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Bibliography on: Symbiosis

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ESP: PubMed Auto Bibliography 20 Nov 2019 at 01:46 Created: 

Symbiosis

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

Created with PubMed® Query: symbiosis NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-11-19

Zhang B, Leonard SP, Li Y, et al (2019)

Obligate bacterial endosymbionts limit thermal tolerance of insect host species.

Proceedings of the National Academy of Sciences of the United States of America pii:1915307116 [Epub ahead of print].

The thermal tolerance of an organism limits its ecological and geographic ranges and is potentially affected by dependence on temperature-sensitive symbiotic partners. Aphid species vary widely in heat sensitivity, but almost all aphids are dependent on the nutrient-provisioning intracellular bacterium Buchnera, which has evolved with aphids for 100 million years and which has a reduced genome potentially limiting heat tolerance. We addressed whether heat sensitivity of Buchnera underlies variation in thermal tolerance among 5 aphid species. We measured how heat exposure of juvenile aphids affects later survival, maturation time, and fecundity. At one extreme, heat exposure of Aphis gossypii enhanced fecundity and had no effect on the Buchnera titer. In contrast, heat suppressed Buchnera populations in Aphis fabae, which suffered elevated mortality, delayed development and reduced fecundity. Likewise, in Acyrthosiphon kondoi and Acyrthosiphon pisum, heat caused rapid declines in Buchnera numbers, as well as reduced survivorship, development rate, and fecundity. Fecundity following heat exposure is severely decreased by a Buchnera mutation that suppresses the transcriptional response of a gene encoding a small heat shock protein. Similarly, absence of this Buchnera heat shock gene may explain the heat sensitivity of Ap. fabae Fluorescent in situ hybridization revealed heat-induced deformation and shrinkage of bacteriocytes in heat-sensitive species but not in heat-tolerant species. Sensitive and tolerant species also differed in numbers and transcriptional responses of heat shock genes. These results show that shifts in Buchnera heat sensitivity contribute to host variation in heat tolerance.

RevDate: 2019-11-19

Li Y, Tassia MG, Waits DS, et al (2019)

Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi.

BMC biology, 17(1):91 pii:10.1186/s12915-019-0713-x.

BACKGROUND: Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused on adaptations and mechanisms of the bacterial partner. The gutless tubeworms (Siboglinidae, Annelida) are obligate hosts of chemoautotrophic endosymbionts (except for Osedax which houses heterotrophic Oceanospirillales), which rely on the sulfide-oxidizing symbionts for nutrition and growth. Whereas several siboglinid endosymbiont genomes have been characterized, genomes of hosts and their adaptations to this symbiosis remain unexplored.

RESULTS: Here, we present and characterize adaptations of the cold seep-dwelling tubeworm Lamellibrachia luymesi, one of the longest-lived solitary invertebrates. We sequenced the worm's ~ 688-Mb haploid genome with an overall completeness of ~ 95% and discovered that L. luymesi lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. Interestingly, the host is known to carry hydrogen sulfide to thiotrophic endosymbionts using hemoglobin. We also found an expansion of hemoglobin B1 genes, many of which possess a free cysteine residue which is hypothesized to function in sulfide binding. Contrary to previous analyses, the sulfide binding mediated by zinc ions is not conserved across tubeworms. Thus, the sulfide-binding mechanisms in sibgolinids need to be further explored, and B1 globins might play a more important role than previously thought. Our comparative analyses also suggest the Toll-like receptor pathway may be essential for tolerance/sensitivity to symbionts and pathogens. Several genes related to the worm's unique life history which are known to play important roles in apoptosis, cell proliferation, and aging were also identified. Last, molecular clock analyses based on phylogenomic data suggest modern siboglinid diversity originated in 267 mya (± 70 my) support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126 mya for vestimentiferans.

CONCLUSIONS: Here, we elucidate several specific adaptations along various molecular pathways that link phenome to genome to improve understanding of holobiont evolution. Our findings of adaptation in genomic mechanisms to reducing environments likely extend to other chemosynthetic symbiotic systems.

RevDate: 2019-11-19
CmpDate: 2019-11-19

Peng X, Liu H, Chen P, et al (2019)

A Chromosome-Scale Genome Assembly of Paper Mulberry (Broussonetia papyrifera) Provides New Insights into Its Forage and Papermaking Usage.

Molecular plant, 12(5):661-677.

Paper mulberry (Broussonetia papyrifera) is a well-known woody tree historically used for Cai Lun papermaking, one of the four great inventions of ancient China. More recently, Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents. In this study, we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches, including Illumina and PacBio sequencing platform as well as Hi-C, optical, and genetic maps. The assembled Paper mulberry genome consists of 386.83 Mb, which is close to the estimated size, and 99.25% (383.93 Mb) of the assembly was assigned to 13 pseudochromosomes. Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families, respectively, accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry. Moreover, the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine, forage, papermaking, and barkcloth making. We also identified the root-associated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation. Collectively, these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition. Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making, and as forage. These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide.

RevDate: 2019-11-19
CmpDate: 2019-11-19

Fromont C, Adair KL, AE Douglas (2019)

Correlation and causation between the microbiome, Wolbachia and host functional traits in natural populations of drosophilid flies.

Molecular ecology, 28(7):1826-1841.

Resident microorganisms are known to influence the fitness and traits of animals under controlled laboratory conditions, but the relevance of these findings to wild animals is uncertain. This study investigated the host functional correlates of microbiota composition in a wild community of three sympatric species of mycophagous drosophilid flies, Drosophila falleni, Drosophila neotestacea and Drosophila putrida. Specifically, we quantified bacterial communities and host transcriptomes by parallel 16S rRNA gene amplicon sequencing and RNA-Seq of individual flies. Among-fly variation in microbiota composition did not partition strongly by sex or species, and included multiple modules, that is, sets of bacterial taxa whose abundance varied in concert across different flies. The abundance of bacteria in several modules varied significantly with multiple host transcripts, especially in females, but the identity of the correlated host transcriptional functions differed with host species, including epithelial barrier function in D. falleni, muscle function in D. putrida, and insect growth and development in D. neotestacea. In D. neotestacea, which harbours the endosymbionts Wolbachia and Spiroplasma, Wolbachia promotes the abundance of Spiroplasma, and is positively correlated with abundance of Lactobacillales and Bacteroidales. Furthermore, most correlations between host gene expression and relative abundance of bacterial modules were co-correlated with abundance of Wolbachia (but not Spiroplasma), indicative of an interdependence between host functional traits, microbiota composition and Wolbachia abundance in this species. These data suggest that, in these natural populations of drosophilid flies, different host species interact with microbial communities in functionally different ways that can vary with the abundance of endosymbionts.

RevDate: 2019-11-18

Poehlman WL, Schnabel EL, Chavan SA, et al (2019)

Identifying Temporally Regulated Root Nodulation Biomarkers Using Time Series Gene Co-Expression Network Analysis.

Frontiers in plant science, 10:1409.

Root nodulation results from a symbiotic relationship between a plant host and Rhizobium bacteria. Synchronized gene expression patterns over the course of rhizobial infection result in activation of pathways that are unique but overlapping with the highly conserved pathways that enable mycorrhizal symbiosis. We performed RNA sequencing of 30 Medicago truncatula root maturation zone samples at five distinct time points. These samples included plants inoculated with Sinorhizobium medicae and control plants that did not receive any Rhizobium. Following gene expression quantification, we identified 1,758 differentially expressed genes at various time points. We constructed a gene co-expression network (GCN) from the same data and identified link community modules (LCMs) that were comprised entirely of differentially expressed genes at specific time points post-inoculation. One LCM included genes that were up-regulated at 24 h following inoculation, suggesting an activation of allergen family genes and carbohydrate-binding gene products in response to Rhizobium. We also identified two LCMs that were comprised entirely of genes that were down regulated at 24 and 48 h post-inoculation. The identity of the genes in these modules suggest that down-regulating specific genes at 24 h may result in decreased jasmonic acid production with an increase in cytokinin production. At 48 h, coordinated down-regulation of a specific set of genes involved in lipid biosynthesis may play a role in nodulation. We show that GCN-LCM analysis is an effective method to preliminarily identify polygenic candidate biomarkers of root nodulation and develop hypotheses for future discovery.

RevDate: 2019-11-18
CmpDate: 2019-11-18

Moskowitz JE, S Devkota (2019)

Determinants of Microbial Antibiotic Susceptibility: The Commensal Gut Microbiota Perspective.

Cell host & microbe, 26(5):574-576.

Ng et al. (2019) unravel the complex factors that shape commensal gut microbiota susceptibility and resilience to antibiotics. These findings depict the microbiota's malleable dynamics resulting from compositional changes, environmental variability, and dietary shifts, further informing potential strategies to mitigate incomplete microbiome recovery accompanying antibiotic treatment.

RevDate: 2019-11-18
CmpDate: 2019-11-18

Mushegian AA, K Tougeron (2019)

Animal-Microbe Interactions in the Context of Diapause.

The Biological bulletin, 237(2):180-191.

Dormancy and diapause are key adaptations in many organisms, enabling survival of temporarily or seasonally unsuitable environmental conditions. In this review, we examine how our understanding of programmed developmental and metabolic arrest during diapause intersects with the increasing body of knowledge about animal co-development and co-evolution with microorganisms. Host-microbe interactions are increasingly understood to affect a number of metabolic, physiological, developmental, and behavioral traits and to mediate adaptations to various environments. Therefore, it is timely to consider how microbial factors might affect the expression and evolution of diapause in a changing world. We examine how a range of host-microbe interactions, from pathogenic to mutualistic, may have an impact on diapause phenotypes. Conversely, we examine how the discontinuities that diapause introduces into animal host generations can affect the ecology of microbial communities and the evolution of host-microbe interactions. We discuss these issues as they relate to physiology, evolution of development, local adaptation, disease ecology, and environmental change. Finally, we outline research questions that bridge the historically distinct fields of seasonal ecology and host-microbe interactions.

RevDate: 2019-11-18
CmpDate: 2019-11-18

Youle RJ (2019)

Mitochondria-Striking a balance between host and endosymbiont.

Science (New York, N.Y.), 365(6454):.

Mitochondria are organelles with their own genome that arose from α-proteobacteria living within single-celled Archaea more than a billion years ago. This step of endosymbiosis offered tremendous opportunities for energy production and metabolism and allowed the evolution of fungi, plants, and animals. However, less appreciated are the downsides of this endosymbiosis. Coordinating gene expression between the mitochondrial genomes and the nuclear genome is imprecise and can lead to proteotoxic stress. The clonal reproduction of mitochondrial DNA requires workarounds to avoid mutational meltdown. In metazoans that developed innate immune pathways to thwart bacterial and viral infections, mitochondrial components can cross-react with pathogen sensors and invoke inflammation. Here, I focus on the numerous and elegant quality control processes that compensate for or mitigate these challenges of endosymbiosis.

RevDate: 2019-11-18
CmpDate: 2019-11-18

Li YH, Wang R, Sui XH, et al (2019)

Bradyrhizobium nanningense sp. nov., Bradyrhizobium guangzhouense sp. nov. and Bradyrhizobium zhanjiangense sp. nov., isolated from effective nodules of peanut in Southeast China.

Systematic and applied microbiology, 42(5):126002.

Nine slow-growing rhizobia isolated from effective nodules on peanut (Arachis hypogaea) were characterized to clarify the taxonomic status using a polyphasic approach. They were assigned to the genus Bradyrhizobium on the basis of 16S rRNA sequences. MLSA of concatenated glnII-recA-dnaK genes classified them into three species represented by CCBAU 53390T, CCBAU 51670T and CCBAU 51778T, which presented the closest similarity to B. guangxiense CCBAU 53363T, B. guangdongense CCBAU 51649T and B. manausense BR 3351T, B. vignae 7-2T and B. forestalis INPA 54BT, respectively. The dDDH (digital DNA-DNA hybridization) and ANI (Average Nucleotide Identity) between the genomes of the three representative strains and type strains for the closest Bradyrhizobium species were less than 42.1% and 91.98%, respectively, below the threshold of species circumscription. Effective nodules could be induced on peanut and Lablab purpureus by all representative strains, while Vigna radiata formed effective nodules only with CCBAU 53390T and CCBAU 51778T. Phenotypic characteristics including sole carbon sources and growth features supported the phylogenetic results. Based on the genotypic and phenotypic features, strains CCBAU 53390T, CCBAU 51670T and CCBAU 51778T are designated the type strains of three novel species, for which the names Bradyrhizobium nanningense sp. nov., Bradyrhizobium guangzhouense sp. nov. and Bradyrhizobium zhanjiangense sp. nov. are proposed, respectively.

RevDate: 2019-11-18
CmpDate: 2019-11-18

Bouhnik O, ElFaik S, Alami S, et al (2019)

Ensifer fredii symbiovar vachelliae nodulates endemic Vachellia gummifera in semiarid Moroccan areas.

Systematic and applied microbiology, 42(5):125999.

The purpose of this work was to study the genetic diversity of the nodule-forming bacteria associated with native populations of Vachellia gummifera growing wild in Morocco. The nearly complete 16S rRNA gene sequences from three selected strains, following ARDRA and REP-PCR results, revealed they were members of the genus Ensifer and the sequencing of the housekeeping genes recA, gyrB, dnaK and rpoB, and their concatenated phylogenetic analysis, showed that the 3 strains belong to the species E. fredii. Based on the nodC and nodA phylogenies, the 3 strains clearly diverged from the type and other reference strains of E. fredii and formed a clearly separated cluster. The strains AGA1, AGA2 and AGB23 did not form nodules on Glycine max, Phaseolus vulgaris and Medicago truncatula, and effectively nodulated V. gummifera, Acacia cyanophylla, Prosopis chilensis and Leucaena leucocephala. Based on similarities of the nodC and nodA symbiotic genes and differences in the host range, the strains isolated from Moroccan endemic V. gummifera may form a different symbiovar within Ensifer species, for which the name "vachelliae" is proposed.

RevDate: 2019-11-18
CmpDate: 2019-11-18

Walker RE, Walker CG, Camargo CA, et al (2019)

Nasal microbial composition and chronic otitis media with effusion: A case-control study.

PloS one, 14(2):e0212473 pii:PONE-D-18-25440.

OBJECTIVES: Chronic otitis media with effusion (COME) in children can cause prolonged hearing loss, which is associated with an increased risk of learning delays and behavioural problems. Dispersal of bacterial pathogens from the nasal passages to the middle ear is implicated in COME. We sought to determine whether there is an association between nasal microbial composition and COME in children.

