCR assay were used to identify candidate genes encoding proteins that interact with NopP. In some germplasms, NopP positively and negatively affected the NN and NDW, while NopP had different effects on NN and NDW in other germplasms. The QTL region in chromosome 12 was further analyzed. The expression patterns of candidate genes Glyma.12g031200 and Glyma.12g073000 were determined by qRT-PCR, and were confirmed to be influenced by NopP.

RevDate: 2018-11-07

Compton KK, Hildreth SB, Helm RF, et al (2018)

Sinorhizobium meliloti Chemoreceptor McpV Senses Short-Chain Carboxylates via Direct Binding.

Journal of bacteriology, 200(23): pii:JB.00519-18.

Sinorhizobium meliloti is a soil-dwelling endosymbiont of alfalfa that has eight chemoreceptors to sense environmental stimuli during its free-living state. The functions of two receptors have been characterized, with McpU and McpX serving as general amino acid and quaternary ammonium compound sensors, respectively. Both receptors use a dual Cache (calcium channels and chemotaxis receptors) domain for ligand binding. We identified that the ligand-binding periplasmic region (PR) of McpV contains a single Cache domain. Homology modeling revealed that McpVPR is structurally similar to a sensor domain of a chemoreceptor with unknown function from Anaeromyxobacter dehalogenans, which crystallized with acetate in its binding pocket. We therefore assayed McpV for carboxylate binding and S. meliloti for carboxylate sensing. Differential scanning fluorimetry identified 10 potential ligands for McpVPR Nine of these are monocarboxylates with chain lengths between two and four carbons. We selected seven compounds for capillary assay analysis, which established positive chemotaxis of the S. meliloti wild type, with concentrations of peak attraction at 1 mM for acetate, propionate, pyruvate, and glycolate, and at 100 mM for formate and acetoacetate. Deletion of mcpV or mutation of residues essential for ligand coordination abolished positive chemotaxis to carboxylates. Using microcalorimetry, we determined that dissociation constants of the seven ligands with McpVPR were in the micromolar range. An McpVPR variant with a mutation in the ligand coordination site displayed no binding to isobutyrate or propionate. Of all the carboxylates tested as attractants, only glycolate was detected in alfalfa seed exudates. This work examines the relevance of carboxylates and their sensor to the rhizobium-legume interaction.IMPORTANCE Legumes share a unique association with certain soil-dwelling bacteria known broadly as rhizobia. Through concerted interorganismal communication, a legume allows intracellular infection by its cognate rhizobial species. The plant then forms an organ, the root nodule, dedicated to housing and supplying fixed carbon and nutrients to the bacteria. In return, the engulfed rhizobia, differentiated into bacteroids, fix atmospheric N2 into ammonium for the plant host. This interplay is of great benefit to the cultivation of legumes, such as alfalfa and soybeans, and is initiated by chemotaxis to the host plant. This study on carboxylate chemotaxis contributes to the understanding of rhizobial survival and competition in the rhizosphere and aids the development of commercial inoculants.

RevDate: 2018-11-07
CmpDate: 2018-11-07

Eisenhauer N, Lanoue A, Strecker T, et al (2017)

Root biomass and exudates link plant diversity with soil bacterial and fungal biomass.

Scientific reports, 7:44641 pii:srep44641.

Plant diversity has been shown to determine the composition and functioning of soil biota. Although root-derived organic inputs are discussed as the main drivers of soil communities, experimental evidence is scarce. While there is some evidence that higher root biomass at high plant diversity increases substrate availability for soil biota, several studies have speculated that the quantity and diversity of root inputs into the soil, i.e. though root exudates, drive plant diversity effects on soil biota. Here we used a microcosm experiment to study the role of plant species richness on the biomass of soil bacteria and fungi as well as fungal-to-bacterial ratio via root biomass and root exudates. Plant diversity significantly increased shoot biomass, root biomass, the amount of root exudates, bacterial biomass, and fungal biomass. Fungal biomass increased most with increasing plant diversity resulting in a significant shift in the fungal-to-bacterial biomass ratio at high plant diversity. Fungal biomass increased significantly with plant diversity-induced increases in root biomass and the amount of root exudates. These results suggest that plant diversity enhances soil microbial biomass, particularly soil fungi, by increasing root-derived organic inputs.

RevDate: 2018-11-06

Wiedenmann J, C D'Angelo (2018)

Symbiosis: High-Carb Diet of Reef Corals as Seen from Space.

Current biology : CB, 28(21):R1263-R1265.

High levels of phytoplankton visible in satellite imagery are correlated with an increased uptake of carbon compounds by corals. This suggests that corals rely less on carbon production by photosynthetic symbionts when other resources are plentiful, and that the changes in the acquisition mode of carbon can be inferred by remote-sensing techniques.

RevDate: 2018-11-06
CmpDate: 2018-11-06

Bisch G, Neuvonen MM, Pierce NE, et al (2018)

Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale.

Genome biology and evolution, 10(7):1687-1704.

Many insects rely on bacterial symbionts to supply essential amino acids and vitamins that are deficient in their diets, but metabolic comparisons of closely related gut bacteria in insects with different dietary preferences have not been performed. Here, we demonstrate that herbivorous ants of the genus Dolichoderus from the Peruvian Amazon host bacteria of the family Bartonellaceae, known for establishing chronic or pathogenic infections in mammals. We detected these bacteria in all studied Dolichoderus species, and found that they reside in the midgut wall, that is, the same location as many previously described nutritional endosymbionts of insects. The genomic analysis of four divergent strains infecting different Dolichoderus species revealed genes encoding pathways for nitrogen recycling and biosynthesis of several vitamins and all essential amino acids. In contrast, several biosynthetic pathways have been lost, whereas genes for the import and conversion of histidine and arginine to glutamine have been retained in the genome of a closely related gut bacterium of the carnivorous ant Harpegnathos saltator. The broad biosynthetic repertoire in Bartonellaceae of herbivorous ants resembled that of gut bacteria of honeybees that likewise feed on carbohydrate-rich diets. Taken together, the broad distribution of Bartonellaceae across Dolichoderus ants, their small genome sizes, the specific location within hosts, and the broad biosynthetic capability suggest that these bacteria are nutritional symbionts in herbivorous ants. The results highlight the important role of the host nutritional biology for the genomic evolution of the gut microbiota-and conversely, the importance of the microbiota for the nutrition of hosts.

RevDate: 2018-11-06
CmpDate: 2018-11-06

Faria VG, Martins NE, Schlötterer C, et al (2018)

Readapting to DCV Infection without Wolbachia: Frequency Changes of Drosophila Antiviral Alleles Can Replace Endosymbiont Protection.

Genome biology and evolution, 10(7):1783-1791.

There is now ample evidence that endosymbionts can contribute to host adaptation to environmental challenges. However, how endosymbiont presence affects the adaptive trajectory and outcome of the host is yet largely unexplored. In Drosophila, Wolbachia confers protection to RNA virus infection, an effect that differs between Wolbachia strains and can be targeted by selection. Adaptation to RNA virus infections is mediated by both Wolbachia and the host, raising the question of whether adaptive genetic changes in the host vary with the presence/absence of the endosymbiont. Here, we address this question using a polymorphic D. melanogaster population previously adapted to DCV infection for 35 generations in the presence of Wolbachia, from which we removed the endosymbiont and followed survival over the subsequent 20 generations of infection. After an initial severe drop, survival frequencies upon DCV selection increased significantly, as seen before in the presence of Wolbachia. Whole-genome sequencing, revealed that the major genes involved in the first selection experiment, pastrel and Ubc-E2H, continued to be selected in Wolbachia-free D. melanogaster, with the frequencies of protective alleles being closer to fixation in the absence of Wolbachia. Our results suggest that heterogeneity in Wolbachia infection status may be sufficient to maintain polymorphisms even in the absence of costs.

RevDate: 2018-11-06
CmpDate: 2018-11-06

Timmis K, Jebok F, Molinari G, et al (2017)

Microbiome yarns: microbiome basis of memory,,.

Microbial biotechnology, 10(6):1283-1292.

RevDate: 2018-11-05

Xu Y, Liu F, Li X, et al (2018)

The mycorrhiza-induced maize ZmPt9 gene affects root development and phosphate availability in nonmycorrhizal plant.

Plant signaling & behavior [Epub ahead of print].

The arbuscular mycorrhizal (AM)-induced ZmPt9 gene is an orthologous to some AM-inducible phosphate (Pi) transporter genes involved in Pi-starvation responses. Promoter GFP assay confirmed its transcript was localized surrounding arbuscule in arbuscule-containing cells. But this gene was not an AM fungi-specific gene. Its function in nonmycorrhizal seedlings was verified through phenotypic analysis of ZmPt9-overexpression Arabidopsis. Overexpression of ZmPt9 in Arabidopsis exhibited increased primary root length and lateral root formation. Furthermore, ZmPt9-overexpression Arabidopsis plants contained more phosphorus (P) than that of wild type. The affection of ZmPt9 in nonmycorrhizal Arabidopsis leads to the hypothesis that symbiosis-inducible genes are also involved in root development and Pi accumulation in AM-independent manner.

RevDate: 2018-11-04

Hendrikx T, B Schnabl (2018)

Antimicrobial proteins: intestinal guards to protect against liver disease.

Journal of gastroenterology pii:10.1007/s00535-018-1521-8 [Epub ahead of print].

Alterations of gut microbes play a role in the pathogenesis and progression of many disorders including liver and gastrointestinal diseases. Both qualitative and quantitative changes in gut microbiota have been associated with liver disease. Intestinal dysbiosis can disrupt the integrity of the intestinal barrier leading to pathological bacterial translocation and the initiation of an inflammatory response in the liver. In order to sustain symbiosis and protect from pathological bacterial translocation, antimicrobial proteins (AMPs) such as a-defensins and C-type lectins are expressed in the gastrointestinal tract. In this review, we provide an overview of the role of AMPs in different chronic liver disease such as alcoholic steatohepatitis, non-alcoholic fatty liver disease, and cirrhosis. In addition, potential approaches to modulate the function of AMPs and prevent bacterial translocation are discussed.

RevDate: 2018-11-05

Meng F, Xi L, Liu D, et al (2018)

Effects of light intensity on oxygen distribution, lipid production and biological community of algal-bacterial granules in photo-sequencing batch reactors.

Bioresource technology, 272:473-481 pii:S0960-8524(18)31491-3 [Epub ahead of print].

The effects of light intensity (0-225 µmol m-2 s-1) on oxygen distribution, lipid production and biological community structure of algal-bacterial granules were investigated in six identical photo-sequencing batch reactors (with a dark/light cycle of 12 h/12 h). Typically green algal-bacterial granules could be developed at a light intensity of ≥135 µmol m-2 s-1. The lipid content was significantly increased under higher light intensity, while the percentage of saturated fatty acid methyl esters was remarkably decreased. Results showed that light intensity ≥90 µmol m-2 s-1 yielded enough O2 production from algae, creating aerobic/anoxic zone (0.3-0.6 mg-O2/L) in the core of granules and thus efficient algal-bacterial symbiosis system. Enhanced nitrogen and phosphorus removals were achieved in the reactors with stronger light illumination, probably attributable to the enrichment of ammonia oxidizing bacteria (Comamonadaceae and Nitrosomonadaceae) and algae (Navicula and Stigeoclonium). Illuminance ≥180 µmol m-2 s-1 was found to be unfavorable for Nitrospiraceae.

RevDate: 2018-11-03

Kim TH, Kim D, Gautam A, et al (2018)

CpG-DNA exerts antibacterial effects by protecting immune cells and producing bacteria-reactive antibodies.

Scientific reports, 8(1):16236 pii:10.1038/s41598-018-34722-y.