METHODS: A case-control study of children aged 3 and 4 years was conducted. Cases undergoing placement of tympanostomy tubes for COME were compared to healthy controls. Nasal swabs were collected and a questionnaire was administered. The V1-3 region of the 16S rRNA gene was amplified, and sequenced on the Illumina MiSeq.

RESULTS: 73 children with COME had a lower Shannon diversity index than 105 healthy controls (1.62 [.80] versus 1.88 [.84], respectively; P = .046). The nasal microbiota of cases and controls differed in composition using Bray-Curtis dissimilarity (p = 0.002). Children with COME had a higher abundance of otopathogens and lower abundance of commensals including alpha haemolytic Streptococci and Lactococcus. Cluster analysis revealed 4 distinct nasal microbial profiles. Profiles that were Corynebacterium-dominated (aOR 4.18 [95%CI, 1.68-10.39], Streptococcus-dominated (aOR 3.12 [95%CI, 1.08-9.06], or Moraxella-dominated (aOR 4.70 [95%CI, 1.73-12.80] were associated with COME, compared to a more mixed microbial profile when controlling for age, ethnicity, and recent antibiotics use.

CONCLUSIONS: Children with COME have a less diverse nasal microbial composition with a higher abundance of pathogens, compared to healthy children who have a more mixed bacterial profile with a higher abundance of commensals. Further research is required to determine how nasal microbiota may relate to the pathogenesis or maintenance of COME, and whether modification of the nasal microbiota can prevent or treat children at risk of COME.

RevDate: 2019-11-18
CmpDate: 2019-11-18

Biscéré T, Ferrier-Pagès C, Gilbert A, et al (2018)

Evidence for mitigation of coral bleaching by manganese.

Scientific reports, 8(1):16789.

Unprecedented mass coral bleaching events due to global warming and overall seawater pollution have been observed worldwide over the last decades. Although metals are often considered as toxic substances for corals, some are essential at nanomolar concentrations for physiological processes such as photosynthesis and antioxidant defenses. This study was designed to elucidate, the individual and combined effects of nanomolar seawater enrichment in manganese (Mn) and iron (Fe), on the main physiological traits of Stylophora pistillata, maintained under normal growth and thermal stress conditions. We provide, for the first time, evidence that Mn is a key trace element for coral symbionts, enhancing cellular chlorophyll concentrations, photosynthetic efficiency and gross photosynthetic rates at ambient temperature. Our experiment also highlights the key role of Mn in increasing coral resistance to heat stress-induced bleaching. While Mn-enriched corals did not bleach and did not reduce their rates of photosynthesis and calcification, control corals experienced significant bleaching. On the contrary to Mn, Fe enrichment not only impaired calcification but induced significant bleaching. Such information is an important step towards a better understanding of the response of corals to seawater enrichment in metals. It can also explain, to some extent, species susceptibility to environmental stress.

RevDate: 2019-11-17

Ngom M, Cissoko M, Gray K, et al (2020)

Establishment of Actinorhizal Symbiosis in Response to Ethylene, Salicylic Acid, and Jasmonate.

Methods in molecular biology (Clifton, N.J.), 2085:117-130.

Phytohormones play a crucial role in regulating plant developmental processes. Among them, ethylene and jasmonate are known to be involved in plant defense responses to a wide range of biotic stresses as their levels increase with pathogen infection. In addition, these two phytohormones have been shown to inhibit plant nodulation in legumes. Here, exogenous salicylic acid (SA), jasmonate acid (JA), and ethephon (ET) were applied to the root system of Casuarina glauca plants before Frankia inoculation, in order to analyze their effects on the establishment of actinorhizal symbiosis. This protocol further describes how to identify putative ortholog genes involved in ethylene and jasmonate biosynthesis and/or signaling pathways in plant, using the Arabidopsis Information Resource (TAIR), Legume Information System (LIS), and Genevestigator databases. The expression of these genes in response to the bacterium Frankia was analyzed using the gene atlas for Casuarina-Frankia symbiosis (SESAM web site).

RevDate: 2019-11-17

Basso V, C Veneault-Fourrey (2020)

Role of Jasmonates in Beneficial Microbe-Root Interactions.

Methods in molecular biology (Clifton, N.J.), 2085:43-67.

The phytohormone jasmonate (JA) modulates various defense and developmental responses of plants, and is implied in the integration of multiple environmental signals. Given its centrality in regulating plant physiology according to external stimuli, JA influences the establishment of interactions between plant roots and beneficial bacteria or fungi. In many cases, moderate JA signaling promotes the onset of mutualism, while massive JA signaling inhibits it. The output also depends on the compatibility between microbe and host plant and on nutritional or environmental cues. Also, JA biosynthesis and perception participate in the systemic regulation of mutualistic interactions and in microbe-induced resistance to biotic and abiotic stress. Here, we review our current knowledge of the role of JA biosynthesis, signaling, and responses during mutualistic root-microbe interactions.

RevDate: 2019-11-16

Petti S, G Lodi (2019)

The controversial natural history of oral Herpes Simplex Virus Type 1 infection.

Oral diseases [Epub ahead of print].

The natural history of oral Herpes Simplex virus Type-1 (HSV-1) infection in the immunocompetent host is complex and rich in controversial phenomena. Namely, the role of unapparent transmission in primary infection acquisition, the high frequency of asymptomatic primary and recurrent infections, the lack of immunogenicity of HSV-1 internalized in the soma (cell body) of the sensory neurons of the Trigeminal Ganglion, the lytic activity of HSV-1 in the soma of neurons that is limited in the sensory neurons of the Trigeminal Ganglion and often uncontrolled in the other neurons, the role of keratin in promoting the development of recurrence episodes in immunocompetent hosts, the virus-host Nash equilibrium, the paradoxical HSV-1 seronegative individuals who shed HSV-1 trough saliva, the limited efficacy of anti-HSV vaccines, and why the oral route of infection is the least likely to produce severe complications. The natural history of oral HSV-1 infection is also an history of symbiosis between humans and virus that may switch from mutualism to parasitism and vice versa. This balance is typical of microorganisms that are highly co-evolved with humans and its knowledge is essential to oral healthcare providers to perform adequate diagnosis and provide proper individual-based HSV-1 infection therapy.

RevDate: 2019-11-16

Banerjee J, Roy S, Dhas Y, et al (2019)

Senescence-associated miR-34a and miR-126 in middle-aged Indians with type 2 diabetes.

Clinical and experimental medicine pii:10.1007/s10238-019-00593-4 [Epub ahead of print].

Rapid urbanization and unhealthy dietary patterns critically increase the risk of type 2 diabetes (T2D) in middle-aged Indians. However, despite recent evidence of senescence-associated microRNAs (SA-miRNAs) in regulating complex pathways of ageing, their expressions in middle-aged Indians with T2D remain unexplored. Hence we aimed to investigate the changes in expressions of SA-miRNAs miR-34a and miR-126 in middle-aged T2D patients. A total of 30 T2D patients and 30 controls were recruited of age 31-50 years. The expressions of plasma miR-34a and miR-126 were determined by quantitative PCR. Oxidized LDL (OxLDL) and malondialdehyde (MDA) levels were quantified using enzyme-linked immunosorbent assay (ELISA). The effect of different glucose concentrations on miR-34a, miR-126, senescence-associated, and oxidative stress-responsive genes were also studied in an in vitro model of mice pancreatic β-cells. MiR-34a was significantly upregulated, whereas miR-126 was nonsignificantly reduced in T2D patients as compared to controls. T2D patients showed elevated levels of oxidative stress markers than controls. Analysis of cultured mice pancreatic β-cells exposed to high glucose showed significant upregulation of miR-34a, miR-126, p53, and superoxide dismutase 2 (SOD2). We found that circulating miR-34a levels and oxidative stress markers levels were elevated in the middle-aged Indians with T2D as compared to controls. The presence of diabetes may aggravate the normal ageing process in the middle-aged Indians. These SA-miRNAs can also be used to check the cellular dysfunctions and ageing of pancreatic β-cells.

RevDate: 2019-11-16

Robin A, Pradier C, Sanguin H, et al (2019)

How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation.

Mycorrhiza pii:10.1007/s00572-019-00917-y [Epub ahead of print].

Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.

RevDate: 2019-11-15

Younginger BS, ML Friesen (2019)

Connecting signals and benefits through partner choice in plant-microbe interactions.

FEMS microbiology letters pii:5626345 [Epub ahead of print].

Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model for these general principles, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies, which rely upon bacteria that only vary in nitrogen-fixation ability, ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we include a model which shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.

RevDate: 2019-11-15

Plett KL, Singan VR, Wang M, et al (2019)

Inorganic nitrogen availability alters Eucalyptus grandis receptivity to the ectomycorrhizal fungus Pisolithus albus but not symbiotic nitrogen transfer.

The New phytologist [Epub ahead of print].

Forest trees are able to thrive in nutrient poor soils in part because they obtain growth-limiting nutrients, especially nitrogen (N), through mutualistic symbiosis with ectomycorrhizal (ECM) fungi. Addition of inorganic N into these soils is known to disrupt this mutualism and reduce the diversity of ECM fungi. Despite its ecological impact, the mechanisms governing the observed effects of elevated inorganic N on mycorrhizal communities remain unknown. We address this by using a compartmentalized in vitro system to independently alter nutrients to each symbiont. Using stable isotopes, we traced the nutrient flux under different nutrient regimes between Eucalyptus grandis and its ectomycorrhizal symbiont, Pisolithus albus. We demonstrate that giving E. grandis independent access to N causes a significant reduction in root colonization by P. albus. Transcriptional analysis suggests that the observed reduction in colonization may be caused, in part, by altered transcription of microbe perception genes and defence genes. We show that delivery of N to host leaves is not increased by host nutrient deficiency but by fungal nutrient availability. Overall, this advances our understanding of the effects of N fertilization on ECM fungi and the factors governing nutrient transfer in the E. grandis - P. microcarpus interaction.

RevDate: 2019-11-15

Grimaldi DA, Peñalver E, Barrón E, et al (2019)

Direct evidence for eudicot pollen-feeding in a Cretaceous stinging wasp (Angiospermae; Hymenoptera, Aculeata) preserved in Burmese amber.

Communications biology, 2:408 pii:652.

Angiosperms and their insect pollinators form a foundational symbiosis, evidence for which from the Cretaceous is mostly indirect, based on fossils of insect taxa that today are anthophilous, and of fossil insects and flowers that have apparent anthophilous and entomophilous specializations, respectively. We present exceptional direct evidence preserved in mid-Cretaceous Burmese amber, 100 mya, for feeding on pollen in the eudicot genus Tricolporoidites by a basal new aculeate wasp, Prosphex anthophilos, gen. et sp. nov., in the lineage that contains the ants, bees, and other stinging wasps. Plume of hundreds of pollen grains wafts from its mouth and an apparent pollen mass was detected by micro-CT in the buccal cavity: clear evidence that the wasp was foraging on the pollen. Eudicots today comprise nearly three-quarters of all angiosperm species. Prosphex feeding on Tricolporoidites supports the hypothesis that relatively small, generalized insect anthophiles were important pollinators of early angiosperms.

RevDate: 2019-11-15
CmpDate: 2019-11-15

Medina G, Leyán P, da Silva CV, et al (2019)

Intra-amoebic localization of Arcobacter butzleri as an endocytobiont of Acanthamoeba castellanii.

Archives of microbiology, 201(10):1447-1452.

Acanthamoeba castellanii is a free-living amoeba found mainly in humid environments and Arcobacter butzleri is an emerging zoonotic pathogen, both can establish in vitro endosymbiotic relationships in the absence of bacterial replication. We analyzed the localization of A. butzleri within A. castellanii establishing their association with endoplasmic reticulum vesicles and mitochondria. Through confocal microscopy, we observed that during the early stages of endosymbiosis, there is not colocalization between amoebic vacuoles containing A. butzleri and mitochondria or ER vesicles of A. castellanii. Considering that energy production of this bacterium occurs via metabolism of amino acids or the tricarboxylic acid cycle, these results contribute to explain the absence of bacterial replication, since A. butzleri would not have access to the nutrients found in endoplasmic reticulum vesicles and mitochondria. In addition, we observe that A. butzleri induces significantly the actin polymerization of A. castellanii during the early stages of endosymbiosis.

RevDate: 2019-11-15
CmpDate: 2019-11-15

Hartmann AC, Marhaver KL, Klueter A, et al (2019)

Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host.

Molecular ecology, 28(1):141-155.

Theory suggests that the direct transmission of beneficial endosymbionts (mutualists) from parents to offspring (vertical transmission) in animal hosts is advantageous and evolutionarily stable, yet many host species instead acquire their symbionts from the environment (horizontal acquisition). An outstanding question in marine biology is why some scleractinian corals do not provision their eggs and larvae with the endosymbiotic dinoflagellates that are necessary for a juvenile's ultimate survival. We tested whether the acquisition of photosynthetic endosymbionts (family Symbiodiniaceae) during the planktonic larval stage was advantageous, as is widely assumed, in the ecologically important and threatened Caribbean reef-building coral Orbicella faveolata. Following larval acquisition, similar changes occurred in host energetic lipid use and gene expression regardless of whether their symbionts were photosynthesizing, suggesting the symbionts did not provide the energetic benefit characteristic of the mutualism in adults. Larvae that acquired photosymbionts isolated from conspecific adults on their natal reef exhibited a reduction in swimming, which may interfere with their ability to find suitable settlement substrate, and also a decrease in survival. Larvae exposed to two cultured algal species did not exhibit differences in survival, but decreased their swimming activity in response to one species. We conclude that acquiring photosymbionts during the larval stage confers no advantages and can in fact be disadvantageous to this coral host. The timing of symbiont acquisition appears to be a critical component of a host's life history strategy and overall reproductive fitness, and this timing itself appears to be under selective pressure.

RevDate: 2019-11-15
CmpDate: 2019-11-15

Kim H, Keum S, Hasan A, et al (2018)

Identification of an entomopathogenic bacterium, Xenorhabdus ehlersii KSY, from Steinernema longicaudum GNUS101 and its immunosuppressive activity against insect host by inhibiting eicosanoid biosynthesis.

Journal of invertebrate pathology, 159:6-17.