CpG-DNA activates various immune cells, contributing to the host defense against bacteria. Here, we examined the biological function of CpG-DNA in the production of bacteria-reactive antibodies. The administration of CpG-DNA increased survival in mice following infection with methicillin-resistant S. aureus and protected immune cell populations in the peritoneal cavity, bone marrow, and spleen. CpG-DNA injection likewise increased bacteria-reactive antibodies in the mouse peritoneal fluid and serum, which was dependent on TLR9. B cells isolated from the peritoneal cavity produced bacteria-reactive antibodies in vitro following CpG-DNA administration that enhanced the phagocytic activity of the peritoneal cells. The bacteria-reactive monoclonal antibody enhanced phagocytosis in vitro and protected mice after S. aureus infection. Therefore, we suggest that CpG-DNA enhances the antibacterial activity of the immune system by protecting immune cells and triggering the production of bacteria-reactive antibodies. Consequently, we believe that monoclonal antibodies could aid in the treatment of antibiotic-resistant bacterial infections.

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

Liu YH, Wang ET, Jiao YS, et al (2018)

Symbiotic characteristics of Bradyrhizobium diazoefficiens USDA 110 mutants associated with shrubby sophora (Sophora flavescens) and soybean (Glycine max).

Microbiological research, 214:19-27.

Site-specific insertion plasmid pVO155 was used to knockout the genes involved in the alternation of host range of strain Bradyrhizobium diazoefficiens USDA 110 from its original determinate-nodule-forming host soybean (Glycine max), to promiscuous and indeterminate-nodule-forming shrubby legume sophora (Sophora flavescens). Symbiotic phenotypes of these mutants inoculated to these two legumes, were compared to those infected by wild-type strain USDA 110. Six genes of the total fourteen Tn5 transposon mutated genes were broken using the pVO155 plasmid. Both Tn5 and pVO155-inserted mutants could nodulate S. flavescens with different morphologies of low-efficient indeterminate nodules. One to several rod or irregular bacteroids, containing different contents of poly-β-hydroxybutyrate or polyphosphate were found within the symbiosomes in nodulated cells of S. flavescens infected by the pVO155-inserted mutants. Moreover, none of bacteroids were observed in the pseudonodules of S. flavescens, infected by wild-type strain USDA 110. These mutants had the nodulation ability with soybean but the symbiotic efficiency reduced to diverse extents. These findings enlighten the complicated interactions between rhizobia and legumes, i. e., mutation of genes involved in metabolic pathways, transporters, chemotaxis and mobility could alter the rhizobial entry and development of the bacteroid inside the nodules of a new host legume.

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

Yoshida Y (2018)

The cellular machineries responsible for the division of endosymbiotic organelles.

Journal of plant research, 131(5):727-734.

Chloroplasts (plastids) and mitochondria evolved from endosymbiotic bacteria. These organelles perform vital functions in photosynthetic eukaryotes, such as harvesting and converting energy for use in biological processes. Consistent with their evolutionary origins, plastids and mitochondria proliferate by the binary fission of pre-existing organelles. Here, I review the structures and functions of the supramolecular machineries driving plastid and mitochondrial division, which were discovered and first studied in the primitive red alga Cyanidioschyzon merolae. In the past decade, intact division machineries have been isolated from plastids and mitochondria and examined to investigate their underlying structure and molecular mechanisms. A series of studies has elucidated how these division machineries assemble and transform during the fission of these organelles, and which of the component proteins generate the motive force for their contraction. Plastid- and mitochondrial-division machineries have important similarities in their structures and mechanisms despite sharing no component proteins, implying that these division machineries evolved in parallel. The establishment of these division machineries might have enabled the host eukaryotic ancestor to permanently retain these endosymbiotic organelles by regulating their binary fission and the equal distribution of resources to daughter cells. These findings provide key insights into the establishment of endosymbiotic organelles and have opened new avenues of research into their evolution and mechanisms of proliferation.

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

Takahashi K, Homma K, Dorezal J, et al (2018)

Nitrogen acquisition, net production and allometry of Alnus fruticosa at a young moraine in Koryto Glacier Valley, Kamchatka, Russian Far East.

Journal of plant research, 131(5):759-769.

Alders (Alnus spp.) often dominate at nutrient-poor sites by symbiotic relations with atmospheric nitrogen-fixing bacteria. However, little is known about quantitative relationships between root nodule as a nitrogen acquisition organ and leaf as a carbon acquisition organ. To examine carbon allocation, nitrogen acquisition and net production in nutrient-poor conditions, we examined allocation patterns among organs of shrub Alnus fruticosa at a young 80-year-old moraine in Kamchatka. Slopes of double-log allometric equations were significantly smaller than 1.0 for the root mass, leaf mass and root nodule mass against stem mass, and for the root nodule mass against root mass, indicating that smaller individuals invested disproportionally more biomass into resource-acquiring leaf and root tissues than to supportive tissues compared to older individuals. The slope of allometric equation of root depth against stem height was 0.542, indicating that smaller/younger individuals allocate disproportionally more biomass into root length growth than stem height growth. On the contrary, the root nodule mass isometrically scaled to leaf mass. The whole-plant nitrogen content also isometrically scaled to root nodule mass, indicating that a certain ratio of nitrogen acquisition depended on root nodules, irrespective of plant size. Although the net production per plant increased with the increase in stem mass, the slope of the double-log regression was smaller than 1.0. On the contrary, the net production per plant isometrically increased with leaf mass, root nodule mass and leaf nitrogen content per plant. Since the leaf mass isometrically scaled to root nodule mass, growth of each individual occurred at the leaves and root nodules in a coordinated manner. It is suggested that their isometric increase contributes to the increase in net production per plant for A. fruticosa in nutrient-poor conditions.

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

Michalik A, Szwedo J, Stroiński A, et al (2018)

Symbiotic cornucopia of the monophagous planthopper Ommatidiotus dissimilis (Fallén, 1806) (Hemiptera: Fulgoromorpha: Caliscelidae).

Protoplasma, 255(5):1317-1329.

In contrast to Cicadomorpha, in which numerous symbiotic bacteria have been identified and characterized, the symbionts of fulgoromorphans are poorly known. Here, we present the results of histological, ultrastructural, and molecular analyses of the symbiotic system of the planthopper Ommatidiotus dissimilis. Amplification, cloning, and sequencing of bacterial 16S RNA genes have revealed that O. dissimilis is host to five types of bacteria. Apart from bacteria Sulcia and Vidania, which are regarded as ancestral symbionts of Fulgoromorpha, three additional types of bacteria belonging to the genera Sodalis, Wolbachia, and Rickettsia have been detected. Histological and ultrastructural investigations have shown that bacteria Sulcia, Vidania, and Sodalis house separate bacteriocytes, whereas bacteria Wolbachia and Rickettsia are dispersed within various insect tissue. Additionally, bacteria belonging to the genus Vidania occupy the bacteriome localized in the lumen of the hindgut. Both molecular and microscopic analyses have revealed that all the symbionts are transovarially transmitted between generations.

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

Almeida RP, R Stouthamer (2018)

Phylogeny of the Trichogramma endosymbiont Wolbachia, an alpha-proteobacteria (Rickettsiae).

Brazilian journal of biology = Revista brasleira de biologia, 78(3):421-428.

Wolbachia (Hertig) endosymbionts are extensively studied in a wide range of organisms and are known to be transmitted through the egg cytoplasm to the offsping. Wolbachia may cause several types of reproductive modifications in arthropods. In Trichogramma species, parthenogenesis-inducing Wolbachia bacteria allow females wasps to produce daughters from unfertilized eggs and these bacteria are present in at least 9% of all Trichogramma species. Phylogenetic studies have led to the subdivision of the Wolbachia clade in five supergroups (A, B, C, D and E) and Wolbachia from Trichogramma belong to supergroup B. Here, using the wsp gene, four groups of Wolbachia that infect Trichogramma species were distinguished and the addition of a new group "Ato" was suggested due to the addition of Wolbachia from Trichogramma atopovirilia (Oatman and Platner). Specific primers were designed and tested for the "Ato" group. Seventy-five percent of all evaluated Wolbachia strains from Trichogramma fell within "Sib" group.

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

Rivilla R, Martín M, J Lloret (2017)

What makes rhizobia rhizosphere colonizers?.

Environmental microbiology, 19(11):4379-4381.

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

Moissl-Eichinger C, Pausan M, Taffner J, et al (2018)

Archaea Are Interactive Components of Complex Microbiomes.

Trends in microbiology, 26(1):70-85.

Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.

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

Wu YY, Westwater C, Xiao E, et al (2018)

Establishment of oral bacterial communities in germ-free mice and the influence of recipient age.

Molecular oral microbiology, 33(1):38-46.

The acquisition of the oral microbiome is a complex process. We examined how the timing of microbial exposure alters bacterial colonization of the tooth surface. Germ-free mice were conventionalized by exposure to specific pathogen-free (SPF) mice to acquire a commensal microbiome over three distinct 4-week periods, 0-4 weeks of age (Conv0-4w), 4-8 weeks (Conv4-8w), or 8-12 weeks (Conv8-12w). Bacterial DNA was extracted from the tooth surface and analyzed by 16S rDNA sequencing. Total bacteria and inflammatory cytokine expression in gingiva were determined by quantitative real-time polymerase chain reaction. After co-housing with SPF mice, Conv0-4w and Conv4-8w mice had low bacterial diversity, whereas Conv8-12w mice had high bacterial diversity that was similar to that of SPF donor mice, as determined by both operational taxonomic units and the Shannon Index. Cluster analysis with unweighted Unifrac distance also supported these trends. This was surprising as the amount of maturation time, 4 weeks, was equal in all conventionalized mice and tooth eruption was largely completed by 4 weeks. This suggests that host factors that occur after tooth eruption have a significant effect on the microbial tooth colonization.

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

Yuan SL, Li R, Chen HF, et al (2017)

RNA-Seq analysis of nodule development at five different developmental stages of soybean (Glycine max) inoculated with Bradyrhizobium japonicum strain 113-2.

Scientific reports, 7:42248 pii:srep42248.

Nodule development directly affects nitrogen fixation efficiency during soybean growth. Although abundant genome-based information related to nodule development has been released and some studies have reported the molecular mechanisms that regulate nodule development, information on the way nodule genes operate in nodule development at different developmental stages of soybean is limited. In this report, notably different nodulation phenotypes in soybean roots inoculated with Bradyrhizobium japonicum strain 113-2 at five developmental stages (branching stage, flowering stage, fruiting stage, pod stage and harvest stage) were shown, and the expression of nodule genes at these five stages was assessed quantitatively using RNA-Seq. Ten comparisons were made between these developmental periods, and their differentially expressed genes were analysed. Some important genes were identified, primarily encoding symbiotic nitrogen fixation-related proteins, cysteine proteases, cystatins and cysteine-rich proteins, as well as proteins involving plant-pathogen interactions. There were no significant shifts in the distribution of most GO functional annotation terms and KEGG pathway enrichment terms between these five development stages. A cystatin Glyma18g12240 was firstly identified from our RNA-seq, and was likely to promote nodulation and delay nodule senescence. This study provides molecular material for further investigations into the mechanisms of nitrogen fixation at different soybean developmental stages.

RevDate: 2018-11-02

Apremont V, Cambon-Bonavita MA, Cueff-Gauchard V, et al (2018)

Gill chamber and gut microbial communities of the hydrothermal shrimp Rimicaris chacei Williams and Rona 1986: A possible symbiosis.

PloS one, 13(11):e0206084 pii:PONE-D-18-11674.

Rimicaris chacei Williams and Rona 1986, formerly named as Chorocaris chacei, is a caridean shrimp living in deep-sea hydrothermal ecosystems. This shrimp is endemic to the Mid Atlantic Ridge (MAR) and lives at the periphery of aggregates of its well-known congeneric R. exoculata Williams and Rona 1986. Contrasting with the very dense and mobile clusters formed by R. exoculata, R. chacei lives in small groups of several individuals that are not very mobile. Although devoid of the characteristic hypertrophied cephalothorax of R. exoculata, which harbors the ectosymbionts, a microbial community has also been reported in the cephalothorax of R. chacei. Previous data on morphology, behavior and isotopic values indicate a diet based on a combination of feeding on its epibiotic bacteria and scavenging or occasional predation. In this study, our objective was to describe, for the first time, the distribution, morphology and phylogeny of the microbial communities associated with R. chacei. This species is significantly less studied than R. exoculata, but nevertheless represents the only other known example of symbiosis in crustaceans of MAR hydrothermal vent sites. Microbial communities have been observed at the same locations as in R. exoculata (mouthparts, branchiostegites and digestive tract). However, in R. chacei, the surfaces occupied by the bacteria are smaller. The main lineages are affiliated to Epsilon and Gammaproteobacteria in the cephalothorax and to Deferribacteres, Mollicutes, Epsilon and Gammaproteobacteria in the digestive tract. Comparison with the well-described bacterial communities of R. exoculata and hypotheses about the role of these communities in R. chacei are discussed.

RevDate: 2018-11-02

Kreisinger J, Schmiedová L, Petrželková A, et al (2018)

Fecal microbiota associated with phytohaemagglutinin-induced immune response in nestlings of a passerine bird.

Ecology and evolution, 8(19):9793-9802 pii:ECE34454.

The vertebrate gastrointestinal tract is inhabited by a diverse community of bacteria, the so-called gut microbiota (GM). Research on captive mammalian models has revealed tight mutual interactions between immune functions and GM. However, our knowledge of GM versus immune system interactions in wild populations and nonmammalian species remains poor. Here, we focus on the association between GM community structure and immune response measured via the phytohaemagglutinin (PHA) skin swelling test in 12-day-old nestlings of a passerine bird, the barn swallow (Hirundo rustica). The PHA test, a widely used method in field ecoimmunology, assesses cell-mediated immunity. GM structure was inferred based on high-throughput 16S rRNA sequencing of microbial communities in fecal samples. We did not find any association between PHA response and GM diversity; however, our data revealed that the intensity of PHA response was correlated with differences in GM composition at the whole-community level. Ten bacterial operational taxonomic units corresponding to both putative commensal and pathogens were identified as drivers of the compositional variation. In conclusion, our study suggests existence of GM versus immune system interactions in a free-living nonmammalian species, which corresponds with previous research on captive vertebrates.

RevDate: 2018-11-02

Piculell BJ, Eckhardt LG, JD Hoeksema (2018)

Genetically determined fungal pathogen tolerance and soil variation influence ectomycorrhizal traits of loblolly pine.

Ecology and evolution, 8(19):9646-9656 pii:ECE34355.

Selection on genetically correlated traits within species can create indirect effects on one trait by selection on another. The consequences of these trait correlations are of interest because they may influence how suites of traits within species evolve under differing selection pressures, both natural and artificial. By utilizing genetic families of loblolly pine either tolerant (t) or susceptible (s) to two different suites of pathogenic fungi responsible for causing either pine decline or fusiform rust disease, we investigated trait variation and trait correlations within loblolly pine (Pinus taeda L.) by determining how ectomycorrhizal (EM) colonization relates to pathogen susceptibility. We detected interactions between susceptibility to pathogenic fungi and soil inoculation source on loblolly pine compatibility with the EM fungi Thelephora, and on relative growth rate of loblolly pine. Additionally, we detected spatial variation in the loblolly pine-EM fungi interaction, and found that variation in colonization rates by some members of the EM community is not dictated by genetic variation in the host plant but rather soil inoculation source alone. The work presented here illustrates the potential for indirect selection on compatibility with symbiotic EM fungi as a result of selection for resistance to fungal pathogens. Additionally, we present evidence that the host plant does not have a single "mycorrhizal trait" governing interactions with all EM fungi, but rather that it can interact with different fungal taxa independently. Synthesis. An understanding of the genetic architecture of essential traits in focal species is crucial if we are to anticipate and manage the results of natural and artificial selection. As demonstrated here, an essential but often overlooked symbiosis (that between plants and mycorrhizal fungi) may be indirectly influenced by directed selection on the host plant.

RevDate: 2018-11-02

Conradi M, Bandera E, Mudrova SV, et al (2018)

Five new coexisting species of copepod crustaceans of the genus Spaniomolgus (Poecilostomatoida: Rhynchomolgidae), symbionts of the stony coral Stylophorapistillata (Scleractinia).


Spaniomolgus is a symbiotic genus of copepods of the poecilostomatoid family Rhynchomolgidae and is known to be associated with shallow-water reef-building hermatypic corals. Three species of this genus were previously found only in washings of Acropora and Stylophora in northern Madagascar. Four coral morphotypes of Stylophorapistillata (Pocilloporidae) were collected by SCUBA at 1 to 28 m depth in five sites in the Saudi Arabian Red Sea in 2013. Copepods found on these colonies were studied using light, confocal and scanning electron microscopy. Five new, and one known, species of the genus Spaniomolgus were discovered in washings and inside the galls of the hermatypic coral S.pistillata. The description of these new species (Spaniomolgusglobussp. n., S.stylophorussp. n., S.dentatussp. n., S.maculatussp. n., and S.acutussp. n.) and a key for the identification of all of its congeners is provided herein.

RevDate: 2018-11-02

Tso GHW, Reales-Calderon JA, Tan ASM, et al (2018)

Experimental evolution of a fungal pathogen into a gut symbiont.

Science (New York, N.Y.), 362(6414):589-595.

Gut microbes live in symbiosis with their hosts, but how mutualistic animal-microbe interactions emerge is not understood. By adaptively evolving the opportunistic fungal pathogen Candida albicans in the mouse gastrointestinal tract, we selected strains that not only had lost their main virulence program but also protected their new hosts against a variety of systemic infections. This protection was independent of adaptive immunity, arose as early as a single day postpriming, was dependent on increased innate cytokine responses, and was thus reminiscent of "trained immunity." Because both the microbe and its new host gain some advantages from their interaction, this experimental system might allow direct study of the evolutionary forces that govern the emergence of mutualism between a mammal and a fungus.

RevDate: 2018-11-02

Ankati S, Rani TS, AR Podile (2018)

Partner-triggered proteome changes in the cell wall of Bacillus sonorensis and roots of groundnut benefit each other.

Microbiological research, 217:91-100.

Plant growth promoting rhizobacteria (PGPR) promote plant growth and activate defense response against phytopathogens. At the subcellular level plant-PGPR interaction is less understood, which would be essential for future improvement(s) of PGPR formulations. In a rigorous screening process, that also involved efficient PGPR strains, Bacillus sonorensis RS4 was selected to study partner-triggered interactions. The potential of B. sonorensis RS4 to improve growth of groundnut, efficiency to colonize roots, and influence on root topology was assessed. Twenty four cell wall proteins of B. sonorensis RS4 [in presence of groundnut root exudates (REs)], and 22 groundnut root proteins (in RS4-bacterized plants) were differentially expressed. The alterations in cell wall proteins of B. sonorensis RS4 were primarily related to the amino acids synthesis, chemotaxis, antioxidant-metabolism, carbohydrate metabolism, transporters, and antibiosis-related secondary metabolites. Root proteins that were differentially expressed during the interaction may be involved in plant growth, defense responses, and in transportation. The changes in B. sonorensis RS4 cell wall proteome and groundnut root proteome, suggest that at least a part of the proteome changes triggered by each of the partners appear to play a significant role in helping each other akin to symbiosis.

RevDate: 2018-11-02

Ying H, Cooke I, Sprungala S, et al (2018)

Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages.

Genome biology, 19(1):175 pii:10.1186/s13059-018-1552-8.

BACKGROUND: Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear.

RESULTS: Draft genome assemblies and annotations were generated for three coral species: Galaxea fascicularis (Complexa), Fungia sp., and Goniastrea aspera (Robusta). Whilst phylogenetic analyses strongly support a deep split between Complexa and Robusta, synteny analyses reveal a high level of gene order conservation between all corals, but not between corals and sea anemones or between sea anemones. HOX-related gene clusters are, however, well preserved across all of these combinations. Differences between species are apparent in the distribution and numbers of protein domains and an apparent correlation between number of HSP20 proteins and stress tolerance. Uniquely amongst animals, a complete histidine biosynthesis pathway is present in robust corals but not in complex corals or sea anemones. This pathway appears to be ancestral, and its retention in the robust coral lineage has important implications for coral nutrition and symbiosis.

CONCLUSIONS: The availability of three new coral genomes enabled recognition of a de novo histidine biosynthesis pathway in robust corals which is only the second identified biosynthetic difference between corals. These datasets provide a platform for understanding many aspects of coral biology, particularly the interactions of corals with their endosymbionts.

RevDate: 2018-11-02
CmpDate: 2018-11-02

Harumoto T, B Lemaitre (2018)

Male-killing toxin in a bacterial symbiont of Drosophila.

Nature, 557(7704):252-255.

Several lineages of symbiotic bacteria in insects selfishly manipulate host reproduction to spread in a population 1 , often by distorting host sex ratios. Spiroplasma poulsonii2,3 is a helical and motile, Gram-positive symbiotic bacterium that resides in a wide range of Drosophila species 4 . A notable feature of S. poulsonii is male killing, whereby the sons of infected female hosts are selectively killed during development1,2. Although male killing caused by S. poulsonii has been studied since the 1950s, its underlying mechanism is unknown. Here we identify an S. poulsonii protein, designated Spaid, whose expression induces male killing. Overexpression of Spaid in D. melanogaster kills males but not females, and induces massive apoptosis and neural defects, recapitulating the pathology observed in S. poulsonii-infected male embryos5-11. Our data suggest that Spaid targets the dosage compensation machinery on the male X chromosome to mediate its effects. Spaid contains ankyrin repeats and a deubiquitinase domain, which are required for its subcellular localization and activity. Moreover, we found a laboratory mutant strain of S. poulsonii with reduced male-killing ability and a large deletion in the spaid locus. Our study has uncovered a bacterial protein that affects host cellular machinery in a sex-specific way, which is likely to be the long-searched-for factor responsible for S. poulsonii-induced male killing.

RevDate: 2018-11-02
CmpDate: 2018-11-02

Howe M, Keefover-Ring K, KF Raffa (2018)

Pine Engravers Carry Bacterial Communities Whose Members Reduce Concentrations of Host Monoterpenes With Variable Degrees of Redundancy, Specificity, and Capability.

Environmental entomology, 47(3):638-645.

Bark beetles are eruptive forest insects that have the potential to cause landscape level mortality to conifer forests. The pine engraver, Ips pini (Say) (Coleoptera: Curculionidae), is the predominant pest of mature red pine (Pinus resinosa Aiton) plantations throughout the Great Lakes region of North America. Pine engraver attack elicits a localized response by host trees in which concentrations of terpenes rapidly exceed the tolerance levels of beetles and their fungal associates. We considered how bacterial associates degrade these toxins from the perspective of the symbiont communities of individual beetles. We demonstrate that 1) most pine engravers harbor bacterial communities that reduce monoterpene concentrations in vivo; 2) several individual bacterial isolates can reduce monoterpenes even at high concentrations; and 3) bacteria isolated from pine engravers are similar to those found in other bark beetles. Bacteria isolated from pine engravers decreased concentrations of (-)-α-pinene, myrcene, and 3-carene. Most beetles carried at least one bacterial isolate that reduced concentrations of at least one monoterpene. Different bacteria vary in the uppermost concentrations at which they can degrade monoterpenes. The community of bacteria associated with an individual beetle appears to have some manner of functional redundancy that could collectively increase the likelihood of successful host colonization.

RevDate: 2018-11-02
CmpDate: 2018-11-02

Ludvigsen J, Amdam GV, Rudi K, et al (2018)

Detection and Characterization of Streptomycin Resistance (strA-strB) in a Honeybee Gut Symbiont (Snodgrassella alvi) and the Associated Risk of Antibiotic Resistance Transfer.

Microbial ecology, 76(3):588-591.

Use of antibiotics in medicine and farming contributes to increasing numbers of antibiotic-resistant bacteria in diverse environments. The ability of antibiotic resistance genes (ARG) to transfer between bacteria genera contributes to this spread. It is difficult to directly link antibiotic exposure to the spread of ARG in a natural environment where environmental settings and study populations cannot be fully controlled. We used managed honeybees in environments with contrasting streptomycin exposure (USA: high exposure, Norway: low exposure) and mapped the prevalence and spread of transferrable streptomycin resistance genes. We found a high prevalence of strA-strB genes in the USA compared to Norway with 17/90 and 1/90 positive samples, respectively (p < 0.00007). We identified strA-strB genes on a transferrable transposon Tn5393 in the honeybee gut symbiont Snodgrassella alvi. Such transfer of resistance genes increases the risk of the spread to new environments as honeybees are moved to new pollination sites.