Steinernema longicaudum GNUS101, an entomopathogenic nematode, was isolated from soils in Korea. Its internal transcribed space sequence was highly similar to the known S. longicaudum species. Infective juveniles (IJs) of S. longicaudum were highly virulent to lepidopteran and coleopteran insects. Two different bacteria were isolated from the hemolymph of lepidopteran larvae infected with S. longicaudum. They exhibited blue and red colonies on nutrient bromothymol blue agar. The red-colored bacterium was identified as Enterococcus mundtii KHY while the blue-colored bacterium was identified as Xenorhabdus ehlersii KSY based on 16S rRNA sequencing and biochemical characters. The bacterial species showed different growth rates, with X. ehlersii KSY growing more slowly than E. mundtii KHY. Both bacteria were entomopathogenic, but showed differences in suppressing host immune responses. X. ehlersii KSY, but not E. mundtii KHY, showed inhibitory activity against cellular immune responses of Spodoptera exigua larvae including hemocyte-spreading behavior and nodule formation in bacteria-cultured broth. Its immunosuppressive activity was reversed by adding arachidonic acid, an eicosanoid biosynthesis precursor. Furthermore, organic extracts of X. ehlersii KSY using hexane or ethyl acetate showed inhibitory activity against cellular immune responses of S. exigua larvae. Arachidonic acid addition to S. exigua larvae infected with X. ehlersii significantly rescued the survival rate of target insect. Of the two bacteria isolated from S. longicaudum GNUS101, only X. ehlersii induced immunosuppression of target insect by inhibiting eicosanoid biosynthesis.

RevDate: 2019-11-13

Hakim S, Mirza BS, Imran A, et al (2019)

Illumina sequencing of 16S rRNA tag shows disparity in rhizobial and non-rhizobial diversity associated with root nodules of mung bean (Vigna radiata L.) growing in different habitats in Pakistan.

Microbiological research, 231:126356 pii:S0944-5013(19)30970-X [Epub ahead of print].

In Rhizobium-legume symbiosis, the nodule is the most frequently studied compartment, where the endophytic/symbiotic microbiota demands critical investigation for development of specific inocula. We identified the bacterial diversity within root nodules of mung bean from different growing areas of Pakistan using Illumina sequencing of 16S rRNA gene. We observed specific OTUs related to specific site where Bradyrhizobium was found to be the dominant genus comprising of 82-94% of total rhizobia in nodules with very minor fraction of sequences from other rhizobia at three sites. In contrast, Ensifer (Sinorhizobium) was single dominant genus comprising 99.9% of total rhizobial sequences at site four. Among non-rhizobial sequences, the genus Acinetobacter was abundant (7-18% of total sequences), particularly in Bradyrhizobium-dominated nodule samples. Rhizobia and non-rhizobial PGPR isolated from nodule samples include Ensifer, Bradyrhizobium, Acinetobacter, Microbacterium and Pseudomonas strains. Co-inoculation of multi-trait PGPR Acinetobacter sp. VrB1 with either of the two rhizobia in field exhibited more positive effect on nodulation and plant growth than single-strain inoculation which favors the use of Acinetobacter as an essential component for development of mung bean inoculum. Furthermore, site-specific dominance of rhizobia and non-rhizobia revealed in this study may contribute towards decision making for development and application of specific inocula in different habitats.

RevDate: 2019-11-13

Forrester NJ, TL Ashman (2019)

Autopolyploidy alters nodule-level interactions in the legume-rhizobium mutualism.

American journal of botany [Epub ahead of print].

PREMISE: Polyploidy is a major genetic driver of ecological and evolutionary processes in plants, yet its effects on plant interactions with mutualistic microbes remain unresolved. The legume-rhizobium symbiosis regulates global nutrient cycles and plays a role in the diversification of legume species. In this mutualism, rhizobia bacteria fix nitrogen in exchange for carbon provided by legume hosts. This exchange occurs inside root nodules, which house bacterial cells and represent the interface of legume-rhizobium interactions. Although polyploidy may directly impact the legume-rhizobium mutualism, no studies have explored how it alters the internal structure of nodules.

METHODS: We created synthetic autotetraploids using Medicago sativa subsp. caerulea. Neotetraploid plants and their diploid progenitors were singly inoculated with two strains of rhizobia, Sinorhizobium meliloti and S. medicae. Confocal microscopy was used to quantify internal traits of nodules produced by diploid and neotetraploid plants.

RESULTS: Autotetraploid plants produced larger nodules with larger nitrogen fixation zones than diploids for both strains of rhizobia, although the significance of these differences was limited by power. Neotetraploid M. sativa subsp. caerulea plants also produced symbiosomes that were significantly larger, nearly twice the size, than those present in diploids.

CONCLUSIONS: This study sheds light on how polyploidy directly affects a plant-bacterium mutualism and uncovers novel mechanisms. Changes in plant-microbe interactions that directly result from polyploidy likely contribute to the increased ability of polyploid legumes to establish in diverse environments.

RevDate: 2019-11-13

Ford Denison R (2019)

Evolutionary trade-offs are key to beneficial manipulation of crops by microbes.

American journal of botany [Epub ahead of print].

RevDate: 2019-11-13

Kreth J, Abdelrahman YM, J Merritt (2020)

Multiplex Imaging of Polymicrobial Communities-Murine Models to Study Oral Microbiome Interactions.

Methods in molecular biology (Clifton, N.J.), 2081:107-126.

Similar to other mucosal surfaces of the body, the oral cavity hosts a diverse microbial flora that live in polymicrobial biofilm communities. It is the ecology of these communities that are the primary determinants of oral health (symbiosis) or disease (dysbiosis). As such, both symbiosis and dysbiosis are inherently polymicrobial phenomena. In an effort to facilitate studies of polymicrobial communities within rodent models, we developed a suite of synthetic luciferases suitable for multiplexed in situ analyses of microbial ecology and specific gene expression. Using this approach, it is feasible to noninvasively measure multiple luciferase signals in vivo with both spatial and temporal resolution. In the following chapter, we describe the relevant details and protocols used to establish a biophotonic imaging platform for the study of experimental polymicrobial oral biofilms and abscesses in mice. The protocols described here are specifically tailored for use with oral streptococci, but the general strategies are adaptable for a wide range of polymicrobial infection studies using other species.

RevDate: 2019-11-13

Rimington WR, Pressel S, Duckett JG, et al (2019)

Evolution and networks in ancient and widespread symbioses between Mucoromycotina and liverworts.

Mycorrhiza pii:10.1007/s00572-019-00918-x [Epub ahead of print].

Like the majority of land plants, liverworts regularly form intimate symbioses with arbuscular mycorrhizal fungi (Glomeromycotina). Recent phylogenetic and physiological studies report that they also form intimate symbioses with Mucoromycotina fungi and that some of these, like those involving Glomeromycotina, represent nutritional mutualisms. To compare these symbioses, we carried out a global analysis of Mucoromycotina fungi in liverworts and other plants using species delimitation, ancestral reconstruction, and network analyses. We found that Mucoromycotina are more common and diverse symbionts of liverworts than previously thought, globally distributed, ancestral, and often co-occur with Glomeromycotina within plants. However, our results also suggest that the associations formed by Mucoromycotina fungi are fundamentally different because, unlike Glomeromycotina, they may have evolved multiple times and their symbiotic networks are un-nested (i.e., not forming nested subsets of species). We infer that the global Mucoromycotina symbiosis is evolutionarily and ecologically distinctive.

RevDate: 2019-11-13

Kolbasova GD, ES Mekhova (2019)

Myzostoma khanhkhoaensis (Myzostomida), a new myzostomid species from the Nhatrang Bay, Vietnam.

Zootaxa, 4691(3):zootaxa.4691.3.4 pii:zootaxa.4691.3.4.

A new myzostome species, described here as Myzostoma khanhkhoaensis sp. nov., was collected in Nhatrang Bay, central Vietnam, during investigation of symbionts associated with crinoids. Myzostoma khanhkhoaensis sp. nov. was found only on Clarkcomanthus albinotus Rowe, Hoggett, Birtles Vail, 1986 in dense groups of up to 25 specimens. This species closely matches the colour pattern of the host by adjusting its cryptic colour and infects the distal part of crinoid arms, causing them to become curved. This is the first record of myzostomes that induce deformation of skeletal elements without the formation of galls or cysts. Morphologically M. khanhkhoaensis sp. nov. is close to M. cuniculus and M. pseudocuniculus but clearly differs from both of them by the shape of caudal blade and chaetae. Molecular-genetics analysis based on CO1, 16S and 18S DNA placed M. khanhkhoaensis sp. nov. in a clade including M. cuniculus, M. pseudocuniculus and M. indocuniculus.

RevDate: 2019-11-13

Najjar RS, RG Feresin (2019)

Plant-Based Diets in the Reduction of Body Fat: Physiological Effects and Biochemical Insights.

Nutrients, 11(11): pii:nu11112712.

Obesity affects over one-third of Americans and increases the risk of cardiovascular disease and type II diabetes. Interventional trials have consistently demonstrated that consumption of plant-based diets reduces body fat in overweight and obese subjects, even when controlling for energy intake. Nonetheless, the mechanisms underlying this effect have not been well-defined. This review discusses six major dietary mechanisms that may lead to reduced body fat. These include (1) reduced caloric density, (2) improved gut microbiota symbiosis, (3) increased insulin sensitivity, (4) reduced trimethylamine-N-oxide (TMAO), (5) activation of peroxisome proliferator-activated receptors (PPARs), and (6) over-expression of mitochondrial uncoupling proteins. Collectively, these factors improve satiety and increase energy expenditure leading to reduced body weight.

RevDate: 2019-11-13

Anker A, S DE Grave (2019)

Further records of burrow-associated palaemonid shrimps (Decapoda: Palaemonidae).

Zootaxa, 4612(1):zootaxa.4612.1.13 pii:zootaxa.4612.1.13.

Despite the ubiquitous nature of symbiosis in palaemonid shrimps (Caridea: Palaemonidae) which live in or on varied invertebrate hosts, such as echinoderms, sponges, ascidians, hard and soft corals, etc., very few taxa have been recorded living in burrows constructed by other animals. This is in sharp contrast to the rich burrow-dwelling diversity in the Alpheidae, in which numerous genera associate with a great variety of burrowing animals, including stomatopods (Hayashi 2002; Ďuriš Anker 2014), echiurans (Anker et al. 2005, 2015), other alpheid shrimps (e.g. De Grave 2004; Anker Marin 2006), and especially numerous ghost and mud shrimps (e.g. Anker, 2011; Anker Lazarus 2015).

RevDate: 2019-11-13

Anker A, H Ashrafi (2019)

Salmoneus durisi sp. nov., an infaunal alpheid shrimp probably associated with callianassid ghost shrimps in the tropical Indo-West Pacific (Malacostraca: Decapoda: Caridea).

Zootaxa, 4651(1):zootaxa.4651.1.4 pii:zootaxa.4651.1.4.

A new species of the alpheid shrimp genus Salmoneus Holthuis, 1955, probably an obligate associate of ghost shrimp burrows, is described based on material from Oman (type locality: Darsait near Muscat), Iran and the Philippines. Salmoneus durisi sp. nov. is characterised principally by both chelipeds enlarged, robust, with ventral and dorsal margins of chelae carrying long fine setae, and with minor chela fingers armed with a few large teeth on cutting edges. All specimens of Salmoneus durisi sp. nov. were collected either directly from burrows of larger decapod crustaceans with the aid of a suction pump, or by exposing burrows dug under large subtidal rocks. The Iranian specimen was found together with its presumed host, Neocallichirus calmani (Nobili, 1904). Two additional specimens from Indonesia and the Solomon Islands are tentatively assigned to S. cf. durisi sp. nov., awaiting further studies.

RevDate: 2019-11-13

Anker A (2019)

On three symbiotic species of the alpheid shrimp genus Salmoneus Holthuis, 1955 from the Indo-West Pacific, including one new to science (Malacostraca: Decapoda: Caridea).

Zootaxa, 4651(1):zootaxa.4651.1.3 pii:zootaxa.4651.1.3.

Three species of the alpheid shrimp genus Salmoneus Holthuis, 1955 associated with burrows of other decapod crustaceans are reported from various Indo-West Pacific localities. Salmoneus venustus sp. nov. is described based on material collected at two distant localities, Nha Trang Bay, southern Vietnam, the type locality of the new species, and the Yiti-Sifah region east of Muscat, northern Oman. Both specimens were collected with the aid of a suction pump applied to burrow entrances or mounds in muddy sand; the holotype was possibly associated with burrows of the callianassid ghost shrimp, Glypturus sp. Salmoneus venustus sp. nov. shares many characteristics with S. latirostris (Coutière, 1897), including the red banding of the pleon, but can be distinguished from S. latirostris and all other species of the genus by a unique combination of morphological characters. The large-sized Salmoneus brucei Komai, 2009 is reported from Sumba, central Indonesia, representing a significant southward extension of the species' previously known distribution range and the first record since its original description. The callianassid ghost shrimp Lepidophthalmus cf. rosae (Nobili, 1904) is recorded as a new host of S. brucei. Finally, Salmoneus colinorum De Grave, 2004, associated with burrows of larger snapping shrimps from the Alpheus malabaricus Fabricius, 1798 species complex, is reported for the first time from Madang, Papua New Guinea, representing an eastward extension of the species' previously known distribution range.

RevDate: 2019-11-13

Goto R, M Tanaka (2019)

Worm-riding clam: description of Montacutona sigalionidcola sp. nov. (Bivalvia: Heterodonta: Galeommatidae) from Japan and its phylogenetic position.

Zootaxa, 4652(3):zootaxa.4652.3.4 pii:zootaxa.4652.3.4.

A new galeommatid bivalve, Montacutona sigalionidcola sp. nov., is described from an intertidal flat in the southern end of the Kii Peninsula, Honshu Island, Japan. Unlike other members of the genus, this species is a commensal with the burrowing scale worm Pelogenia zeylanica (Willey) (Annelida: Sigalionidae) that lives in fine sand sediments. Specimens were always found attached to the dorsal surface of the anterior end of the host body. This species has a ligament lithodesma between diverging hinge teeth, which is characteristic of Montacutona Yamamoto Habe. However, it is morphologically distinguished from the other members of this genus in having elongate-oval shells with small gape at the posteroventral margin and lacking an outer demibranch. Molecular phylogenetic analysis based on the four-gene combined dataset (18S + 28S + H3 + COI) indicated that this species is monophyletic with Montacutona, Nipponomontacuta Yamamoto Habe and Koreamya Lützen, Hong Yamashita, which are commensals with sea anemones or Lingula brachiopods. This result suggests that host shifting across different phyla occurred at least twice in this clade.

RevDate: 2019-11-13
CmpDate: 2019-11-13

Konecka E, Z Olszanowski (2019)

First Evidence of Intracellular Bacteria Cardinium in Thermophilic Mite Microzetorchestes emeryi (Acari: Oribatida): Molecular Screening of Bacterial Endosymbiont Species.

Current microbiology, 76(9):1038-1044.

We undertook the issue of the distribution of intracellular bacteria among Oribatida (Acari). Six genera of bacteria were detected by PCR and Sanger DNA sequencing: Wolbachia, Cardinium, Rickettsia, Spiroplasma, Arsenophonus, and Hamiltonella. Our research, for the first time, revealed the presence of Cardinium in Microzetorchestes emeryi in two subpopulations separated from each other by 300 m. The percentages of infected animals were the same in both subpopulations-ca. 20%. The identity of 16S rDNA sequences of Cardinium between these two subpopulations of M. emeryi was 97%. Phylogenetic analysis showed that the Cardinium in M. emeryi was clustered into the group A. The occurrence of M. emeryi in Poland has not been reported before and our report is the first one. Cardinium maybe help the thermophilic M. emeryi to adapt to low temperatures in the Central Europe.

RevDate: 2019-11-14
CmpDate: 2019-11-14

Horváthová T, Babik W, Kozłowski J, et al (2019)

Vanishing benefits - The loss of actinobacterial symbionts at elevated temperatures.

Journal of thermal biology, 82:222-228.

Only a few insect species are known to engage in symbiotic associations with antibiotic-producing Actinobacteria and profit from this kind of protection against pathogens. However, it still remains elusive how widespread the symbiotic interactions with Actinobacteria in other organisms are and how these partnerships benefit the hosts in terms of the growth and survival. We characterized a drastic temperature-induced change in the occurrence of Actinobacteria in the gut of the terrestrial isopod Porcellio scaber reared under two different temperature (15 °C and 22 °C) and oxygen conditions (10% and 22% O2) using 16S rRNA gene sequencing. We show that the relative abundance of actinobacterial gut symbionts correlates with increased host growth at lower temperature. Actinobacterial symbionts were almost completely absent at 22 °C under both high and low oxygen conditions. In addition, we identified members of nearly half of the known actinobacterial families in the isopod microbiome, and most of these include members that are known to produce antibiotics. Our study suggests that hosting diverse actinobacterial symbionts may provide conditions favorable for host growth. These findings show how a temperature-driven decline in microbiome diversity may cause a loss of beneficial functions with negative effects on ectotherms.

RevDate: 2019-11-14
CmpDate: 2019-11-14

Vaughan DB, Grutter AS, KS Hutson (2018)

Cleaner shrimp are a sustainable option to treat parasitic disease in farmed fish.

Scientific reports, 8(1):13959.

Chemical use is widespread in aquaculture to treat parasitic diseases in farmed fish. Cleaner fish biocontrols are increasingly used in fish farming as an alternative to medicines. However, cleaner fish are susceptible to some of their clients' parasites and their supply is largely dependent on wild harvest. In comparison, cleaner shrimp are not susceptible to fish ectoparasites and they can be reliably bred in captivity. The effectiveness of shrimp in reducing parasites on farmed fish remained unexplored until now. We tested four cleaner shrimp species for their ability to reduce three harmful parasites (a monogenean fluke, a ciliate protozoan, and a leech) on a farmed grouper. All shrimp reduced parasites on fish and most reduced the free-living early-life environmental stages - a function not provided by cleaner fish. Cleaner shrimp are sustainable biocontrol candidates against parasites of farmed fish, with the peppermint cleaner shrimp reducing parasites by up to 98%.

RevDate: 2019-11-12

Stieb SM, de Busserolles F, Carleton KL, et al (2019)

A detailed investigation of the visual system and visual ecology of the Barrier Reef anemonefish, Amphiprion akindynos.

Scientific reports, 9(1):16459 pii:10.1038/s41598-019-52297-0.

Vision plays a major role in the life of most teleosts, and is assumingly well adapted to each species ecology and behaviour. Using a multidisciplinary approach, we scrutinised several aspects of the visual system and ecology of the Great Barrier Reef anemonefish, Amphiprion akindynos, including its orange with white patterning, retinal anatomy and molecular biology, its symbiosis with anemones and sequential hermaphroditism. Amphiprion akindynos possesses spectrally distinct visual pigments and opsins: one rod opsin, RH1 (498 nm), and five cone opsins, SWS1 (370 nm), SWS2B (408 nm), RH2B (498 nm), RH2A (520 nm), and LWS (554 nm). Cones were arranged in a regular mosaic with each single cone surrounded by four double cones. Double cones mainly expressed RH2B (53%) in one member and RH2A (46%) in the other, matching the prevailing light. Single cones expressed SWS1 (89%), which may serve to detect zooplankton, conspecifics and the host anemone. Moreover, a segregated small fraction of single cones coexpressed SWS1 with SWS2B (11%). This novel visual specialisation falls within the region of highest acuity and is suggested to increase the chromatic contrast of Amphiprion akindynos colour patterns, which might improve detection of conspecifics.

RevDate: 2019-11-12

Mergaert P, Kereszt A, E Kondorosi (2019)

Gene Expression in Nitrogen-Fixing Symbiotic Nodule Cells in Medicago truncatula and Other Nodulating Plants.

The Plant cell pii:tpc.19.00494 [Epub ahead of print].

Root nodules formed by plants of the nitrogen-fixing clade (NFC) are symbiotic organs whose function is the maintenance and metabolic integration of large populations of nitrogen-fixing bacteria. These organs feature unique characteristics and processes, including their tissue organization, the presence of specific infection structures called infection threads, endocytotic uptake of bacteria, symbiotic cells that carry thousands of intracellular bacteria without signs of immune response, and the integration of symbiont and host metabolism. The early stages of the nodulation process are governed by a small set of well-defined functions, which together constitute the common symbiosis signaling pathway (CSSP). The CSSP activates a set of transcription factors (TFs) that orchestrate nodule organogenesis and infection. The later stages of nodule development require the activation of hundreds to thousands of genes, mostly expressed in the symbiotic cells. Many of these symbiotic cell-expressed genes are only active in these cells, reflecting the uniqueness of nodules as plant structures. While it is at present poorly understood how the nodule-specific transcriptome is activated and connected to early CSSP-signaling, candidate TFs have been identified by transcriptome approaches and the importance of epigenetic and chromatin-based regulation has been demonstrated. We further discuss how gene regulation analyses have advanced our understanding of nodule organogenesis and functioning of the symbiotic cells as well as the evolution of symbiosis in the NFC.

RevDate: 2019-11-12

Burlaka AP, Ganusevich II, Vovk AV, et al (2019)

Redox state of adipose tissue for patients with gastric cancer and its connection with the body mass index and distance from the tumor.

Obesity research & clinical practice pii:S1871-403X(18)30604-5 [Epub ahead of print].

Excess body weight has been causally linked to an increased risk of different cancer types, including gastric cancer but the mechanisms underlying this relationship are not well understood. Superoxide generation rate, activity of complex I in electron transport chain of mitochondria, activity of matrix metalloproteinase (MMP-2 and 9) of adipose tissues (AT) of patients with gastric cancer in AT located adjacent to tumor (ATAT) and at a distance of 3 cm (ATD) are measured to follow the connection of the redox state with some of the microenvironment indicators (HIF-1α, CD68, Plin5), body mass index (BMI) and cancer metastasis. Superoxide generation rate in ATAT positively correlates with BMI (r = 0.59, p < 0.05) being 4 times higher than in control (p < 0.05). MMP-2, 9 activities in ATAT positively correlate with BMI (r = 0.67, p < 0.05) being 3.3-4.0 higher than in control (p < 0.05). In ATD a statistically significant increase of MMP-2 activity is found. In ATAT for the group of patients with distant metastasis (M1) the superoxide generation rate, MMP-2, 9 activities are about 2 times higher (p < 0.05) than in the subgroup without distant metastases (M0). M1 is also characterized by the increased values of HIF-1α+ (factor 1.25), CD68+ (factor 1.4) and Plin5+ (factor 2.1) compared to M0 category in tumor tissues (p < 0.05). The results can be used for better understanding the mechanism(s) of symbiosis of tumor and adipose tissues as well as serve as a basis for new therapeutic approaches.

RevDate: 2019-11-12
CmpDate: 2019-11-12

Gohain A, Sarma RK, Debnath R, et al (2019)

Phylogenetic affiliation and antimicrobial effects of endophytic actinobacteria associated with medicinal plants: prevalence of polyketide synthase type II in antimicrobial strains.

Folia microbiologica, 64(4):481-496.

The most diverse and versatile endophytic actinobacteria are relatively unexplored potential sources of bioactive metabolites useful for different medical, agricultural, and other commercial applications. Their diversity in symbiotic association with traditionally utilized medicinal plants of northeast India is scantly available. The present investigation assessed the genetic diversity of endophytic actinobacteria (n = 120) distributed around the root, stem, and leaf tissues of six selected medicinal plants (Emblica officinalis, Terminalia chebula, T. arjuna, Murraya koenigii, Rauwolfia serpentina, and Azadirachta indica) from three different protected areas of evergreen forest-the Gibbon Wildlife Sanctuary (GWS), the Kaziranga National Park (KNP), and the North East Ecological Park (NEEP) of Assam, India. The samples were collected in two seasons (summer and winter). The overall phylogenetic analysis showed significant genetic diversity with 18 distinct genera belonging to 12 families. Overall, the occurrence of Streptomyces genus was predominant across all three sampling sites (76.66%), in both the sampling season (summer and winter). Shannon's and Simpson's diversity estimates showed their presence at A. indica (1.496, 0.778), R. serpentina (1.470, 0.858), and E. officinalis (0.975, 0.353). Among the site sampled, GWS had the most diverse community of actinobacteria (Shannon = 0.86 and Simpson = 0.557). The isolates were antagonistically more active against the investigated plant pathogenic bacteria than fungal pathogens. Further analysis revealed the prevalence of polyketide synthase genes (PKS) type II (84%) and PKS type I (16%) in the genome of the antimicrobial isolates. The overall findings confirmed the presence of biosynthetically active diverse actinobacterial members in the selected medicinal plants which offer potential opportunities towards the exploration of biologically active compounds.

RevDate: 2019-11-12
CmpDate: 2019-11-12

Clare EL, Fazekas AJ, Ivanova NV, et al (2019)

Approaches to integrating genetic data into ecological networks.

Molecular ecology, 28(2):503-519.

As molecular tools for assessing trophic interactions become common, research is increasingly focused on the construction of interaction networks. Here, we demonstrate three key methods for incorporating DNA data into network ecology and discuss analytical considerations using a model consisting of plants, insects, bats and their parasites from the Costa Rica dry forest. The simplest method involves the use of Sanger sequencing to acquire long sequences to validate or refine field identifications, for example of bats and their parasites, where one specimen yields one sequence and one identification. This method can be fully quantified and resolved and these data resemble traditional ecological networks. For more complex taxonomic identifications, we target multiple DNA loci, for example from a seed or fruit pulp sample in faeces. These networks are also well resolved but gene targets vary in resolution and quantification is difficult. Finally, for mixed templates such as faecal contents of insectivorous bats, we use DNA metabarcoding targeting two sequence lengths (157 and 407 bp) of one gene region and a MOTU, BLAST and BIN association approach to resolve nodes. This network type is complex to generate and analyse, and we discuss the implications of this type of resolution on network analysis. Using these data, we construct the first molecular-based network of networks containing 3,304 interactions between 762 nodes of eight trophic functions and involving parasitic, mutualistic and predatory interactions. We provide a comparison of the relative strengths and weaknesses of these data types in network ecology.

RevDate: 2019-11-12
CmpDate: 2019-11-12

González-Varo JP, Arroyo JM, P Jordano (2019)

The timing of frugivore-mediated seed dispersal effectiveness.

Molecular ecology, 28(2):219-231.

The seed dispersal effectiveness framework allows assessing mutualistic services from frugivorous animals in terms of quantity and quality. Quantity accounts for the number of seeds dispersed and quality for the probability of recruitment of dispersed seeds. Research on this topic has largely focused on the spatial patterns of seed deposition because seed fates often vary between microhabitats due to differences in biotic and abiotic factors. However, the temporal dimension has remained completely overlooked despite these factors-and even local disperser assemblages-can change dramatically during long fruiting periods. Here, we test timing effects on seed dispersal effectiveness, using as study case a keystone shrub species dispersed by frugivorous birds and with a fruiting period of 9 months. We evaluated quantity and quality in different microhabitats of a Mediterranean forest and different periods of the fruiting phenophase. We identified the bird species responsible for seed deposition through DNA barcoding and evaluated the probability of seedling recruitment through a series of field experiments on sequential demographic processes. We found that timing matters: The disperser assemblage was temporally structured, seed viability decreased markedly during the plant's fruiting phenophase, and germination was lower for viable seeds dispersed in the fruiting peak. We show how small contributions to seed deposition by transient migratory species can result in a relevant effectiveness if they disperse seeds in a high-quality period for seedling recruitment. This study expands our understanding of seed dispersal effectiveness, highlighting the importance of timing and infrequent interactions for population and community dynamics.

RevDate: 2019-11-12
CmpDate: 2019-11-12

Doña J, Proctor H, Serrano D, et al (2019)

Feather mites play a role in cleaning host feathers: New insights from DNA metabarcoding and microscopy.

Molecular ecology, 28(2):203-218.

Parasites and other symbionts are crucial components of ecosystems, regulating host populations and supporting food webs. However, most symbiont systems, especially those involving commensals and mutualists, are relatively poorly understood. In this study, we have investigated the nature of the symbiotic relationship between birds and their most abundant and diverse ectosymbionts: the vane-dwelling feather mites. For this purpose, we studied the diet of feather mites using two complementary methods. First, we used light microscopy to examine the gut contents of 1,300 individual feather mites representing 100 mite genera (18 families) from 190 bird species belonging to 72 families and 19 orders. Second, we used high-throughput sequencing (HTS) and DNA metabarcoding to determine gut contents from 1,833 individual mites of 18 species inhabiting 18 bird species. Results showed fungi and potentially bacteria as the main food resources for feather mites (apart from potential bird uropygial gland oil). Diatoms and plant matter appeared as rare food resources for feather mites. Importantly, we did not find any evidence of feather mites feeding upon bird resources (e.g., blood, skin) other than potentially uropygial gland oil. In addition, we found a high prevalence of both keratinophilic and pathogenic fungal taxa in the feather mite species examined. Altogether, our results shed light on the long-standing question of the nature of the relationship between birds and their vane-dwelling feather mites, supporting previous evidence for a commensalistic-mutualistic role of feather mites, which are revealed as likely fungivore-microbivore-detritivore symbionts of bird feathers.

RevDate: 2019-11-11

Konečný J, Hršelová H, Bukovská P, et al (2019)

Correlative evidence for co-regulation of phosphorus and carbon exchanges with symbiotic fungus in the arbuscular mycorrhizal Medicago truncatula.