RevDate: 2018-11-02
CmpDate: 2018-11-02

Carrasco D, Desurmont GA, Laplanche D, et al (2018)

With or without you: Effects of the concurrent range expansion of an herbivore and its natural enemy on native species interactions.

Global change biology, 24(2):631-643.

Global climatic changes may lead to the arrival of multiple range-expanding species from different trophic levels into new habitats, either simultaneously or in quick succession, potentially causing the introduction of manifold novel interactions into native food webs. Unraveling the complex biotic interactions between native and range-expanding species is critical to understand the impact of climate change on community ecology, but experimental evidence is lacking. In a series of laboratory experiments that simulated direct and indirect species interactions, we investigated the effects of the concurrent arrival of a range-expanding insect herbivore in Europe, Spodoptera littoralis, and its associated parasitoid Microplitis rufiventris, on the native herbivore Mamestra brassicae, and its associated parasitoid Microplitis mediator, when co-occurring on a native plant, Brassica rapa. Overall, direct interactions between the herbivores were beneficial for the exotic herbivore (higher pupal weight than the native herbivore), and negative for the native herbivore (higher mortality than the exotic herbivore). At the third trophic level, both parasitoids were unable to parasitize the herbivore they did not coexist with, but the presence of the exotic parasitoid still negatively affected the native herbivore (increased mortality) and the native parasitoid (decreased parasitism rate), through failed parasitism attempts and interference effects. Our results suggest different interaction scenarios depending on whether S. littoralis and its parasitoid arrive to the native tritrophic system separately or concurrently, as the negative effects associated with the presence of the parasitoid were dependent on the presence of the exotic herbivore. These findings illustrate the complexity and interconnectedness of multitrophic changes resulting from concurrent species arrival to new environments, and the need for integrating the ecological effects of such arrivals into the general theoretical framework of global invasion patterns driven by climatic change.

RevDate: 2018-11-02
CmpDate: 2018-11-02

Weigel BL, PM Erwin (2017)

Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila.

Scientific reports, 7:43247 pii:srep43247.

Microbial symbionts in sponges are ubiquitous, forming complex and highly diverse host-specific communities. Conspecific sponges display remarkable stability in their symbiont communities, both spatially and temporally, yet extreme fluctuations in environmental factors can cause shifts in host-symbiont associations. We previously demonstrated that the marine sponge Hymeniacidon heliophila displayed significant community-level differences in microbial symbiont diversity, structure and composition when sampled from intertidal and subtidal environments. Here, we conducted a 70-day reciprocal transplant experiment to directly test the effect of tidal exposure on the microbiome of H. heliophila, using next-generation Illumina sequencing of 16S rRNA gene sequences to characterize symbiont communities. While sponges transplanted between habitats displayed shifts in microbial communities after 70 days, temporal variation was the dominant factor affecting microbial community composition. Further, we identified core symbionts that persisted across these spatio-temporal scales and used a metagenomic approach to show that these dominant members of the microbiome of H. heliophila represent nitrogen cycling taxa that have the potential to contribute to a diverse array of nitrogen transformations in the sponge holobiont. Together, these results indicate that despite moderate spatio-temporal shifts in symbiont composition, core symbiont functions (e.g. nitrogen cycling) can be maintained in sponge microbiomes through functional redundancy.

RevDate: 2018-11-02
CmpDate: 2018-11-02

Rayner S, Bruhn S, Vallhov H, et al (2017)

Identification of small RNAs in extracellular vesicles from the commensal yeast Malassezia sympodialis.

Scientific reports, 7:39742 pii:srep39742.

Malassezia is the dominant fungus in the human skin mycobiome and is associated with common skin disorders including atopic eczema (AE)/dermatitis. Recently, it was found that Malassezia sympodialis secretes nanosized exosome-like vesicles, designated MalaEx, that carry allergens and can induce inflammatory cytokine responses. Extracellular vesicles from different cell-types including fungi have been found to deliver functional RNAs to recipient cells. In this study we assessed the presence of small RNAs in MalaEx and addressed if the levels of these RNAs differ when M. sympodialis is cultured at normal human skin pH versus the elevated pH present on the skin of patients with AE. The total number and the protein concentration of the released MalaEx harvested after 48 h culture did not differ significantly between the two pH conditions nor did the size of the vesicles. From small RNA sequence data, we identified a set of reads with well-defined start and stop positions, in a length range of 16 to 22 nucleotides consistently present in the MalaEx. The levels of small RNAs were not significantly differentially expressed between the two different pH conditions indicating that they are not influenced by the elevated pH level observed on the AE skin.

RevDate: 2018-11-01

Parasyri A, Papazi A, Stamatis N, et al (2018)

Lichen as Micro-Ecosystem: Extremophilic Behavior with Astrobiotechnological Applications.

Astrobiology [Epub ahead of print].

This work demonstrates the tolerance of lichen Pleurosticta acetabulum under extreme conditions similar to those encountered in extraterrestrial environments. Specifically, the impact of three extreme Mars-like conditions-complete dehydration, extremely low temperature (-196°C/77K), and oxygen depletion-on lichens was investigated. The symbiosis of mycobiont and photobiont partners creates a micro-ecosystem that ensures viability of both symbiotic partners under prolonged desiccation and extremely low temperatures without any cultivation care. Changes in the molecular structure and function of the photosynthetic apparatus, in the level of chlorophylls, polyamines, fatty acids, carbohydrates, ergosterol, efflux of K+, and DNA methylation ensure the ecological integrity of the system and offer resistance of lichens to above-mentioned extreme environmental conditions. For the first time, we also demonstrate that the unprecedented polyextremophilic characteristic of lichens could be linked to biotechnological applications, following exposure to these extreme conditions, such that their ability to produce a high yield of hydrogen was unchanged. All these support that lichens are (a) ideal model systems for a space mission to inhabit other planets, supporting also the aspect that the panspermia theory could be extended to incorporate in the traveling entities not only single organisms but micro-ecosystems like lichens, and (b) ideal model systems for astrobiotechnological applications (hydrogen production), such as in the development of bioregeneration systems for extraterrestrial environments.

RevDate: 2018-11-01

Cunning R, Bay RA, Gillette P, et al (2018)

Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution.

Scientific reports, 8(1):16134 pii:10.1038/s41598-018-34459-8.

Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral 'core' genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.

RevDate: 2018-11-01

Russell SL, McCartney E, CM Cavanaugh (2018)

Transmission strategies in a chemosynthetic symbiosis: detection and quantification of symbionts in host tissues and their environment.

Proceedings. Biological sciences, 285(1890): pii:rspb.2018.2157.

Transmission of bacteria vertically through host tissues ensures offspring acquire symbionts; however, horizontal transmission is an effective strategy for many associations and plays a role in some vertically transmitted symbioses. The bivalve Solemya velum and its gammaproteobacterial chemosynthetic symbionts exhibit evolutionary evidence of both transmission modes, but the dominant strategy on an ecological time scale is unknown. To address this, a specific primer set was developed and validated for the S. velum symbiont using a novel workflow called specific marker design (SMD). Symbionts were quantified in spawned eggs and sediment and seawater samples from S. velum habitats with qPCR. Each egg was estimated to contain 50-100 symbiont genomes. By contrast, symbiont DNA was found at low abundance/occurrence in sediment and seawater, often co-occurring with host mitochondrial DNA, obscuring its origin. To ascertain when eggs become infected, histological sections of S. velum tissues were labelled for symbiont 16S rRNA via in situ hybridization. This revealed symbionts in the ovary walls and mature oocytes, suggesting association in late oogenesis. These data support the hypothesis that S. velum symbionts are vertically transmitted every host generation, thus genetic signatures of horizontal transmission are driven by ecologically infrequent events. This knowledge furthers our understanding of vertical and horizontal mode integration and provides insights across animal-bacterial chemosynthetic symbioses.

RevDate: 2018-11-01
CmpDate: 2018-11-01

Van Oosten MJ, Di Stasio E, Cirillo V, et al (2018)

Root inoculation with Azotobacter chroococcum 76A enhances tomato plants adaptation to salt stress under low N conditions.

BMC plant biology, 18(1):205 pii:10.1186/s12870-018-1411-5.

BACKGROUND: The emerging roles of rhizobacteria in improving plant nutrition and stress protection have great potential for sustainable use in saline soils. We evaluated the function of the salt-tolerant strain Azotobacter chroococcum 76A as stress protectant in an important horticultural crop, tomato. Specifically we hypothesized that treatment of tomato plants with A. chroococcum 76A could improve plant performance under salinity stress and sub-optimal nutrient regimen.

RESULTS: Inoculation of Micro Tom tomato plants with A. chroococcum 76A increased numerous growth parameters and also conferred protective effects under both moderate (50 mM NaCl) and severe (100 mM NaCl) salt stresses. These benefits were mostly observed under reduced nutrient regimen and were less appreciable in optimal nitrogen conditions. Therefore, the efficiency of A. chroococcum 76A was found to be dependent on the nutrient status of the rhizosphere. The expression profiles of LEA genes indicated that A. chroococcum 76A treated plants were more responsive to stress stimuli when compared to untreated controls. However, transcript levels of key nitrogen assimilation genes revealed that the optimal nitrogen regimen, in combination with the strain A. chroococcum 76A, may have saturated plant's ability to assimilate nitrogen.

CONCLUSIONS: Roots inoculation with A. chroococcum 76A tomato promoted tomato plant growth, stress tolerance and nutrient assimilation efficiency under moderate and severe salinity. Inoculation with beneficial bacteria such as A. chroococcum 76A may be an ideal solution for low-input systems, where environmental constraints and limited chemical fertilization may affect the potential yield.

RevDate: 2018-11-01
CmpDate: 2018-11-01

Rillig MC, Lehmann A, Lehmann J, et al (2018)

Soil Biodiversity Effects from Field to Fork.

Trends in plant science, 23(1):17-24.

Our knowledge of soil biodiversity in agriculture in general is currently increasing rapidly. However, almost all studies have stopped with the quantification of soil biodiversity effects on crops at harvest time, ignoring subsequent processes along the agrifood chain until food arrives on our plates. Here we develop a conceptual framework for the study of such postharvest effects. We present the main mechanisms (direct and indirect) via which soil biodiversity can influence crop quality aspects and give examples of how effects at harvest time may become attenuated through postharvest operations and how biodiversity may also affect some of these operations (i.e., storage) themselves. Future research with a broader focus has the potential to unveil how soil biodiversity may benefit from what ends up on our forks.

RevDate: 2018-10-31

Rey T, André O, Nars A, et al (2018)

Lipo-chitooligosaccharide signalling blocks a rapid pathogen-induced ROS burst without impeding immunity.

The New phytologist [Epub ahead of print].

Molecular signals released by microbes at the surface of plant roots and leaves largely determine host responses, notably by triggering either immunity or symbiosis. How these signalling pathways cross-talk upon coincident perception of pathogens and symbionts is poorly described in plants forming symbiosis. Nitrogen fixing symbiotic Rhizobia spp. and Arbuscular Mycorrhizal fungi produce Lipo-chitooligosaccharides (LCOs) to initiate host symbiotic programs. In Medicago truncatula roots, the perception of LCOs leads to reduced efflux of Reactive Oxygen Species (ROS). In contrast, pathogen perception generally triggers a strong ROS burst and activates defence gene expression. Here we show that incubation of M. truncatula seedlings with culture filtrate (CF) of the legume pathogen Aphanomyces euteiches alone or simultaneously with Sinorhizobium meliloti LCOs, resulted in a strong ROS release. However, this response was completely inhibited if CF was added after pre-incubation of seedlings with LCOs. In contrast, expression of immunity-associated genes in response to CF and disease resistance to A. euteiches remained unaffected by LCO treatment of M. truncatula roots. Our findings suggest that symbiotic plants evolved ROS inhibition response to LCOs to facilitate early steps of symbiosis whilst maintaining parallel defence mechanisms toward pathogens. This article is protected by copyright. All rights reserved.

RevDate: 2018-10-31

Loizia P, Neofytou N, AA Zorpas (2018)

The concept of circular economy strategy in food waste management for the optimization of energy production through anaerobic digestion.

Environmental science and pollution research international pii:10.1007/s11356-018-3519-4 [Epub ahead of print].

Food waste management (FWM) is considered to be an extremely important social issue besides an environmental one. Worldwide, it is estimated that 1.3 billion t/year of foods are disposed of in landfills (including edible and inedible foods). Moreover, FAO indicated that if food waste (FW) was a country, it could be the 3rd biggest CO2 producer after China and the USA with more than 3.5-4.2 billion of t equivalence CO2. Each citizen in the entire EU produces approximately 179 kg/year FW equal more or less with 600 €/year. This paper focuses on the concept of circular economy (CE) and how can we optimize and improve the production of biogas from UASB-R (upflow anaerobic sludge blanket reactor) using FW and natural minerals (clinoptilolite). The study was elaborated through laboratory scale experiments using different mixtures of FW, liquid waste from slaughterhouse (LWS), and natural clinoptilolite (Cli). The amount of biogas produced and the methane content of biogas were used as indicators in order to monitor and asses the performance of the anaerobic digester. The results of the present study were encouraging towards the use of FW in existing anaerobic treatment plants, suggesting selective collection at source of FW, diversion from landfills, and use as a secondary resource for energy recovery through a transition to a CE. The results indicate that the use of FW with zeolite duplicates the production of CH4 within the same days of production compared with the control sample.

RevDate: 2018-10-31
CmpDate: 2018-10-31

Pavlidi N, Gioti A, Wybouw N, et al (2017)

Transcriptomic responses of the olive fruit fly Bactrocera oleae and its symbiont Candidatus Erwinia dacicola to olive feeding.

Scientific reports, 7:42633 pii:srep42633.

The olive fruit fly, Bactrocera oleae, is the most destructive pest of olive orchards worldwide. The monophagous larva has the unique capability of feeding on olive mesocarp, coping with high levels of phenolic compounds and utilizing non-hydrolyzed proteins present, particularly in the unripe, green olives. On the molecular level, the interaction between B. oleae and olives has not been investigated as yet. Nevertheless, it has been associated with the gut obligate symbiotic bacterium Candidatus Erwinia dacicola. Here, we used a B.oleae microarray to analyze the gene expression of larvae during their development in artificial diet, unripe (green) and ripe (black) olives. The expression profiles of Ca. E. dacicola were analyzed in parallel, using the Illumina platform. Several genes were found overexpressed in the olive fly larvae when feeding in green olives. Among these, a number of genes encoding detoxification and digestive enzymes, indicating a potential association with the ability of B. oleae to cope with green olives. In addition, a number of biological processes seem to be activated in Ca. E. dacicola during the development of larvae in olives, with the most notable being the activation of amino-acid metabolism.

RevDate: 2018-10-30
CmpDate: 2018-10-30

Kamani J, Harrus S, Nachum-Biala Y, et al (2018)

Pathogenic and endosymbiont apicomplexans in Ctenocephalides felis (Siphonaptera: Pulicidae) from cats in Jerusalem, Israel.

Comparative immunology, microbiology and infectious diseases, 57:29-33.

This study was conducted to determine the prevalence of pathogenic and endosymbiont apicomplexans in the cat flea, Ctenocephalides felis (Bouché) infesting 185 stray cats in Jerusalem, Israel using PCR assay and sequencing approach. Two pathogens, Hepatozoon felis and Babesia vogeli and an endosymbiont Steinina ctenocephali were detected in 1.9%, 0.2% and 5.8% of 685 C. felis evaluated respectively. There was a significant association (p < 0.05) between the prevalence of H. felis and the sex of cats hosting the fleas as well as the season of sampling but not for age or health status of the cats or sex of the fleas tested. Prevalence of S. ctenocephali was significantly (p < 0.001) associated with season, being higher in the warm season. This report represents the first molecular detection of S. ctenocephali in C. felis. Further studies to determine the potential role of C. felis in the epidemiology of H. felis and B. vogeli are warranted.

RevDate: 2018-10-30
CmpDate: 2018-10-30

Setsungnern A, Treesubsuntorn C, P Thiravetyan (2018)

Chlorophytum comosum-bacteria interactions for airborne benzene remediation: Effect of native endophytic Enterobacter sp. EN2 inoculation and blue-red LED light.

Plant physiology and biochemistry : PPB, 130:181-191.

This study was performed to determine the effect of plant-endophytic Enterobacter sp. EN2 interactions and blue-red LED light conditions on gaseous benzene removal by plants. It was found that under consecutive benzene fumigation for three cycles (18 days), inoculation of the strain EN2 into sterilized and non-sterilized native C. comosum resulted in significantly increased gaseous benzene removal compared to that in non-inoculated groups under the same light conditions (P < 0.05). Remarkably, EN2 colonization in inoculated plants under LED conditions was higher than under fluorescence conditions as the EN2 could grow better under LED conditions. Strain EN2 possesses NADPH that is used to facilitate benzene degradation and modulate plant growth under benzene stress by bacterial IAA production and ACC deaminase activity; higher IAA and lower ethylene levels were found in inoculated plants compared to non-inoculated ones. These contributed to better benzene removal efficiency. Interestingly, under fumigation for 16 cycles (67 days), there was no difference in gaseous benzene removal between inoculated plants and non-inoculated plants under the same light conditions at initial benzene concentrations of 5 ppm. This is probably due to EN2 reaching maximum growth under all treatments. However, C. comosum exhibited better benzene removal under LED conditions than under fluorescence conditions during 16 cycles, possibly due to better photosynthetic performance and plant growth, leading to more NADPH, and eventually enhanced benzene removal efficiency. Hence, the most efficient acceleration of benzene removal was provided by inoculation of strain EN2 onto C. comosum under blue-red LED light conditions.

RevDate: 2018-10-30
CmpDate: 2018-10-30

Tsai YM, Chang A, CH Kuo (2018)

Horizontal Gene Acquisitions Contributed to Genome Expansion in Insect-Symbiotic Spiroplasma clarkii.

Genome biology and evolution, 10(6):1526-1532.

Genome reduction is a recurring theme of symbiont evolution. The genus Spiroplasma contains species that are mostly facultative insect symbionts. The typical genome sizes of those species within the Apis clade were estimated to be ∼1.0-1.4 Mb. Intriguingly, Spiroplasma clarkii was found to have a genome size that is >30% larger than the median of other species within the same clade. To investigate the molecular evolution events that led to the genome expansion of this bacterium, we determined its complete genome sequence and inferred the evolutionary origin of each protein-coding gene based on the phylogenetic distribution of homologs. Among the 1,346 annotated protein-coding genes, 641 were originated from within the Apis clade while 233 were putatively acquired from outside of the clade (including 91 high-confidence candidates). Additionally, 472 were specific to S. clarkii without homologs in the current database (i.e., the origins remained unknown). The acquisition of protein-coding genes, rather than mobile genetic elements, appeared to be a major contributing factor of genome expansion. Notably, >50% of the high-confidence acquired genes are related to carbohydrate transport and metabolism, suggesting that these acquired genes contributed to the expansion of both genome size and metabolic capability. The findings of this work provided an interesting case against the general evolutionary trend observed among symbiotic bacteria and further demonstrated the flexibility of Spiroplasma genomes. For future studies, investigation on the functional integration of these acquired genes, as well as the inference of their contribution to fitness could improve our knowledge of symbiont evolution.

RevDate: 2018-10-30
CmpDate: 2018-10-30

Kinjo Y, Bourguignon T, Tong KJ, et al (2018)

Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches.

Genome biology and evolution, 10(6):1622-1630.

Almost all examined cockroaches harbor an obligate intracellular endosymbiont, Blattabacterium cuenoti. On the basis of genome content, Blattabacterium has been inferred to recycle nitrogen wastes and provide amino acids and cofactors for its hosts. Most Blattabacterium strains sequenced to date harbor a genome of ∼630 kbp, with the exception of the termite Mastotermes darwiniensis (∼590 kbp) and Cryptocercus punctulatus (∼614 kbp), a representative of the sister group of termites. Such genome reduction may have led to the ultimate loss of Blattabacterium in all termites other than Mastotermes. In this study, we sequenced 11 new Blattabacterium genomes from three species of Cryptocercus in order to shed light on the genomic evolution of Blattabacterium in termites and Cryptocercus. All genomes of Cryptocercus-derived Blattabacterium genomes were reduced (∼614 kbp), except for that associated with Cryptocercus kyebangensis, which comprised 637 kbp. Phylogenetic analysis of these genomes and their content indicates that Blattabacterium experienced parallel genome reduction in Mastotermes and Cryptocercus, possibly due to similar selective forces. We found evidence of ongoing genome reduction in Blattabacterium from three lineages of the C. punctulatus species complex, which independently lost one cysteine biosynthetic gene. We also sequenced the genome of the Blattabacterium associated with Salganea taiwanensis, a subsocial xylophagous cockroach that does not vertically transmit gut symbionts via proctodeal trophallaxis. This genome was 632 kbp, typical of that of nonsubsocial cockroaches. Overall, our results show that genome reduction occurred on multiple occasions in Blattabacterium, and is still ongoing, possibly because of new associations with gut symbionts in some lineages.

RevDate: 2018-10-30
CmpDate: 2018-10-30

Qi W, Cascarano MC, Schlapbach R, et al (2018)

Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity.

Genome biology and evolution, 10(6):1363-1374.

Endozoicomonas bacteria are generally beneficial symbionts of diverse marine invertebrates including reef-building corals, sponges, sea squirts, sea slugs, molluscs, and Bryozoans. In contrast, the recently reported Ca. Endozoicomonas cretensis was identified as a vertebrate pathogen, causing epitheliocystis in fish larvae resulting in massive mortality. Here, we described the Ca. E. cretensis draft genome, currently undergoing genome decay as evidenced by massive insertion sequence (IS element) expansion and pseudogene formation. Many of the insertion sequences are also predicted to carry outward-directed promoters, implying that they may be able to modulate the expression of neighbouring coding sequences (CDSs). Comparative genomic analysis has revealed many Ca. E. cretensis-specific CDSs, phage integration and novel gene families. Potential virulence related CDSs and machineries were identified in the genome, including secretion systems and related effector proteins, and systems related to biofilm formation and directed cell movement. Mucin degradation would be of importance to a fish pathogen, and many candidate CDSs associated with this pathway have been identified. The genome may reflect a bacterium in the process of changing niche from symbiont to pathogen, through expansion of virulence genes and some loss of metabolic capacity.

RevDate: 2018-10-30
CmpDate: 2018-10-30

He Y, Yang Z, Li M, et al (2017)

Effects of a dark septate endophyte (DSE) on growth, cadmium content, and physiology in maize under cadmium stress.

Environmental science and pollution research international, 24(22):18494-18504.

Dark septate endophytes (DSE) are widely distributed in plant roots grown in stressful habitats, especially in heavy metal-polluted soils. But little is known about the physiological interactions between DSE and plants under heavy metal stress. In the present study, the growth, Cd content, and physiological response of Zea mays L. to a root-colonized DSE, Exophiala pisciphila, were analyzed under Cd stress (0, 5, 10, 20, and 40 mg/kg) in a sand culture experiment. Under high Cd (10, 20, and 40 mg/kg) stress, the DSE colonization in roots increased the maize growth, kept more Cd in roots, and decreased Cd content in shoots. The DSE colonization improved the photosynthesis and induced notable changes on phytohormones but had no significant effect on the antioxidant capability in the maize leaves. Moreover, there were significant positive correlations between the gibberellic acid (GA) content and transpiration rate, zeatin riboside (ZR) content, and photosynthetic rate in maize leaves. These results indicated that the DSE's ability to promote plant growth was related to a decrease on Cd content and the regulation on phytohormone balance and photosynthetic activities in maize leaves.