PloS one, 14(11):e0224938 pii:PONE-D-19-13765.

Research efforts directed to elucidation of mechanisms behind trading of resources between the partners in the arbuscular mycorrhizal (AM) symbiosis have seen a considerable progress in the recent years. Yet, despite of the recent developments, some key questions still remain unanswered. For example, it is well established that the strictly biotrophic AM fungus releases phosphorus to- and receives carbon molecules from the plant symbiont, but the particular genes, and their products, responsible for facilitating this exchange, are still not fully described, nor are the principles and pathways of their regulation. Here, we made a de novo quest for genes involved in carbon transfer from the plant to the fungus using genome-wide gene expression array targeting whole root and whole shoot gene expression profiles of mycorrhizal and non-mycorrhizal Medicago truncatula plants grown in a glasshouse. Using physiological intervention of heavy shading (90% incoming light removed) and the correlation of expression levels of MtPT4, the mycorrhiza-inducible phosphate transporter operating at the symbiotic interface between the root cortical cells and the AM fungus, and our candidate genes, we demonstrate that several novel genes may be involved in resource tradings in the AM symbiosis established by M. truncatula. These include glucose-6-phosphate/phosphate translocator, polyol/monosaccharide transporter, DUR3-like, nucleotide-diphospho-sugar transferase or a putative membrane transporter. Besides, we also examined the expression of other M. truncatula phosphate transporters (MtPT1-3, MtPT5-6) to gain further insights in the balance between the "direct" and the "mycorrhizal" phosphate uptake pathways upon colonization of roots by the AM fungus, as affected by short-term carbon/energy deprivation. In addition, the role of the novel candidate genes in plant cell metabolism is discussed based on available literature.

RevDate: 2019-11-11

Collens A, Kelley E, LA Katz (2019)

The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis.

Journal of experimental zoology. Part B, Molecular and developmental evolution [Epub ahead of print].

John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host-associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way-by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.

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

Seto M, Y Iwasa (2019)

The fitness of chemotrophs increases when their catabolic by-products are consumed by other species.

Ecology letters, 22(12):1994-2005.

Chemotrophic microorganisms synthesise biomass by utilising energy obtained from a set of chemical reactions that convert resources to by-products, forming catabolic interactions. The amount of energy obtained per catabolic reaction decreases with the abundance of the by-product named as the 'abundant resource premium'. Consider two species, Species 1 and 2, Species 1 obtains energy from a reaction that converts resource A to by-product B. Species 2 then utilises B as its resource, extracting energy from a reaction that converts B to C. Thus, the presence of Species 2 reduces the abundance of B, which improves the fitness of Species 1 by increasing the energy acquisition per reaction of A to B. We discuss the population dynamic implication of this effect and its importance in expanding a realised niche, boosting material flow through the ecosystem and providing mutualistic interactions among species linked by the material flow. Introducing thermodynamics into population ecology could offer us fundamental ecological insights into understanding the ecology of chemotrophic microorganisms dominating the subsurface realm.

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

Klepa MS, Urquiaga MCO, Somasegaran P, et al (2019)

Bradyrhizobium niftali sp. nov., an effective nitrogen-fixing symbiont of partridge pea [Chamaecrista fasciculata (Michx.) Greene], a native caesalpinioid legume broadly distributed in the USA.

International journal of systematic and evolutionary microbiology, 69(11):3448-3459.

Information about the symbionts of legumes of the Caesalpinioideae subfamily is still limited, and we performed a polyphasic approach with three Bradyrhizobium strains-CNPSo 3448T, CNPSo 3394 and CNPSo 3442-isolated from Chamaecrista fasciculata, a native legume broadly distributed in the USA. In the phylogenetic analysis of both the 16S rRNA gene and the intergenic transcribed spacer, the CNPSo strains were clustered within the Bradyrhizobium japonicumsuperclade. Multilocus sequence analysis with six housekeeping genes-glnII, gyrB, recA, rpoB, atpD and dnaK-indicated that Bradyrhizobium diazoefficiens is the closest species, with 83 % of nucleotide identity. In the genome analyses of CNPSo 3448T, average nucleotide identity and digital DNA-DNA hybridization results confirmed higher similarity with B. diazoefficiens, with values estimated of 93.35 and 51.50 %, respectively, both below the threshold of the same species, confirming that the CNPSo strains represent a new lineage. BOX-PCR profiles indicated high intraspecific genetic diversity between the CNPSo strains. In the analyses of the symbiotic genes nodC and nifH the CNPSo strains were clustered with Bradyrhizobium arachidis, Bradyrhizobium forestalis, Bradyrhizobium cajani, Bradyrhizobium kavangense and Bradyrhizobium vignae, indicating a different phylogenetic history compared to the conserved core genes. Other physiological (C utilization, tolerance to antibiotics and abiotic stresses), chemical (fatty acid profile) and symbiotic (nodulation host range) properties were evaluated and are described. The data from our study support the description of the CNPSo strains as the novel species Bradyrhizobiumniftali sp. nov., with CNPSo 3448T (=USDA 10051T=U687T=CL 40T) designated as the type strain.

RevDate: 2019-11-10

Kowallis KA, Duvall SW, Zhao W, et al (2020)

Manipulation of Bacterial Signaling Using Engineered Histidine Kinases.

Methods in molecular biology (Clifton, N.J.), 2077:141-163.

Two-component systems allow bacteria to respond to changes in environmental or cytosolic conditions through autophosphorylation of a histidine kinase (HK) and subsequent transfer of the phosphate group to its downstream cognate response regulator (RR). The RR then elicits a cellular response, commonly through regulation of transcription. Engineering two-component system signaling networks provides a strategy to study bacterial signaling mechanisms related to bacterial cell survival, symbiosis, and virulence, and to develop sensory devices in synthetic biology. Here we focus on the principles for engineering the HK to identify unknown signal inputs, test signal transmission mechanisms, design small molecule sensors, and rewire two-component signaling networks.

RevDate: 2019-11-10

Pawlowski ML, Vuong TD, Valliyodan B, et al (2019)

Whole-genome resequencing identifies quantitative trait loci associated with mycorrhizal colonization of soybean.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik pii:10.1007/s00122-019-03471-5 [Epub ahead of print].

KEY MESSAGE: A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with colonization of soybean by an arbuscular mycorrhizal fungus (Rhizophagus intraradices). Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. Arbuscular mycorrhizal fungi (AMF) form associations with over 80% of all terrestrial plant species and assist their host plants by increasing their nutrient uptake, drought tolerance, and resilience against pathogens and pests. Genotypic variation of crop plants to AMF colonization has been identified in crops, including soybean; however, the genetics controlling levels of AMF colonization in soybean are unknown. The overall goal of our study was to identify genomic regions associated with mycorrhizal colonization in soybean using genome-wide association analysis. A diverse panel of 350 exotic soybean genotypes inoculated with Rhizophagus intraradices were microscopically evaluated for root colonization using a modified gridline intersect method. Root colonization differed significantly (P < 0.001) among genotypes and ranged from 11 to 70%. A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with R. intraradices colonization that explained 24% of the phenotypic variance. Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. The results showed there was a significant genetic component to the level of colonization by R. intraradices in soybean. This information may be useful in the development of AMF-sensitive soybean cultivars to enhance nutrient uptake, drought tolerance, and disease resistance in the crop.

RevDate: 2019-11-09

He J, Zhang C, Dai H, et al (2019)

A LysM Receptor Heteromer Mediates Perception of Arbuscular Mycorrhizal Symbiotic Signal in Rice.

Molecular plant pii:S1674-2052(19)30363-6 [Epub ahead of print].

Symbiotic microorganisms improve nutrient uptake by plants. To initiate mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, plants perceive Myc factors, including lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (CO4/CO5), secreted by AM fungi. However, the molecular mechanism of Myc factors perception remains elusive. Here, we identified a heteromer of LysM receptor-like kinases, OsMYR1/OsLYK2 and OsCERK1, that mediates perception of AM fungi in rice. CO4 directly binds to OsMYR1, promoting the dimerization and phosphorylation of this receptor complex. Compared to control plants, Osmyr1 and Oscerk1 mutant rice plants are less sensitive to Myc factors and show decreased AM colonization. We engineered transgenic rice by expressing chimeric receptors that respectively replaced the ectodomains of OsMYR1 and OsCERK1 with those from the homologous Nod factor receptors MtNFP and MtLYK3 of Medicago truncatula. Transgenic plants displayed increased calcium oscillations in response to Nod factors compared to control rice. Our findings reveal a mechanism for mycorrhizal symbiotic signal perception in rice, and the ectopic expression of chimeric Nod/Myc receptors achieves a potentially important step towards generating cereals that host nitrogen-fixing bacteria.

RevDate: 2019-11-09

Sgibnev A, E Kremleva (2019)

Probiotics in addition to metronidazole for treatment Trichomonas vaginalis in the presence of BV: a randomized, placebo-controlled, double-blind study.

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology pii:10.1007/s10096-019-03731-8 [Epub ahead of print].

The purpose was to evaluate whether probiotics can increase the effectiveness of antimicrobial therapy. Ninety women with Trichomonas vaginalis (TV) in the presence BV were included in the study of regimens for therapy combination with metronidazole and vaginal probiotics. For 7 days, the probiotics group patients received metronidazole at 500 mg twice a day and 1 capsule of probiotic Gynophilus® vaginally twice a day; the placebo group patients in addition to metronidazole received a placebo instead of a probiotic. For the next 7 days, patients in both groups in order restore normal microflora were given the probiotics vaginally. Before the treatment, on the 4th, 8th, and 15th day of therapy complaints, pH and redox potential of the vaginal fluid were recorded, TV detection culturally, microflora of the vagina with the qPCR-RT and microscopically. Adding probiotics to traditional therapy of TV in the presence of BV increased the likelihood of cure from TV (88.6 and 42.9% in the probiotic and placebo groups, respectively) and from BV (63.6 and 11.9%, respectively). We have found that the addition of probiotics to antimicrobial therapy causes the decrease in the inflammatory response and significant changes in the vagina's physicochemical parameters (decreased of the pH values, increased of the redox potential) already on the fourth day of the therapy. The changes in the metronidazole's antimicrobial action implementation when a probiotic is added are the reason of increasing the TV therapy's effectiveness in the BV presence.

RevDate: 2019-11-09

Nakakuni M, Yamasaki Y, Yoshitake N, et al (2019)

Methyl Ether-Derivatized Sterols and Coprostanol Produced via Thermochemolysis Using Tetramethylammonium Hydroxide (TMAH).

Molecules (Basel, Switzerland), 24(22): pii:molecules24224040.

Sterols are widely distributed in nature from lipids in organisms to sediments. As a conventional method, extraction and derivatization with TMS have been applied for sterol analysis, requiring a long preparation time for gas chromatography-mass spectrometry analysis. In this study, for sterol analysis, thermochemolysis using tetramethylammonium hydroxide (TMAH) was applied. This method performs hydrolysis and methylation simultaneously; thus, free and ether-bonding sterols can be analyzed as sterol methyl ethers in a relatively short time period. A sediment sample from a tideland (the Yatsu tideland, Japan) was analyzed using the TMAH method, and we detected more than 10 sterols, which include cholest-5-en-3β-ol (cholesterol), 24-ethylcholest-5-en-3β-ol (sitosterol), 24-methylcholesta-5,22E-3β-ol (brassicasterol), 24-ethylcholesta-5,24(28)Z-dien-3β-ol (isofucosterol), 4α,23,24-trimethyl-5α(H)-cholest-22E-en-3β- ol (dinosterol), and 5β(H)-cholestan-3β-ol (coprostanol). The detection of the various sterols can be attributed to multiple natural and artificial sources around the Yatsu tideland. In this paper, the mass spectra of these sterols are provided together with an interpretation of their fragmentation patterns. Additionally, the fecal pollution in the Yatsu tideland is discussed in the context of the detection of coprostanol.

RevDate: 2019-11-08

Margarita V, Marongiu A, Diaz N, et al (2019)

Prevalence of double-stranded RNA virus in Trichomonas vaginalis isolated in Italy and association with the symbiont Mycoplasma hominis.

Parasitology research pii:10.1007/s00436-019-06469-6 [Epub ahead of print].

The flagellated protozoon Trichomonas vaginalis, responsible for trichomoniasis, can establish a symbiotic relationship with the bacterium Mycoplasma hominis and can harbor double-stranded RNA Trichomonasvirus (TVV). In this study, we investigated by real-time PCR the prevalence of the four TVVs and of M. hominis among 48 T. vaginalis strains isolated in Italy, and we evaluated a possible association with metronidazole resistance. Fifty percent of the analyzed trichomonad strains tested positive for at least one TVV T. vaginalis, with TVV2 being the most prevalent, followed by TVV1 and TVV3. Two T. vaginalis strains were infected by TVV4, detected in Europe for the first time. Interestingly, we found more than one TVV species in 75% of positive trichomonad strains. M. hominis was present in 81.25% of T. vaginalis isolates tested, and no statistically significant association was observed with the infection by any TVV. Metronidazole sensitivity of T. vaginalis isolates was evaluated in vitro, and no correlation was observed between minimal lethal concentration and the presence of TVVs. This is the first report on TVV infection of T. vaginalis in Italy. Even if no association of TVV positive isolates with the presence of the symbiont M. hominis or with metronidazole resistance was observed, further studies are needed to shed light on the effective role of infecting microorganisms on the pathophysiology of T. vaginalis.

RevDate: 2019-11-08

Lanci L, Zanella E, Jovane L, et al (2019)

Dataset of characteristic remanent magnetization and magnetic properties of early Pliocene sediments from IODP Site U1467 (Maldives platform).

Data in brief, 27:104666 pii:104666.

This data article describes data of magnetic stratigraphy and anisotropy of isothermal remanent magnetization (AIRM) from "Magnetic properties of early Pliocene sediments from IODP Site U1467 (Maldives platform) reveal changes in the monsoon system" [1]. Acquisition of isothermal magnetization on pilot samples and anisotropy of isothermal remanent magnetization are reported as raw data; magnetostratigraphic data are reported as characteristic magnetization (ChRM).

RevDate: 2019-11-08

Cui L, Guo F, Zhang J, et al (2019)

Synergy of arbuscular mycorrhizal symbiosis and exogenous Ca2+ benefits peanut (Arachis hypogaea L.) growth through the shared hormone and flavonoid pathway.

Scientific reports, 9(1):16281 pii:10.1038/s41598-019-52630-7.