RevDate: 2018-10-30
CmpDate: 2018-10-30

Wan PJ, Tang YH, Yuan SY, et al (2017)

Reference genes for quantitative real-time PCR analysis in symbiont Entomomyces delphacidicola of Nilaparvata lugens (Stål).

Scientific reports, 7:42206 pii:srep42206.

Nilaparvata lugens (Stål) (Hemiptera: Delphacidae) is a major rice pest that harbors an endosymbiont ascomycete fungus, Entomomyces delphacidicola str. NLU (also known as yeast-like symbiont, YLS). Driving by demand of novel population management tactics (e.g. RNAi), the importance of YLS has been studied and revealed, which greatly boosts the interest of molecular level studies related to YLS. The current study focuses on reference genes for RT-qPCR studies related to YLS. Eight previously unreported YLS genes were cloned, and their expressions were evaluated for N. lugens samples of different developmental stages and sexes, and under different nutritional conditions and temperatures. Expression stabilities were analyzed by BestKeeper, geNorm, NormFinder, ΔCt method and RefFinder. Furthermore, the selected reference genes for RT-qPCR of YLS genes were validated using targeted YLS genes that respond to different nutritional conditions (amino acid deprivation) and RNAi. The results suggest that ylsRPS15p/ylsACT are the most suitable reference genes for temporal gene expression profiling, while ylsTUB/ylsACT and ylsRPS15e/ylsGADPH are the most suitable reference gene choices for evaluating nutrition and temperature effects. Validation studies demonstrated the advantage of using endogenous YLS reference genes for YLS studies.

RevDate: 2018-10-29

Correia M, Heleno R, da Silva LP, et al (2018)

First evidence for the joint dispersal of mycorrhizal fungi and plant diaspores by birds.

The New phytologist [Epub ahead of print].

Seed dispersal allows plants to colonize new sites and escape from pathogens and intraspecific competition, maintaining plant genetic diversity and regulating plant distribution. Conversely, most plant species form mutualistic associations with arbuscular mycorrhizal (AM) fungi in a symbiosis established right after seed germination. Since AM fungi are obligate symbionts, using the same dispersal vector as their host should be highly advantageous for their survival, however, the co-dispersal of seeds and AM fungal spores has never been confirmed. We aim to clarify the potential role of European birds, essential dispersers for many plant species, as co-dispersers of seeds and AM fungal spores. To achieve that, 63 bird droppings with intact seeds were placed in sterilized soil and maintained for 4 months in a protected environment to avoid contamination. Additionally, 173 bird droppings and 729 gauze swabs used to clean birds' feet were inspected for AM fungal spores. Although no spores were detected by direct observation of these samples, seven Rubus ulmifolius seedlings obtained from four independent droppings of Erithacus rubecula and Sylvia melanocephala were colonized by AM fungi. Our results show that birds can effectively co-disperse viable seeds and AM fungal spores, potentially over long distances, providing a pivotal mechanism to understand the cosmopolitan distribution of AM fungi. This article is protected by copyright. All rights reserved.

RevDate: 2018-10-29

Korhonen A, Lehto T, Heinonen J, et al (2018)

Whole-plant frost hardiness of mycorrhizal (Hebeloma sp. or Suillus luteus) and non-mycorrhizal Scots pine seedlings.

Tree physiology pii:5146310 [Epub ahead of print].

Ectomycorrhizal trees are common in the cold regions of the world, yet the role of the mycorrhizal symbiosis in plant cold tolerance is poorly known. Moreover, the standard methods for testing plant frost hardiness may not be adequate for roots and mycorrhizas. The aims of this study were to compare the frost hardiness of mycorrhizal and non-mycorrhizal Scots pine (Pinus sylvestris L.) seedlings and to test the use of reverse-flow root hydraulic conductance (Kr) measurement for root frost hardiness determination. Mycorrhizal (Hebeloma sp. or Suillus luteus) and non-mycorrhizal seedlings were grown in controlled-environment chambers for 13 weeks. After this, half of the plants were allotted to a non-hardening treatment (long day and high temperature, same as during the preceding growing season) and the other half to a hardening (short day and low temperature) 'autumn' treatment for 4 weeks. The intact seedlings were exposed to whole-plant freezing tests and the needle frost hardiness was measured by relative electrolyte leakage (REL) method. The seedlings were grown for three more weeks for visual damage assessment and Kr measurements using a high-pressure flow meter (HPFM). Mycorrhizas did not affect the frost hardiness of seedlings in either hardening treatment. The effect of the hardening treatment on frost hardiness was shown by REL and visual assessment of the aboveground parts as well as Kr of roots. Non-mycorrhizal plants were larger than mycorrhizal ones while nitrogen and phosphorus contents (per unit dry mass) were similar in all mycorrhiza treatments. In plants with no frost exposure, the non-mycorrhizal treatment had higher Kr. There was no mycorrhizal effect on plant frost hardiness when nutritional effects were excluded. Further studies are needed on the role of mycorrhizas especially in the recovery of growth and nutrient uptake in cold soils in the spring. The HPFM is useful novel method for assessment of root damage.

RevDate: 2018-10-29
CmpDate: 2018-10-29

Faeth SH, Oberhofer M, Saari S, et al (2017)

Does hybridization of endophytic symbionts in a native grass increase fitness in resource-limited environments?.

Ecology, 98(1):138-149.

Hybridization is common among plants, animals and microbes. However, the ecological consequences of hybridization for microbes are far less understood than for plants and animals. For symbiotic Epichloë fungi, hybridization is widespread and may augment the well-known benefits of the endophytes to their grass hosts, especially in stressful environments. We tested the hybrid fitness hypothesis (HFH) that hybrid endophytes enhance fitness in stressful environments relative to non-hybrid endophytes. In a long-term field experiment, we monitored growth and reproduction of hybrid-infected (H+), non-hybrid infected (NH+), naturally endophyte free (E-) plants and those plants from which the endophyte had been experimentally removed (H- and NH-) in resource-rich and resource-poor environments. Infection by both endophyte species enhanced growth and reproduction. H+ plants outperformed NH+ plants in terms of growth by the end of the experiment, supporting HFH. However, H+ plants only outperformed NH+ plants in the resource-rich treatment, contrary to HFH. Plant genotypes associated with each endophyte species had strong effects on growth and reproduction. Our results provide some support the HFH hypothesis but not based upon adaptation to stressful environments. Our results reinforce the notion of a complex interplay between endophyte and plant genotype and environmental factors that determine fitness of the symbiotum.

RevDate: 2018-10-27

Alcaraz JP, Cinquin P, DK Martin (2018)

Tackling the concept of symbiotic implantable medical devices with nanobiotechnologies.

Biotechnology journal [Epub ahead of print].

This review takes an approach to implanted medical devices that considers whether the intention of the implanted device is to have any communication of energy or materials with the body. The first part describes some specific examples of 3 different classes of implants, analysed with regards to the type of signal sent to cells. Through several examples, we describe that a one way signalling to the body leads to encapsulation or degradation. In most cases, those phenomena do not lead to major problems. However, encapsulation or degradation are critical for new kinds of medical devices capable of duplex communication, which we define in this review as symbiotic devices. The concept we propose is that implanted medical devices that need to be symbiotic with the body also need to be designed with an intended duplex communication of energy and materials with the body. This extends the definition of a biocompatible system to one that requires stable exchange of materials between the implanted device and the body. Having this novel concept in mind will guide research in a new field between medical implant and regenerative medicine to create actual symbiotic devices.

RevDate: 2018-10-26

Baba K, Miyazono A, Matsuyama K, et al (2007)

Occurrence and detrimental effects of the bivalve-inhabiting hydroid Eutima japonica on juveniles of the Japanese scallop Mizuhopecten yessoensis in Funka Bay, Japan: relationship to juvenile massive mortality in 2003.

Marine biology, 151(5):1977-1987.

In November 2003, we first observed prevalent occurrence of a hydroid, Eutima japonica, on soft body tissues of age zero Japanese scallop (Mizuhopecten yessoensis) juveniles cultured in large areas of Funka Bay, Hokkaido. The occurrence coincided with massive death of juvenile scallops. A major objective was to clarify ecological relationships between the symbionts, and to infer the relationship between symbiosis and the massive mortality. To do this, we investigated distributions of association rates of hydroids with juvenile scallops at 15-34 sites over 3 years (2003-2005), with age one adult scallops at 24 sites in 2003, and with mussels at 13 sites in 2004. We studied seasonal changes in association rates with juvenile scallops, and numbers of polyps per juvenile scallop at three sites from November 2003 to June 2004. We also quantified the hydroid impacts on juvenile scallop shell length growth and triglyceride accumulation in the digestive gland. The association rate of E. japonica polyps with juvenile scallops was high in large areas of Funka Bay in 2003, and overlapped the distribution of mussels bearing polyps. Association rates with age one adult scallops were very low in November 2003, even at the sites where polyps were very common on juvenile scallops. Levels of hydroid occurrence in juvenile scallops varies by year. We found that hydroids presence in juvenile scallops declined drastically in 2004 and 2005. The association rates with juvenile scallops, and numbers of polyps per juvenile scallop declined during winter, until they disappeared completely in the following June. Since polyps were rare in adult scallops, we believe that infection of juvenile scallops was probably initiated from the planulae produced by medusae released from polyps growing on Mytilus spp., especially M. galloprovincialis. Subsequently, the inhabitation spread intraspecifically and interspecifically. In juvenile scallops, inhabitation of polyps reduced shell length growth by 43%, and triglyceride accumulation in digestive glands by 24-47%. Inhabitation of E. japonica on juvenile scallop is best regarded as parasitism, rather than inquilinism or commensalism. Occurrence of polyps was probably not a direct lethal factor for juvenile scallops, because there were some sites where association rates were high, but mortalities were low. Massive mortalities in 2003 may have resulted from simultaneous impacts of heavy polyp load and stresses caused by the way in which the animals were handled (transferred from cages for pre-intermediate culture to cages for intermediate culture), because the massive mortality occurred within a month of the transfer. The presence of polyps in juvenile scallops does not affect the quality of the product in Funka Bay, because market size scallops are hydroid-free.

RevDate: 2018-10-26

Tan WH, Reyes ML, Hoang KL, et al (2018)

How symbiosis and ecological context influence the variable expression of transgenerational wing induction upon fungal infection of aphids.

PloS one, 13(10):e0201865 pii:PONE-D-18-21477.

Aphids, like most animals, mount a diverse set of defenses against pathogens. For aphids, two of the best studied defenses are symbiont-conferred protection and transgenerational wing induction. Aphids can harbor bacterial symbionts that provide protection against pathogens, parasitoids and predators, as well as against other environmental stressors. In response to signals of danger, aphids also protect not themselves but their offspring by producing more winged than unwinged offspring as a way to ensure that their progeny may be able to escape deteriorating conditions. Such transgenerational wing induction has been studied most commonly as a response to overcrowding of host plants and presence of predators, but recent evidence suggests that pea aphids (Acyrthosiphon pisum) may also begin to produce a greater proportion of winged offspring when infected with fungal pathogens. Here, we explore this phenomenon further by asking how protective symbionts, pathogen dosage and environmental conditions influence this response. Overall, while we find some evidence that protective symbionts can modulate transgenerational wing induction in response to fungal pathogens, we observe that transgenerational wing induction in response to fungal infection is highly variable. That variability cannot be explained entirely by symbiont association, by pathogen load or by environmental stress, leaving the possibility that a complex interplay of genotypic and environmental factors may together influence this trait.

RevDate: 2018-10-26

Becana M, Wienkoop S, MA Matamoros (2018)

Sulfur Transport and Metabolism in Legume Root Nodules.

Frontiers in plant science, 9:1434.

Sulfur is an essential nutrient in plants as a constituent element of some amino acids, metal cofactors, coenzymes, and secondary metabolites. Not surprisingly, sulfur deficiency decreases plant growth, photosynthesis, and seed yield in both legumes and non-legumes. In nodulated legumes, sulfur supply is positively linked to symbiotic nitrogen fixation (SNF) and sulfur starvation causes three additional major effects: decrease of nodulation, inhibition of SNF, and slowing down of nodule metabolism. These effects are due, at least in part, to the impairment of nitrogenase biosynthesis and activity, the accumulation of nitrogen-rich amino acids, and the decline in leghemoglobin, ferredoxin, ATP, and glucose in nodules. During the last decade, some major advances have been made about the uptake and metabolism of sulfur in nodules. These include the identification of the sulfate transporter SST1 in the symbiosomal membrane, the finding that glutathione produced in the bacteroids and host cells is essential for nodule activity, and the demonstration that sulfur assimilation in the whole plant is reprogrammed during symbiosis. However, many crucial questions still remain and some examples follow. In the first place, it is of paramount importance to elucidate the mechanism by which sulfur deficiency limits SNF. It is unknown why homoglutahione replaces glutathione as a major water-soluble antioxidant, redox buffer, and sulfur reservoir, among other relevant functions, only in certain legumes and also in different tissues of the same legume species. Much more work is required to identify oxidative post-translational modifications entailing cysteine and methionine residues and to determine how these modifications affect protein function and metabolism in nodules. Likewise, most interactions of antioxidant metabolites and enzymes bearing redox-active sulfur with transcription factors need to be defined. Solving these questions will pave the way to decipher sulfur-dependent mechanisms that regulate SNF, thereby gaining a deep insight into how nodulated legumes adapt to the fluctuating availability of nutrients in the soil.

RevDate: 2018-10-26

Gifford I, Battenberg K, Vaniya A, et al (2018)

Distinctive Patterns of Flavonoid Biosynthesis in Roots and Nodules of Datisca glomerata and Medicago spp. Revealed by Metabolomic and Gene Expression Profiles.

Frontiers in plant science, 9:1463.

Plants within the Nitrogen-fixing Clade (NFC) of Angiosperms form root nodule symbioses with nitrogen-fixing bacteria. Actinorhizal plants (in Cucurbitales, Fagales, Rosales) form symbioses with the actinobacteria Frankia while legumes (Fabales) form symbioses with proteobacterial rhizobia. Flavonoids, secondary metabolites of the phenylpropanoid pathway, have been shown to play major roles in legume root nodule symbioses: as signal molecules that in turn trigger rhizobial nodulation initiation signals and acting as polar auxin transport inhibitors, enabling a key step in nodule organogenesis. To explore a potentially broader role for flavonoids in root nodule symbioses across the NFC, we combined metabolomic and transcriptomic analyses of roots and nodules of the actinorhizal host Datisca glomerata and legumes of the genus Medicago. Patterns of biosynthetic pathways were inferred from flavonoid metabolite profiles and phenylpropanoid gene expression patterns in the two hosts to identify similarities and differences. Similar classes of flavonoids were represented in both hosts, and an increase in flavonoids generally in the nodules was observed, with differences in flavonoids prominent in each host. While both hosts produced derivatives of naringenin, the metabolite profile in D. glomerata indicated an emphasis on the pinocembrin biosynthetic pathway, and an abundance of flavonols with potential roles in symbiosis. Additionally, the gene expression profile indicated a decrease in expression in the lignin/monolignol pathway. In Medicago sativa, by contrast, isoflavonoids were highly abundant featuring more diverse and derived isoflavonoids than D. glomerata. Gene expression patterns supported these differences in metabolic pathways, especially evident in a difference in expression of cinnamic acid 4-hydroxylase (C4H), which was expressed at substantially lower levels in D. glomerata than in a Medicago truncatula transcriptome where it was highly expressed. C4H is a major rate-limiting step in phenylpropanoid biosynthesis that separates the pinocembrin pathway from the lignin/monolignol and naringenin-based flavonoid branches. Shikimate O-hydroxycinnamoyltransferase, the link between flavonoid biosynthesis and the lignin/monolignol pathway, was also expressed at much lower levels in D. glomerata than in M. truncatula. Our results indicate (a) a likely major role for flavonoids in actinorhizal nodules, and (b) differences in metabolic flux in flavonoid and phenylpropanoid biosynthesis between the different hosts in symbiosis.

RevDate: 2018-10-26

Antonets KS, Onishchuk OP, Kurchak ON, et al (2018)

[Proteomic Profile of the Bacterium Sinorhizobium meliloti Depends on Its Life Form and Host Plant Species].

Molekuliarnaia biologiia, 52(5):898-904.

The importance of root nodule bacteria in biotechnology is determined by their distinctive feature: symbiotic nitrogen fixation resulting in the production of organic nitrogen-containing compounds. While interacting with host legume plants, the cells of these bacteria undergo global changes at all levels of expression of genetic information leading to the formation in root nodules of so-called bacteroids functioning as nitrogen fixation factories. The molecular mechanisms underlying plant-microbial symbiosis are actively investigated, and one of the most interesting and poorly studied aspects of this problem is the species-specificity of interaction between root nodule bacteria and host plants. In this work we have performed the proteomic analysis of the Sinorhizobium meliloti bacteroids isolated from two legume species: alfalfa (Medicago sativa L.) and yellow sweet clover (Melilotus officinalis L.). It has been shown that the S. meliloti bacteroids produce a lot of proteins (many of them associated with symbiosis) in a host-specific manner, i.e., only in certain host plant species. It has been demonstrated for the first time that the levels of expression in bacteroids of the genes encoding the ExoZ and MscL proteins responsible for the synthesis of surface lipopolysaccha-rides and formation of a large conductance mechanosensitive channel, respectively, depend on a host plant species that confirms the results of proteomic analysis. Overall, our data show that the regulation of bacteroid development by the host plant has species-specific features.

RevDate: 2018-10-26
CmpDate: 2018-10-26

García-Bayona L, LE Comstock (2018)

Bacterial antagonism in host-associated microbial communities.

Science (New York, N.Y.), 361(6408):.

Antagonistic interactions are abundant in microbial communities and contribute not only to the composition and relative proportions of their members but also to the longer-term stability of a community. This Review will largely focus on bacterial antagonism mediated by ribosomally synthesized peptides and proteins produced by members of host-associated microbial communities. We discuss recent findings on their diversity, functions, and ecological impacts. These systems play key roles in ecosystem defense, pathogen invasion, spatial segregation, and diversity but also confer indirect gains to the aggressor from products released by killed cells. Investigations into antagonistic bacterial interactions are important for our understanding of how the microbiota establish within hosts, influence health and disease, and offer insights into potential translational applications.

RevDate: 2018-10-26
CmpDate: 2018-10-26

Reveillaud J, Anderson R, Reves-Sohn S, et al (2018)

Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity.

Microbiome, 6(1):19 pii:10.1186/s40168-018-0411-x.

BACKGROUND: The microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR) in the Caribbean Sea were characterized using microscopy, phylogenetic analyses, and a metagenomic approach.

RESULTS: Bacteria, with a typical Gram negative cell envelope contained within membrane-bound vacuoles, were observed within the trophosome of both tubeworm species. Phylogenetic analysis of the 16S rRNA gene and ITS region suggested MCR individuals harbored highly similar endosymbionts that were > 98% identical, with the exception of two symbionts that showed a 60 bp insertion within the ITS region. All sequences from MCR endosymbionts formed a separate well-supported clade that diverged from those of symbionts of seep and vent vestimentiferans from the Pacific, Gulf of Mexico, and Mediterranean Sea. The metagenomes of the symbionts of two specimens of each tubeworm species were sequenced, and two distinct Gammaproteobacteria metagenome-assembled genomes (MAGs) of more than 4 Mbp assembled. An Average Nucleotide Identity (ANI) of 86.5% between these MAGs, together with distinct 16S rRNA gene and ITS sequences, indicate the presence of multiple endosymbiont phylotypes at the MCR, with one MAG shared between one Escarpia and two Lamellibrachia individuals, indicating these endosymbionts are not specific to either host species. Genes for sulfur and hydrogen oxidation, nitrate reduction (assimilatory and dissimilatory), glycolysis and the Krebs cycle, peptide, sugar, and lipid transporters, and both rTCA and CBB carbon fixation cycles were detected in the MAGs, highlighting key and shared functions with symbiont metagenomes of the vestimentiferans Riftia, Tevnia, and Ridgeia from the Pacific. The potential for a second hydrogen oxidation pathway (via a bidirectional hydrogenase), formate dehydrogenase, a catalase, and several additional peptide transporters were found exclusively in the MCR endosymbiont MAGs.

CONCLUSIONS: The present study adds new evidence that tubeworm endosymbionts can potentially switch from autotrophic to heterotrophic metabolism, or may be mixotrophic, presumably while free-living, and also suggests their versatile metabolic potential may enable both the host and symbionts to exploit a wide range of environmental conditions. Together, the marked gene content and sequence dissimilarity at the rRNA operon and whole genome level between vent and seep symbionts suggest these newly described endosymbionts from the MCR belong to a novel tubeworm endosymbiont genera, introduced as Candidatus Vondammii.

RevDate: 2018-10-26
CmpDate: 2018-10-26

Maire J, Vincent-Monégat C, Masson F, et al (2018)

An IMD-like pathway mediates both endosymbiont control and host immunity in the cereal weevil Sitophilus spp.

Microbiome, 6(1):6 pii:10.1186/s40168-017-0397-9.

Many insects developing on nutritionally unbalanced diets have evolved symbiotic associations with vertically transmitted intracellular bacteria (endosymbionts) that provide them with metabolic components, thereby improving the host's abilities to thrive on such poor ecological niches. While host-endosymbiont coevolutionary constraints are known to entail massive genomic changes in the microbial partner, host's genomic evolution remains elusive, particularly with regard to the immune system. In the cereal weevil Sitophilus spp., which houses Sodalis pierantonius, endosymbionts are secluded in specialized host cells, the bacteriocytes that group together as an organ, the bacteriome. We previously reported that at standard conditions, the bacteriome highly expresses the coleoptericin A (colA) antimicrobial peptide (AMP), which was shown to prevent endosymbiont escape from the bacteriocytes. However, following the insect systemic infection by pathogens, the bacteriome upregulates a cocktail of AMP encoding genes, including colA. The regulations that allow these contrasted immune responses remain unknown. In this short report, we provide evidence that an IMD-like pathway is conserved in two sibling species of cereal weevils, Sitophilus oryzae and Sitophilus zeamais. RNA interference (RNAi) experiments showed that imd and relish genes are essential for (i) colA expression in the bacteriome under standard conditions, (ii) AMP up-regulation in the bacteriome following a systemic immune challenge, and (iii) AMP systemic induction following an immune challenge. Histological analyses also showed that relish inhibition by RNAi resulted in endosymbiont escape from the bacteriome, strengthening the involvement of an IMD-like pathway in endosymbiont control. We conclude that Sitophilus' IMD-like pathway mediates both the bacteriome immune program involved in endosymbiont seclusion within the bacteriocytes and the systemic and local immune responses to exogenous challenges. This work provides a striking example of how a conserved immune pathway, initially described as essential in pathogen clearance, also functions in the control of mutualistic associations.

RevDate: 2018-10-25

Miyokawa R, Tsuda T, Kanaya HJ, et al (2018)

Horizontal Transmission of Symbiotic Green Algae Between Hydra Strains.

The Biological bulletin, 235(2):113-122.

Some hydra strains belonging to the vulgaris group show a symbiotic relationship with green algae Chlorococcum sp. The symbiotic green algae can escape from the host polyps and can form swimming zoospores (which have two flagella) in culture solution. We observed that co-culture with the symbiotic polyps caused horizontal transmission of the symbionts into some non-symbiotic hydra strains that have no symbionts in nature and that belong not only to the vulgaris group but also to other hydra species groups. Although most of the horizontal transmission has ended in transient symbioses, a newly formed symbiosis between the symbiotic Chlorococcum sp. and strain 105 of Hydra vulgaris (Hydra magnipapillata) has been sustained for more than five years and has caused morphological and behavioral changes in the host polyps. We named this strain 105G. The asexual proliferation rate by budding increased under light conditions, although the feeding activity decreased and the polyp size was reduced in strain 105G. This new symbiosis between Chlorococcum sp. and strain 105G of H. vulgaris provides us with an intriguing research system for investigating the origin of symbiosis.