Peanut yield is severely affected by exchangeable calcium ion (Ca2+) deficiency in the soil. Arbuscular mycorrhizal (AM) symbiosis increases the absorption of Ca2+ for host plants. Here, we analyzed the physiological and transcriptional changes in the roots of Arachis hypogaea L. colonized by Funneliformis mosseae under Ca2+-deficient and -sufficient conditions. The results showed that exogenous Ca2+ application increased arbuscular mycorrhizal fungi (AMF) colonization, plant dry weight, and Ca content of AM plants. Simultaneously, transcriptome analysis showed that Ca2+ application further induced 74.5% of differentially expressed gene transcripts in roots of AM peanut seedlings. These genes are involved in AM symbiosis development, hormone biosynthesis and signal transduction, and carotenoid and flavonoid biosynthesis. The transcripts of AM-specific marker genes in AM plants with Ca2+ deprivation were further up-regulated by Ca2+ application. Gibberellic acid (GA3) and flavonoid contents were higher in roots of AM- and Ca2+-treated plants, but salicylic acid (SA) and carotenoid contents specifically increased in roots of the AM plants. Thus, these results suggest that the synergy of AM symbiosis and Ca2+ improves plant growth due to the shared GA- and flavonoid-mediated pathway, whereas SA and carotenoid biosynthesis in peanut roots are specific to AM symbiosis.

RevDate: 2019-11-08

Yuen B, Polzin J, JM Petersen (2019)

Organ transcriptomes of the lucinid clam Loripes orbiculatus (Poli, 1791) provide insights into their specialised roles in the biology of a chemosymbiotic bivalve.

BMC genomics, 20(1):820 pii:10.1186/s12864-019-6177-0.

BACKGROUND: The lucinid clam Loripes orbiculatus lives in a nutritional symbiosis with sulphur-oxidizing bacteria housed in its gills. Although our understanding of the lucinid endosymbiont physiology and metabolism has made significant progress, relatively little is known about how the host regulates the symbiosis at the genetic and molecular levels. We generated transcriptomes from four L. orbiculatus organs (gills, foot, visceral mass, and mantle) for differential expression analyses, to better understand this clam's physiological adaptations to a chemosymbiotic lifestyle, and how it regulates nutritional and immune interactions with its symbionts.

RESULTS: The transcriptome profile of the symbiont-housing gill suggests the regulation of apoptosis and innate immunity are important processes in this organ. We also identified many transcripts encoding ion transporters from the solute carrier family that possibly allow metabolite exchange between host and symbiont. Despite the clam holobiont's clear reliance on chemosynthesis, the clam's visceral mass, which contains the digestive tract, is characterised by enzymes involved in digestion, carbohydrate recognition and metabolism, suggesting that L. orbiculatus has a mixotrophic diet. The foot transcriptome is dominated by the biosynthesis of glycoproteins for the construction of mucus tubes, and receptors that mediate the detection of chemical cues in the environment.

CONCLUSIONS: The transcriptome profiles of gills, mantle, foot and visceral mass provide insights into the molecular basis underlying the functional specialisation of bivalve organs adapted to a chemosymbiotic lifestyle.

RevDate: 2019-11-08
CmpDate: 2019-11-08

Boza G, Worsley SF, Yu DW, et al (2019)

Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability.

PLoS computational biology, 15(5):e1007109 pii:PCOMPBIOL-D-19-00034.

Understanding the mechanisms that promote the assembly and maintenance of host-beneficial microbiomes is an open problem. Empirical evidence supports the idea that animal and plant hosts can combine 'private resources' with the ecological phenomenon known as 'community bistability' to favour some microbial strains over others. We briefly review evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotics to suppress non-beneficial, competitor strains, and (iii) provide resources that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. The faster early growth of preferred strains, combined with the phenomenon of 'community bistability,' allows those strains to continue to dominate the microbiome even after the private resource is withdrawn or made public. This is because after a beneficial colony reaches a sufficiently large size, it can resist invasion by parasites without further private support from the host. We further explicitly model localized microbial interactions and diffusion dynamics, and we show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that there is a wide range of parameters under which hosts can promote the assembly of a self-sustaining defensive microbiome. This in turn supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.

RevDate: 2019-11-08
CmpDate: 2019-11-08

Witchley JN, Penumetcha P, Abon NV, et al (2019)

Candida albicans Morphogenesis Programs Control the Balance between Gut Commensalism and Invasive Infection.

Cell host & microbe, 25(3):432-443.e6.

Candida albicans is a gut commensal and opportunistic pathogen. The transition between yeast and invasive hyphae is central to virulence but has unknown functions during commensal growth. In a mouse model of colonization, yeast and hyphae co-occur throughout the gastrointestinal tract. However, competitive infections of C. albicans homozygous gene disruption mutants revealed an unanticipated, inhibitory role for the yeast-to-hypha morphogenesis program on commensalism. We show that the transcription factor Ume6, a master regulator of filamentation, inhibits gut colonization, not by effects on cell shape, but by activating the expression of a hypha-specific pro-inflammatory secreted protease, Sap6, and a hyphal cell surface adhesin, Hyr1. Like a ume6 mutant, strains lacking SAP6 exhibit enhanced colonization fitness, whereas SAP6-overexpression strains are attenuated in the gut. These results reveal a tradeoff between fungal programs supporting commensalism and virulence in which selection against hypha-specific markers limits the disease-causing potential of this ubiquitous commensal-pathogen.

RevDate: 2019-11-08
CmpDate: 2019-11-08

Liang SH, Anderson MZ, Hirakawa MP, et al (2019)

Hemizygosity Enables a Mutational Transition Governing Fungal Virulence and Commensalism.

Cell host & microbe, 25(3):418-431.e6.

Candida albicans is a commensal fungus of human gastrointestinal and reproductive tracts, but also causes life-threatening systemic infections. The balance between colonization and pathogenesis is associated with phenotypic plasticity, with alternative cell states producing different outcomes in a mammalian host. Here, we reveal that gene dosage of a master transcription factor regulates cell differentiation in diploid C. albicans cells, as EFG1 hemizygous cells undergo a phenotypic transition inaccessible to "wild-type" cells with two functional EFG1 alleles. Notably, clinical isolates are often EFG1 hemizygous and thus licensed to undergo this transition. Phenotypic change corresponds to high-frequency loss of the functional EFG1 allele via de novo mutation or gene conversion events. This phenomenon also occurs during passaging in the gastrointestinal tract with the resulting cell type being hypercompetitive for commensal and systemic infections. A "two-hit" genetic model therefore underlies a key phenotypic transition in C. albicans that enables adaptation to host niches.

RevDate: 2019-11-07

Feng F, Sun J, Radhakrishnan GV, et al (2019)

A combination of chitooligosaccharide and lipochitooligosaccharide recognition promotes arbuscular mycorrhizal associations in Medicago truncatula.

Nature communications, 10(1):5047 pii:10.1038/s41467-019-12999-5.

Plants associate with beneficial arbuscular mycorrhizal fungi facilitating nutrient acquisition. Arbuscular mycorrhizal fungi produce chitooligosaccharides (COs) and lipo-chitooligosaccharides (LCOs), that promote symbiosis signalling with resultant oscillations in nuclear-associated calcium. The activation of symbiosis signalling must be balanced with activation of immunity signalling, which in fungal interactions is promoted by COs resulting from the chitinaceous fungal cell wall. Here we demonstrate that COs ranging from CO4-CO8 can induce symbiosis signalling in Medicago truncatula. CO perception is a function of the receptor-like kinases MtCERK1 and LYR4, that activate both immunity and symbiosis signalling. A combination of LCOs and COs act synergistically to enhance symbiosis signalling and suppress immunity signalling and receptors involved in both CO and LCO perception are necessary for mycorrhizal establishment. We conclude that LCOs, when present in a mix with COs, drive a symbiotic outcome and this mix of signals is essential for arbuscular mycorrhizal establishment.

RevDate: 2019-11-06

Bellantuono AJ, Dougan KE, Granados-Cifuentes C, et al (2019)

Free-living and symbiotic lifestyles of a thermotolerant coral endosymbiont display profoundly distinct transcriptomes under both stable and heat stress conditions.

Molecular ecology [Epub ahead of print].

Reef-building corals depend upon a nutritional endosymbiosis with photosynthetic dinoflagellates of the family Symbiodiniaceae for the majority of their energetic needs. While this mutualistic relationship is impacted by numerous stressors, warming oceans are a predominant threat to coral reefs, placing the future of the world's reefs in peril. Some Symbiodiniaceae species exhibit tolerance to thermal stress, but the in hospite symbiont response to thermal stress is underexplored. To describe the underpinnings of symbiosis and heat stress response, we compared in hospite and free-living transcriptomes of Durusdinium trenchii, a pan-tropical heat-tolerant Symbiodiniaceae species, under stable temperature conditions and acute hyperthermal stress. We discovered that symbiotic state was a larger driver of the transcriptional landscape than heat stress. The majority of differentially expressed transcripts between in hospite and free-living cells were downregulated, suggesting the in hospite condition is associated with the shutdown of numerous processes uniquely required for a free-living lifestyle. In the free-living state, we identified enrichment for numerous cell signaling pathways and other functions related to detecting and responding to a changing environment, as well as transcripts relating to mitosis, meiosis, and motility. In contrast, in hospite cells exhibited enhanced transcriptional activity for photosynthesis and carbohydrate transport as well as chromatin modifications and a disrupted circadian clock. Hyperthermal stress induced drastic alteration of transcriptional activity in hospite, suggesting symbiotic engagement with the host elicited an exacerbated stress response when compared to free-living D. trenchii. Altogether, the dramatic differences in gene expression between in hospite and free-living D. trenchii indicate the importance of considering symbiotic state in investigations of symbiosis and hyperthermal stress in Symbiodiniaceae.

RevDate: 2019-11-06

Simona F, Zhang H, CR Voolstra (2019)

Evidence for a Role of Protein Phosphorylation in the Maintenance of the Cnidarian-Algal Symbiosis.

Molecular ecology [Epub ahead of print].

The endosymbiotic relationship between cnidarians and photosynthetic dinoflagellate algae provides the foundation of coral reef ecosystems. This essential interaction is globally threatened by anthropogenic disturbance. As such, it is important to understand the molecular mechanisms underpinning the cnidarian-algal association. Here we investigated phosphorylation-mediated protein signaling as a mechanism of regulation of the cnidarian-algal interaction, and we report on the generation of the first phosphoproteome for the coral model organism Aiptasia. Using mass spectrometry-based phosphoproteomics in data-independent acquisition allowed consistent quantification of over 3,000 phosphopeptides totaling more than 1,600 phosphoproteins across aposymbiotic (symbiont-free) and symbiotic anemones. Comparison of the symbiotic states showed distinct phosphoproteomic profiles attributable to the differential phosphorylation of 539 proteins that cover a broad range of functions, from receptors to structural and signal transduction proteins. A subsequent pathway enrichment analysis identified the processes of 'protein digestion and absorption,' 'carbohydrate metabolism,' and 'protein folding, sorting, and degradation,' and highlighted differential phosphorylation of the 'phospholipase D signaling pathway' and 'protein processing in the endoplasmic reticulum.' Targeted phosphorylation of the phospholipase D signaling pathway suggests control of glutamate vesicle trafficking across symbiotic compartments, and phosphorylation of the endoplasmic reticulum machinery suggests recycling of symbiosome-associated proteins. Our study shows for the first time that changes in the phosphorylation status of proteins between aposymbiotic and symbiotic Aiptasia anemones play a role in the regulation of the cnidarian-algal symbiosis. This is the first phosphoproteomic study of a cnidarian-algal symbiotic association as well as the first application of quantification by data-independent acquisition in the coral field.

RevDate: 2019-11-06

Zink KE, Tarnowski DA, Mandel MJ, et al (2019)

Optimization of a minimal sample preparation protocol for imaging mass spectrometry of unsectioned juvenile invertebrates.

Journal of mass spectrometry : JMS [Epub ahead of print].

Tissue sections have long been the subject matter for the application of imaging mass spectrometry, but recently the technique has been adapted for many other purposes including bacterial colonies and 3D cell culture. Here, we present a simple preparation method for unsectioned invertebrate tissue without the need for fixing, embedding, or slicing. The protocol was used to successfully prepare a Hawaiian bobtail squid hatchling for analysis, and the resulting data detected ions that correspond to compounds present in the host only during its symbiotic colonization by Vibrio fischeri.

RevDate: 2019-11-06

Alves Monteiro HJ, Brahmi C, Mayfield AB, et al (2019)

Molecular mechanisms of acclimation to long-term elevated temperature exposure in marine symbioses.

Global change biology [Epub ahead of print].

Seawater temperature rise in French Polynesia has repeatedly resulted in the bleaching of corals and giant clams. Because giant clams possess distinctive ectosymbiotic features, they represent a unique and powerful model for comparing molecular pathways involved in 1) maintenance of symbiosis and 2) acquisition of thermo-tolerance among coral reef organisms. Herein, we explored the physiological and transcriptomic responses of the clam hosts and their photosynthetically active symbionts over a 65-day experiment in which clams were exposed to either normal or environmentally relevant elevated seawater temperatures. Additionally, we used metabarcoding data coupled with in situ sampling/survey data to explore the relative importance of holobiont adaptation (i.e., a symbiont community shift) versus acclimation (i.e., physiological changes at the molecular level) in the clams' responses to environmental change. We finally compared transcriptomic data to publicly available genomic datasets for Symbiodiniaceae dinoflagellates (both cultured and in hospite with the coral Pocillopora damicornis) to better tease apart the responses of both hosts and specific symbiont genotypes in this mutualistic association. Gene module preservation analysis revealed that the function of the symbionts' photosystem II was impaired at high temperature, and this response was also found across all holobionts and Symbiodiniaceae lineages examined. Similarly, epigenetic modulation appeared to be a key response mechanism for symbionts in hospite with giant clams exposed to high temperatures, and such modulation was able to distinguish thermo-tolerant from thermo-sensitive Cladocopium goreaui ecotypes; epigenetic processes may, then, represent a promising research avenue for those interested in coral reef conservation in this era of changing global climate.

RevDate: 2019-11-06

Kamra K, Kaur H, Prasad S, et al (2019)

Symposium Report: International Symposium on Ciliate Biology, India Habitat Centre, New Delhi, India, 04-06 April 2018.

The Journal of eukaryotic microbiology [Epub ahead of print].

Ciliated protists have attracted wide interest among researchers from the Indian sub-continent in the last few years. An International Symposium on Ciliate Biology (ISCB) 2018 was held on 04-06 April 2018 at the India Habitat Centre, New Delhi, India. The symposium represented a synergy with International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC), an affiliate society of International Society of Protistologists (ISOP). The symposium provided a platform for Indian and International delegates to exchange knowledge, present their latest research findings and establish collaborations as well as creating a networking opportunity for undergraduate and postgraduate students. Nine foreign delegates from 5 countries and 300 Indian delegates actively participated in the event which included 22 oral and 57 poster presentations.