RevDate: 2018-10-25

Gabaldón T (2018)

Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis.

IUBMB life [Epub ahead of print].

The origin of eukaryotes stands as a major open question in biology. Central to this question is the nature and timing of the origin of the mitochondrion, an ubiquitous eukaryotic organelle originated by the endosymbiosis of an alphaproteobacterial ancestor. Different hypotheses disagree, among other aspects, on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host is debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Here, I will discuss recent findings from phylogenomics analyses of extant genomes that are shedding light into the evolutionary origins of the eukaryotic ancestor, and which suggest a later acquisition of alpha-proteobacterial derived proteins as compared to those with different bacterial ancestries. I argue that simple eukaryogenesis models that assume a binary symbiosis between an archaeon host and an alpha-proteobacterial proto-mitochondrion cannot explain the complex chimeric nature that is inferred for the eukaryotic ancestor. To reconcile existing hypotheses with the new data, I propose the "pre-mitochondrial symbioses" hypothesis that provides a framework for eukaryogenesis scenarios involving alternative symbiotic interactions that predate the acquisition of mitochondria. © 2018 IUBMB Life, 2018.

RevDate: 2018-10-25

Prazeres M (2018)

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia.

Frontiers in microbiology, 9:2404.

Ocean warming is known to cause detrimental effects in coral reef fauna that rely on photo-symbiosis for survival. Microbial associations can facilitate the success of species across a range of environmental conditions, and play a role in the capacity of organisms to respond to climate change. In 2016, the Great Barrier Reef experienced its third mass bleaching event, with sea surface temperature rising to 1.3°C above long-term monthly summer averages. Here, I investigate the effects of ocean warming on the chlorophyll a (chl a) content and microbiome of the large benthic Foraminifera Amphistegina radiata. Samples were collected in January and April 2016, before and after the mass bleaching event. In total, 71 specimens were collected from two different depths (6- and 18-m) to investigate depth-dependant responses associated with changes in chl a and microbiome. Pigment analysis showed a significant reduction in chl a between time points in specimens collected at both depths. Reduction in pigmentation was accompanied by changes in the microbiome, and a significant interaction of depth and time was observed. Genus-level bacterial community associated with A. radiata was significantly different across depth and time. However, ocean warming affected populations at both depths to a similar extent, and resulted in change from a Betaproteobacteria-dominated assemblage in January to a more diverse bacterial community by April. Analysis of presence/absence and relative abundance of bacterial taxa revealed significant differences between time points at both depths analyzed. OTUs classified as Firmicutes, which were either absent, or present in very low relative abundances (<0.1%) across all sample groups in January, were identified in abundances as high as ∼20% in specimens collected from 18-m depth in April. Class-level shifts were observed in shallow-dwelling specimens, from high abundances of Betaproteobacteria to a high abundance and diversity of Actinobacteria. These results demonstrate the sensitivity of LBF to the effects of ocean warming, for which depth did not provide protection, and highlights the capacity of LBF to re-assemble bacterial communities after a disturbance. This study provides the first molecular-based demonstration of changes in foraminifera-associated bacterial assemblages during a bleaching event on a natural reef system.

RevDate: 2018-10-25

Volpe V, Chitarra W, Cascone P, et al (2018)

The Association With Two Different Arbuscular Mycorrhizal Fungi Differently Affects Water Stress Tolerance in Tomato.

Frontiers in plant science, 9:1480.

Arbuscular mycorrhizal (AM) fungi are very widespread, forming symbiotic associations with ∼80% of land plant species, including almost all crop plants. These fungi are considered of great interest for their use as biofertilizer in low-input and organic agriculture. In addition to an improvement in plant nutrition, AM fungi have been reported to enhance plant tolerance to important abiotic and biotic environmental conditions, especially to a reduced availability of resources. These features, to be exploited and applied in the field, require a thorough identification of mechanisms involved in nutrient transfer, metabolic pathways induced by single and multiple stresses, physiological and eco-physiological mechanisms resulting in improved tolerance. However, cooperation between host plants and AM fungi is often related to the specificity of symbiotic partners, the environmental conditions and the availability of resources. In this study, the impact of two AM fungal species (Funneliformis mosseae and Rhizophagus intraradices) on the water stress tolerance of a commercial tomato cultivar (San Marzano nano) has been evaluated in pots. Biometric and eco-physiological parameters have been recorded and gene expression analyses in tomato roots have been focused on plant and fungal genes involved in inorganic phosphate (Pi) uptake and transport. R. intraradices, which resulted to be more efficient than F. mosseae to improve physiological performances, was selected to assess the role of AM symbiosis on tomato plants subjected to combined stresses (moderate water stress and aphid infestation) in controlled conditions. A positive effect on the tomato indirect defense toward aphids in terms of enhanced attraction of their natural enemies was observed, in agreement with the characterization of volatile organic compound (VOC) released. In conclusion, our results offer new insights for understanding the molecular and physiological mechanisms involved in the tolerance toward water deficit as mediated by a specific AM fungus. Moreover, they open new perspectives for the exploitation of AM symbiosis to enhance crop tolerance to abiotic and biotic stresses in a scenario of global change.

RevDate: 2018-10-25

Epstein B, Abou-Shanab RAI, Shamseldin A, et al (2018)

Genome-Wide Association Analyses in the Model Rhizobium Ensifer meliloti.

mSphere, 3(5): pii:3/5/e00386-18.

Genome-wide association studies (GWAS) can identify genetic variants responsible for naturally occurring and quantitative phenotypic variation. Association studies therefore provide a powerful complement to approaches that rely on de novo mutations for characterizing gene function. Although bacteria should be amenable to GWAS, few GWAS have been conducted on bacteria, and the extent to which nonindependence among genomic variants (e.g., linkage disequilibrium [LD]) and the genetic architecture of phenotypic traits will affect GWAS performance is unclear. We apply association analyses to identify candidate genes underlying variation in 20 biochemical, growth, and symbiotic phenotypes among 153 strains of Ensifer meliloti For 11 traits, we find genotype-phenotype associations that are stronger than expected by chance, with the candidates in relatively small linkage groups, indicating that LD does not preclude resolving association candidates to relatively small genomic regions. The significant candidates show an enrichment for nucleotide polymorphisms (SNPs) over gene presence-absence variation (PAV), and for five traits, candidates are enriched in large linkage groups, a possible signature of epistasis. Many of the variants most strongly associated with symbiosis phenotypes were in genes previously identified as being involved in nitrogen fixation or nodulation. For other traits, apparently strong associations were not stronger than the range of associations detected in permuted data. In sum, our data show that GWAS in bacteria may be a powerful tool for characterizing genetic architecture and identifying genes responsible for phenotypic variation. However, careful evaluation of candidates is necessary to avoid false signals of association.IMPORTANCE Genome-wide association analyses are a powerful approach for identifying gene function. These analyses are becoming commonplace in studies of humans, domesticated animals, and crop plants but have rarely been conducted in bacteria. We applied association analyses to 20 traits measured in Ensifer meliloti, an agriculturally and ecologically important bacterium because it fixes nitrogen when in symbiosis with leguminous plants. We identified candidate alleles and gene presence-absence variants underlying variation in symbiosis traits, antibiotic resistance, and use of various carbon sources; some of these candidates are in genes previously known to affect these traits whereas others were in genes that have not been well characterized. Our results point to the potential power of association analyses in bacteria, but also to the need to carefully evaluate the potential for false associations.

RevDate: 2018-10-24

Bongrand C, EG Ruby (2018)

Achieving a multi-strain symbiosis: strain behavior and infection dynamics.

The ISME journal pii:10.1038/s41396-018-0305-8 [Epub ahead of print].

Strain diversity, while now recognized as a key driver underlying partner dynamics in symbioses, is usually difficult to experimentally manipulate and image in hosts with complex microbiota. To address this problem, we have used the luminous marine bacterium Vibrio fischeri, which establishes a symbiosis within the crypts of the nascent light organ of the squid Euprymna scolopes. Competition assays in newly hatched juvenile squid have shown that symbiotic V. fischeri are either niche-sharing "S strains", which share the light organ when co-inoculated with other S strains, or niche-dominant "D strains", which are typically found alone in the light organ after a co-colonization. To understand this D strain advantage, we determined the minimum time that different V. fischeri strains needed to initiate colonization and used confocal microscopy to localize the symbionts along their infection track. Further, we determined whether symbiont-induced host morphogenic events also occurred earlier during a D strain colonization. We conclude that D strains colonized more quickly than S strains. Nevertheless, light-organ populations in field-caught adult squid often contain both D and S strains. We determined experimentally that this symbiont population heterogeneity might be achieved in nature by a serial encounter of different strains in the environment.

RevDate: 2018-10-24
CmpDate: 2018-10-24

Cai H, Bai Y, C Guo (2018)

Comparative genomics of 151 plant-associated bacteria reveal putative mechanisms underlying specific interactions between bacteria and plant hosts.

Genes & genomics, 40(8):857-864.

Although much work has explored how microbes can benefit plant growth, the mechanisms underlying this intriguing process remain largely unknown, especially considering the diversity of bacteria that surrounds plants. The objective of the present study was to identify bacterial genes contributing to plant-microbe associations, beneficial effects, and host specificities. For this purpose, comparative genomics investigation of 151 plant-associated bacteria was performed. A principal component analysis of seven key genomic features revealed patterns in the specific properties of these bacteria: N2-fixing bacteria were more closely related to pathogenic ones than to beneficial bacteria. A common set of genes over-represented in these plant-associated bacteria were found to be remarkably similar in terms of (1) genetic information processing, (2) amino acid metabolism, (3) metabolism of cofactors and vitamins, (4) nucleotide metabolism, (5) human diseases, and (6) metabolism of terpenoids and polyketides. Although we did not detect a common genetic basis for these beneficial effects, further in-depth analysis revealed that each of five beneficial bacterial groups shared specific gene sets. Functional annotation showed that environmental information processing, genetic information processing and cellular processes predominated in these beneficial groups. Hypothesizing that plant-associated bacteria may have overlapping strategies to colonize their plant hosts, we successfully identified many putative genes that determine host specificities. Most of these genes were classified as transcription factors, enzymes, transporters, and chemotaxis regulators. Comparative genomics provides a powerful tool for helping to identify genes that are common among species. Genome-based views of plant-associated bacteria reveal specific interactions between bacteria and plant hosts.

RevDate: 2018-10-24
CmpDate: 2018-10-24

Torres D, Benavidez I, Donadio F, et al (2018)

New insights into auxin metabolism in Bradyrhizobium japonicum.

Research in microbiology, 169(6):313-323.

Bacterial metabolism of phytohormones includes several processes such as biosynthesis, catabolism, conjugation, hydrolysis and homeostatic regulation. However, only biosynthesis and occasionally catabolism are studied in depth in microorganisms. In this work, we evaluated and reconsidered IAA metabolism in Bradyrhizobiumjaponicum E109, one of the most widely used strains for soybean inoculation around the world. The genomic analysis of the strain showed the presence of several genes responsible for IAA biosynthesis, mainly via indole-3-acetonitrile (IAN), indole-3-acetamide (IAM) and tryptamine (TAM) pathways. However; in vitro experiments showed that IAA is not accumulated in the culture medium in significant amounts. On the contrary, a strong degradation activity was observed after exogenous addition of 0.1 mM of IAA, IBA or NAA to the medium. B. japonicum E109 was not able to grow in culture medium containing IAA as a sole carbon source. In YEM medium, the bacteria degraded IAA and hydrolyzed amino acid auxin conjugates with alanine (IAAla), phenylalanine (IAPhe), and leucine (IAPhe), releasing IAA which was quickly degraded. Finally, the presence of exogenous IAA induced physiological changes in the bacteria such as increased biomass and exopolysaccharide production, as well as infection effectiveness and symbiotic behavior in soybean plants.


ESP Quick Facts

ESP Origins

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

ESP Support

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

ESP Rationale

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

ESP Goal

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

ESP Usage

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

ESP Content

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

ESP Help

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

ESP Plans

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

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Papers in Classical Genetics

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

Digital Books

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


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Biographical information about many key scientists.

Selected Bibliographies

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

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