RevDate: 2019-11-06

Kosolapova AO, Belousov MV, Sulatskaya AI, et al (2019)

Two Novel Amyloid Proteins, RopA and RopB, from the Root Nodule Bacterium Rhizobium leguminosarum.

Biomolecules, 9(11): pii:biom9110694.

Amyloids represent protein fibrils with a highly ordered spatial structure, which not only cause dozens of incurable human and animal diseases but also play vital biological roles in Archaea, Bacteria, and Eukarya. Despite the fact that association of bacterial amyloids with microbial pathogenesis and infectious diseases is well known, there is a lack of information concerning the amyloids of symbiotic bacteria. In this study, using the previously developed proteomic method for screening and identification of amyloids (PSIA), we identified amyloidogenic proteins in the proteome of the root nodule bacterium Rhizobium leguminosarum. Among 54 proteins identified, we selected two proteins, RopA and RopB, which are predicted to have β-barrel structure and are likely to be involved in the control of plant-microbial symbiosis. We demonstrated that the full-length RopA and RopB form bona fide amyloid fibrils in vitro. In particular, these fibrils are β-sheet-rich, bind Thioflavin T (ThT), exhibit green birefringence upon staining with Congo Red (CR), and resist treatment with ionic detergents and proteases. The heterologously expressed RopA and RopB intracellularly aggregate in yeast and assemble into amyloid fibrils at the surface of Escherichia coli. The capsules of the R. leguminosarum cells bind CR, exhibit green birefringence, and contain fibrils of RopA and RopB in vivo.

RevDate: 2019-11-05

Cervantes L, Miranda-Sánchez F, Tejerizo GT, et al (2019)

Plasmid pSfr64a and the symbiotic plasmid pSfr64b of Sinorhizobium fredii GR64 control each other's conjugative transfer through quorum-sensing elements.

Plasmid pii:S0147-619X(19)30067-8 [Epub ahead of print].

Rhizobia are nitrogen-fixing symbionts of plants. Their genomes frequently contain large plasmids, some of which are able to perform conjugative transfer. Plasmid pSfr64a from Sinorhizobium fredii GR64 is a conjugative plasmid, whose transfer is regulated by quorum sensing genes encoded by itself (traR64a, traI64a), in the symbiotic plasmid pSfr64b (traR64b, traI64b), and in the chromosome (ngrI). Also, transfer of pSfr64b requires quorum sensing elements encoded in this plasmid (traR64b, traI64b), in pSfr64a (traR64a), and in the chromosome (ngrI). These results demonstrate that pSfr64a and the symbiotic plasmid depend on each other for conjugative transfer. Plasmid pSfr64a from S. fredii GR64 is unable to transfer from the genomic background of Rhizobium etli CFN42. Our results show that the relaxase of pRet42a is able to process the oriT of pSfr64a, and viceversa, underlining their functional similarity and suggesting that in addition to the external signals, the "cytoplasmic environment" may pose a barrier to plasmid dissemination, even if the plasmids are functional in other aspects.

RevDate: 2019-11-05

Durden L, Wang D, Panaccione D, et al (2019)

Decreased Root-Knot Nematode Gall Formation in Roots of the Morning Glory Ipomoea tricolor Symbiotic with Ergot Alkaloid-Producing Fungal Periglandula Sp.

Journal of chemical ecology pii:10.1007/s10886-019-01109-w [Epub ahead of print].

Many species of morning glories (Convolvulaceae) form symbioses with seed-transmitted Periglandula fungal endosymbionts, which produce ergot alkaloids and may contribute to defensive mutualism. Allocation of seed-borne ergot alkaloids to various tissues of several Ipomoea species has been demonstrated, including roots of I. tricolor. The goal of this study was to determine if infection of I. tricolor by the Periglandula sp. endosymbiont affects Southern root-knot nematode (Meloidogyne incognita) gall formation and host plant biomass. We hypothesized that I. tricolor plants infected by Periglandula (E+) would develop fewer nematode-induced galls compared to non-symbiotic plants (E-). E+ or E- status of plant lines was confirmed by testing methanol extracts from individual seeds for endosymbiont-produced ergot alkaloids. To test the effects of Periglandula on nematode colonization, E+ and E- I. tricolor seedlings were grown in soil infested with high densities of M. incognita nematodes (N+) or no nematodes (N-) for four weeks in the greenhouse before harvesting. After harvest, nematode colonization of roots was visualized microscopically, and total gall number and plant biomass were quantified. Four ergot alkaloids were detected in roots of E+ plants, but no alkaloids were found in E- plants. Gall formation was reduced by 50% in E+ plants compared to E- plants, independent of root biomass. Both N+ plants and E+ plants had significantly reduced biomass compared to N- and E- plants, respectively. These results demonstrate Periglandula's defensive role against biotic enemies, albeit with a potential trade-off with host plant growth.

RevDate: 2019-11-05

Gupta N, Ansari A, Dhoke GV, et al (2019)

Computationally designed antibody-drug conjugates self-assembled via affinity ligands.

Nature biomedical engineering pii:10.1038/s41551-019-0470-8 [Epub ahead of print].

Antibody-drug conjugates (ADCs) combine the high specificity of antibodies with cytotoxic payloads. However, the present strategies for the synthesis of ADCs either yield unstable or heterogeneous products or involve complex processes. Here, we report a computational approach that leverages molecular docking and molecular dynamics simulations to design ADCs that self-assemble through the non-covalent binding of the antibody to a payload that we designed to act as an affinity ligand for specific conserved amino acid residues in the antibody. This method does not require modifications to the antibody structure and yields homogenous ADCs that form in less than 8 min. We show that two conjugates, which consist of hydrophilic and hydrophobic payloads conjugated to two different antibodies, retain the structure and binding properties of the antibody and its biological specificity, are stable in plasma and improve anti-tumour efficacy in mice with non-small cell lung tumour xenografts. The relative simplicity of the approach may facilitate the production of ADCs for the targeted delivery of cytotoxic payloads.

RevDate: 2019-11-05

Bjorbækmo MFM, Evenstad A, Røsæg LL, et al (2019)

The planktonic protist interactome: where do we stand after a century of research?.

The ISME journal pii:10.1038/s41396-019-0542-5 [Epub ahead of print].

Microbial interactions are crucial for Earth ecosystem function, but our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39% of all records), followed by symbiosis (29%), parasitism (18%), and 'unresolved interactions' (14%, where it is uncertain whether the interaction is beneficial or antagonistic). Using bipartite networks, we found that protist predators seem to be 'multivorous' while parasite-host and symbiont-host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions. Despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.

RevDate: 2019-11-05

Fonseca-García C, Zayas AE, Montiel J, et al (2019)

Transcriptome analysis of the differential effect of the NADPH oxidase gene RbohB in Phaseolus vulgaris roots following Rhizobium tropici and Rhizophagus irregularis inoculation.

BMC genomics, 20(1):800 pii:10.1186/s12864-019-6162-7.

BACKGROUND: Reactive oxygen species (ROS) are generated by NADPH oxidases known as respiratory burst oxidase homologs (RBOHs) in plants. ROS regulate various cellular processes, including the mutualistic interactions between legumes and nitrogen-fixing bacteria or arbuscular mycorrhizal (AM) fungi. Rboh is a multigene family comprising nine members (RbohA-I) in common bean (Phaseolus vulgaris). The RNA interference-mediated silencing of RbohB (PvRbohB-RNAi) in this species diminished its ROS production and greatly impaired nodulation. By contrast, the PvRbohB-RNAi transgenic roots showed early hyphal root colonization with enlarged fungal hypopodia; therefore, we proposed that PvRbohB positively regulates rhizobial infection (Rhizobium tropici) and inhibits AM colonization by Rhizophagus irregularis in P. vulgaris.

RESULTS: To corroborate this hypothesis, an RNA-Seq transcriptomic analysis was performed to identify the differentially expressed genes in the PvRbohB-RNAi roots inoculated with Rhizobium tropici or Rhizophagus irregularis. We found that, in the early stages, root nodule symbioses generated larger changes of the transcriptome than did AM symbioses in P. vulgaris. Genes related to ROS homeostasis and cell wall flexibility were markedly upregulated in the early stages of rhizobial colonization, but not during AM colonization. Compared with AM colonization, the rhizobia induced the expression of a greater number of genes encoding enzymes involved in the metabolism of auxins, cytokinins, and ethylene, which were typically repressed in the PvRbohB-RNAi roots.

CONCLUSIONS: Our research provides substantial insights into the genetic interaction networks in the early stages of rhizobia and AM symbioses with P. vulgaris, as well as the differential roles that RbohB plays in processes related to ROS scavenging, cell wall remodeling, and phytohormone homeostasis during nodulation and mycorrhization in this legume.

RevDate: 2019-11-05

Trněný O, Vlk D, Macková E, et al (2019)

Allelic Variants for Candidate Nitrogen Fixation Genes Revealed by Sequencing in Red Clover (Trifolium pratense L.).

International journal of molecular sciences, 20(21): pii:ijms20215470.

Plant-rhizobia symbiosis can activate key genes involved in regulating nodulation associated with biological nitrogen fixation (BNF). Although the general molecular basis of the BNF process is frequently studied, little is known about its intraspecific variability and the characteristics of its allelic variants. This study's main goals were to describe phenotypic and genotypic variation in the context of nitrogen fixation in red clover (Trifolium pretense L.) and identify variants in BNF candidate genes associated with BNF efficiency. Acetylene reduction assay validation was the criterion for selecting individual plants with particular BNF rates. Sequences in 86 key candidate genes were obtained by hybridization-based sequence capture target enrichment of plants with alternative phenotypes for nitrogen fixation. Two genes associated with BNF were identified: ethylene response factor required for nodule differentiation (EFD) and molybdate transporter 1 (MOT1). In addition, whole-genome population genotyping by double-digest restriction-site-associated sequencing (ddRADseq) was performed, and BNF was evaluated by the natural 15N abundance method. Polymorphisms associated with BNF and reflecting phenotype variability were identified. The genetic structure of plant accessions was not linked to BNF rate of measured plants. Knowledge of the genetic variation within BNF candidate genes and the characteristics of genetic variants will be beneficial in molecular diagnostics and breeding of red clover.

RevDate: 2019-11-07
CmpDate: 2019-11-07

Chang DZ, Serra L, Lu D, et al (2019)

A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema.

PLoS pathogens, 15(5):e1007626 pii:PPATHOGENS-D-18-01936.

Parasitic helminths release molecular effectors into their hosts and these effectors can directly damage host tissue and modulate host immunity. Excreted/secreted proteins (ESPs) are one category of parasite molecular effectors that are critical to their success within the host. However, most studies of nematode ESPs rely on in vitro stimulation or culture conditions to collect the ESPs, operating under the assumption that in vitro conditions mimic actual in vivo infection. This assumption is rarely if ever validated. Entomopathogenic nematodes (EPNs) are lethal parasites of insects that produce and release toxins into their insect hosts and are a powerful model parasite system. We compared transcriptional profiles of individual Steinernema feltiae nematodes at different time points of activation under in vitro and in vivo conditions and found that some but not all time points during in vitro parasite activation have similar transcriptional profiles with nematodes from in vivo infections. These findings highlight the importance of experimental validation of ESP collection conditions. Additionally, we found that a suite of genes in the neuropeptide pathway were downregulated as nematodes activated and infection progressed in vivo, suggesting that these genes are involved in host-seeking behavior and are less important during active infection. We then characterized the ESPs of activated S. feltiae infective juveniles (IJs) using mass spectrometry and identified 266 proteins that are released by these nematodes. In comparing these ESPs with those previously identified in activated S. carpocapsae IJs, we identified a core set of 52 proteins that are conserved and present in the ESPs of activated IJs of both species. These core venom proteins include both tissue-damaging and immune-modulating proteins, suggesting that the ESPs of these parasites include both a core set of effectors as well as a specialized set, more adapted to the particular hosts they infect.

RevDate: 2019-11-05
CmpDate: 2019-11-05

Rodríguez-Flores CI, Ornelas JF, Wethington S, et al (2019)

Are hummingbirds generalists or specialists? Using network analysis to explore the mechanisms influencing their interaction with nectar resources.

PloS one, 14(2):e0211855 pii:PONE-D-18-12237.

Mutualistic interactions are powerful drivers of biodiversity on Earth that can be represented as complex interaction networks that vary in connection pattern and intensity. One of the most fascinating mutualisms is the interaction between hummingbirds and the plants they visit. We conducted an exhaustive search for articles, theses, reports, and personal communications with researchers (unpublished data) documenting hummingbird visits to flowers of nectar-rewarding plants. Based on information gathered from 4532 interactions between 292 hummingbird species and 1287 plant species, we built an interaction network between nine hummingbird clades and 100 plant families used by hummingbirds as nectar resources at a continental scale. We explored the network architecture, including phylogenetic, morphological, biogeographical, and distributional information. As expected, the network between hummingbirds and their nectar plants was heterogeneous and nested, but not modular. When we incorporated ecological and historical information in the network nodes, we found a generalization gradient in hummingbird morphology and interaction patterns. The hummingbird clades that most recently diversified in North America acted as generalist nodes and visited flowers with ornithophilous, intermediate and non-ornithophilous morphologies, connecting a high diversity of plant families. This pattern was favored by intermediate morphologies (bill, wing, and body size) and by the low niche conservatism in these clades compared to the oldest clades that diversified in South America. Our work is the first effort exploring the hummingbird-plant mutualistic network at a continental scale using hummingbird clades and plant families as nodes, offering an alternative approach to exploring the ecological and evolutionary factors that explain plant-animal interactions at a large scale.

RevDate: 2019-11-06
CmpDate: 2019-11-06

Lam WN, HTW Tan (2019)

The crab spider-pitcher plant relationship is a nutritional mutualism that is dependent on prey-resource quality.

The Journal of animal ecology, 88(1):102-113.

Nutritional mutualisms are one of the three major categories of mutualisms and involve the provision of limiting nutrients (resources) to one species by another. It was recently shown in laboratory experiments that two species of pitcher-dwelling crab spiders (Thomisidae), Thomisus nepenthiphilus and Misumenops nepenthicola, increased capture rates of flesh flies (Sarcophagidae) for their host, Nepenthes gracilis. The spiders ambushed pitcher-visiting flesh flies and dropped their carcasses into pitchers after consuming them. The consumption of shared prey-resources by crab spiders and pitcher plants presents the possibility of parasitism between them. However, ecologically generalizable mechanisms that predict the context-dependent outcomes of such mutualisms are not known. The effectiveness framework (mutualism effectiveness = quality × quantity) is useful for examining the total effect of mutualisms, but its quality component can be difficult to define. We identify the crab spider-pitcher plant interaction as a type of resource conversion mutualism and propose that the quality component in such interactions is the amount of the underlying resource contained in each unit of resource processed. We then used the crab spider-pitcher plant interaction to test the hypothesis that resource conversion mutualisms are more beneficial to the nutrient recipient when operating through high-quality resources (i.e., large prey, in this interaction). We sampled the prey and inquilines of 107 N. gracilis upper pitches in situ and analysed the differences between pitchers that were inhabited or uninhabited by crab spiders, and the differences between nutritional contents of prey that were consumed by crab spiders or not. Pitchers inhabited by T. nepenthiphilus contained higher numbers of several prey taxa, many of which were flying insects. Consumption by T. nepenthiphilus reduced the nutrient contents in all prey examined. Overall, T. nepenthiphilus-assisted prey capture is likely to result in a net nutrient gain for N. gracilis that is proportional to the size of prey consumed by T. nepenthiphilus. Our results suggest that resource conversion mutualisms are more likely to operate through high-quality resources, since the nutrient-processing species necessarily reduces the quality of the resource it processes while increasing its availability to the nutrient recipient species.

RevDate: 2019-11-06
CmpDate: 2019-11-06

Roder AC, SP Stock (2018)

Influence of Xenorhabdus (Gamma-Proteobacteria: Enterobacteriaceae) symbionts on gonad postembryonic development in Steinernema (Nematoda: Steinernematidae) nematodes.

Journal of invertebrate pathology, 153:65-74.

Steinernema nematodes and their Xenorhabdus partners form an obligate mutualistic association. This partnership is insecticidal to a wide range of insects. Steinernema rely on their Xenorhabdus partner to produce toxins inside the insect cadaver to liberate nutrients from the insect, as well as antimicrobials to sterilize the cadaver, thus creating a suitable environment for reproduction. In return, Steinernema vector their Xenorhabdus between insect hosts. Disruption of this partnership may affect the success of both partners. For instance, when Steinernema associates with non-cognate symbionts, their virulence and reproductive fitness are affected. In this study, we examined the effect of symbiotic (cognate and non-cognate) and non-symbiotic bacteria on maturation time, gonad postembryonic development, and sex ratio of first-generation Steinernema adults. Two Steinernema spp. were considered: S. feltiae SN and S. carpocapsae All. In vitro assays were carried out by pairing each nematode sp. with symbiotic (cognate and non-cognate) Xenorhabdus, and with non-symbiotic bacteria (Serratia proteamaculans). Additionally, for comparative purposes, we also considered adult nematodes reared in vivo in Galleria mellonella larvae to assess nematode development under natural conditions. Results from this study showed non-symbiotic Serratia proteamaculans did not support adult development of S. feltiae but it allowed development of S. carpocapsae adults. Sex ratio decreased from 2:1 to 1:1 (female: male) when S. carpocapsae adults were reared with the non-symbiotic S. proteamaculans. Cognate or non-cognate Xenorhabdus spp. and/or strains did not change the sex ratio of any of either Steinernema spp. tested. Morphometric analysis also revealed that bacterial conditions influenced adult size and gonad postembryonic development in both Steinernema species. Body size (length and width), and gonad length in both S. feltiae males and females, were significantly reduced when reared with a non-cognate Xenorhabdus species. In S. carpocapsae, males exhibited an enhanced body size (length and width) and gonad length when reared with a non-cognate X. nematophila strain. S. carpocapsae females also exhibited an enhanced gonad length when reared with a non-cognate X. nematophila strain. S. carpocapsae males and females were underdeveloped when reared with the non-symbiotic S. proteamaculans, and exhibited reduced body sizes and gonad lengths. We conclude that development of first-generation adults of both Steinernema spp. tested, in particular time to adult maturation as well as body and gonad size were directly influenced by the bacterial symbionts they were cultured with. However, response to the culture conditions was species specific.

RevDate: 2019-11-04

Seifert A, Kashi Y, YD Livney (2019)

Delivery to the gut microbiota: A rapidly proliferating research field.

Advances in colloid and interface science, 274:102038 pii:S0001-8686(19)30223-4 [Epub ahead of print].

The post genomic era has brought breakthroughs in our understanding of the complex and fascinating symbiosis we have with our co-evolving microbiota, and its dramatic impact on our physiology, physical and mental health, mood, interpersonal communication, and more. This fast "proliferating" knowledge, particularly related to the gut microbiota, is leading to the development of numerous technologies aimed to promote our health via prudent modulation of our gut microbiota. This review embarks on a journey through the gastrointestinal tract from a biomaterial science and engineering perspective, and focusses on the various state-of-the-art approaches proposed in research institutes and those already used in various industries and clinics, for delivery to the gut microbiota, with emphasis on the latest developments published within the last 5 years. Current and possible future trends are discussed. It seems that future development will progress toward more personalized solutions, combining high throughput diagnostic omic methods, and precision interventions.

RevDate: 2019-11-04

Qin Z, Yu K, Chen B, et al (2019)

Diversity of Symbiodiniaceae in 15 Coral Species From the Southern South China Sea: Potential Relationship With Coral Thermal Adaptability.

Frontiers in microbiology, 10:2343.

It is well-known that the adaptability of coral-Symbiodiniaceae symbiosis to thermal stress varies among coral species, but the cause and/or mechanism behind it are not well-understood. In this study, we aimed to explore this issue based on zooxanthellae density (ZD) and Symbiodiniaceae genus/subclade. Hemocytometry and next-generation sequencing of the internal transcribed spacer region 2 (ITS2) marker gene were used to observe ZDs and Symbiodiniaceae genera/subclades associated with 15 typical coral species in the southern South China Sea (SCS). Average ZDs of all corals were in low levels, ranging from 0.84 to 1.22 × 106 cells cm-2, with a total of five Symbiodiniaceae genera, Symbiodinium, Cladocopium, Durusdinium, Fugacium, and Gerakladium, as well as 24 dominant subclades, were detected and varied among these coral species. Pocillopora verrucosa was dominated by Durusdinium (subclade D1/D1a), and other colonial corals were dominated by Cladocopium, but the subclades were varied among these species. Porites lutea and Montipora efflorescens were dominated by C15, and Echinopora lamellosa, Hydnophora exesa, and Coscinaraea exesa were dominated by C40. Acropora corymbosa, Merulina ampliata, and five species of Faviidae were mainly associated with Cladocopium types of C3u and Cspc. In contrast to other colonial corals, the dominant subclade of solitary Fungia fungites was C27, with high host specificity. Our study indicates that coral thermal stress adaptability is mainly affected by dominant Symbiodiniaceae type instead of ZD in the southern SCS. Some heat-sensitive corals, such as P. verrucosa corals, have acquired a high abundance of heat-tolerant Durusdinium to adapt to thermal stress. This could be the main reason for these corals becoming the dominant corals in this reef region. Background subclades analyses showed significant differences among coral species in subclade quantity and diversity. These suggest that numbers of coral species may have adapted to high environmental temperature by adopting various symbionts and/or associating with heat-tolerant Symbiodiniaceae.

RevDate: 2019-11-04

Muhammad A, Habineza P, Ji T, et al (2019)

Intestinal Microbiota Confer Protection by Priming the Immune System of Red Palm Weevil Rhynchophorus ferrugineus Olivier (Coleoptera: Dryophthoridae).

Frontiers in physiology, 10:1303.

The immune system of animals, including insects, is the vital factor to maintain the symbiotic interactions between animals and their associated microbes. However, the effects of gut microbiota on insect immunity remain mostly elusive. Red palm weevil (RPW), Rhynchophorus ferrugineus Olivier, is a destructive pest of palm trees worldwide, which has forged alliances with its gut microbiota. Here, we found that the aposymbiotic insects succumbed at a significantly faster rate than conventionally reared (CR) ones upon bacterial infection. Physiological assays confirmed that CR insects had stronger antimicrobial activity and higher phenoloxidase activity in contrast to germfree (GF) ones, indicating that the systemic immune responses of GF individuals were compromised markedly. Interestingly, under the bacterial challenge conditions, the reassociation of gut microbiota with GF insects could enhance their survival rate by rescuing their immunocompetence. Furthermore, comparative transcriptome analysis uncovered that 35 immune-related genes, including pathogen recognition receptors, effectors and immune signaling pathway, were significantly downregulated in GF insects as compared to CR ones. Collectively, our findings corrobate that intestinal commensal bacteria have profound immunostimulatory effects on RPW larvae. Therefore, knowledge on the effects of gut microbiota on RPW immune defenses may contribute to of set up efficient control strategies of this pest.

RevDate: 2019-11-04

Primo ED, Cossovich S, Nievas F, et al (2019)

Exopolysaccharide production in Ensifer meliloti laboratory and native strains and their effects on alfalfa inoculation.

Archives of microbiology pii:10.1007/s00203-019-01756-3 [Epub ahead of print].

Bacterial surface molecules have an important role in the rhizobia-legume symbiosis. Ensifer meliloti (previously, Sinorhizobium meliloti), a symbiotic Gram-negative rhizobacterium, produces two different exopolysaccharides (EPSs), termed EPS I (succinoglycan) and EPS II (galactoglucan), with different functions in the symbiotic process. Accordingly, we undertook a study comparing the potential differences in alfalfa nodulation by E. meliloti strains with differences in their EPSs production. Strains recommended for inoculation as well as laboratory strains and native strains isolated from alfalfa fields were investigated. This study concentrated on EPS-II production, which results in mucoid colonies that are dependent on the presence of an intact expR gene. The results revealed that although the studied strains exhibited different phenotypes, the differences did not affect alfalfa nodulation itself. However, subtle changes in timing and efficacy to the effects of inoculation with the different strains may result because of other as-yet unknown factors. Thus, additional research is needed to determine the most effective inoculant strains and the best conditions for improving alfalfa production under agricultural conditions.

RevDate: 2019-11-03

Yahara H, Tanikawa N, Okamoto M, et al (2019)

Characterizing fine-root traits by species phylogeny and microbial symbiosis in 11 co-existing woody species.

Oecologia pii:10.1007/s00442-019-04546-2 [Epub ahead of print].

Understanding the differences in fine-root traits among different species is essential to gain a detailed understanding of resource conservation and acquisition strategies of plants. We aimed to explore whether certain root traits are consistent among subsets of species and characterize species together into meaningful community groups. We selected 11 woody species from different microbial symbiotic groups (ectomycorrhiza, arbuscular mycorrhiza, and rhizobia) and phylogenetic groups (broad-leaved angiosperms and coniferous gymnosperms) from the cool temperate forests of Nagano, Japan. We measured root architectural (branching intensity), morphological (root tissue density and specific root length), chemical (N and K concentrations), and anatomical (total stele and total cortex) traits. Significant differences were observed in all root traits, although many species did not differ from one another. Branching intensity was found to be the greatest variation in the measured root traits across the 11 woody species. The results of a principal component analysis of root traits showed a distinct separation between angiosperms and gymnosperms. We identified clusters of species based on their multidimensional root traits that were consistent with the different phylogenetic microbial association groups. Gymnosperm roots may be more resource conservative, while angiosperm roots may be more acquisitive for water and nutrients. We consider that the advances in root traits combination will make a breakthrough in our ability to differentiate the community groups rather than individual root trait.

RevDate: 2019-11-03

Llopis-Belenguer C, Balbuena JA, Lange K, et al (2019)

Towards a Unified Functional Trait Framework for Parasites.

Trends in parasitology pii:S1471-4922(19)30237-5 [Epub ahead of print].

Trait-based research holds high potential to unveil ecological and evolutionary processes. Functional traits are fitness-related characteristics of individuals, which are measured at individual level and defined without using information external to the individual. Despite the usefulness of the functional approach to understand the performance of individuals in ecosystems, and parasitism being the most common life-history strategy on Earth, studies based on functional traits of parasites are still scarce. Since the choice of functional traits is a critical step for any study, we propose a core list of seven functional traits of metazoan parasites, related to three universal challenges faced by organisms (dispersal, establishment, and persistence), and give guidelines to define appropriate functional traits in future parasite community studies.

RevDate: 2019-11-02

Caldera EJ, Chevrette MG, McDonald BR, et al (2019)

Local adaptation of bacterial symbionts within a geographic mosaic of antibiotic coevolution.

Applied and environmental microbiology pii:AEM.01580-19 [Epub ahead of print].

The geographic mosaic theory of coevolution (GMC) posits that coevolutionary dynamics go beyond local coevolution and are comprised of three components: geographic selection mosaics, coevolutionary hot-spots, and trait remixing. It is unclear whether GMC applies to bacteria, as horizontal gene transfer and cosmopolitan dispersal may violate theoretical assumptions. Here, we test key GMC predictions in an antibiotic-producing bacterial symbiont (genus Pseudonocardia) that protects the crops of neotropical, fungus-farming ants (Apterostigma dentigerum) from a specialized pathogen (genus Escovopsis). We found Pseudonocardia antibiotic inhibition of common Escovopsis was elevated in A. dentigerum colonies from Panama compared to those from Costa Rica. Further, a Panama canal-zone population of Pseudonocardia on Barro Colorado Island (BCI) was locally adapted whereas two neighboring populations were not, consistent with a GMC-predicted selection mosaic and a hot-spot of adaptation surrounded by areas of maladaptation. Maladaptation was shaped by incongruent Pseudonocardia-Escovopsis population genetic structure, whereas local adaptation was facilitated by geographic isolation on BCI after the flooding of the Panama Canal. Genomic assessments of antibiotic potential of 29 Pseudonocardia identified diverse and unique biosynthetic gene clusters in BCI strains despite low genetic diversity in the core genome. The strength of antibiotic inhibition was not correlated with the presence/absence of individual biosynthetic gene clusters or parasite location. Rather, biosynthetic gene clusters have undergone selective sweeps, suggesting that the trait remixing dynamics conferring the long-term maintenance of antibiotic potency rely on evolutionary genetic changes within already-present biosynthetic gene clusters and not simply the horizontal acquisition of novel genetic elements or pathways.IMPORTANCE Recently, coevolutionary theory in macro-organisms has been advanced by the Geographic Mosaic theory of Coevolution (GMC) that considers how geography and local adaptation shape coevolutionary dynamics. Here, we test GMC in an ancient symbiosis where the ant Apterostigma dentigerum cultivates fungi in an agricultural system analogous to human farming. The cultivars are parasitized by the fungus Escovopsis The ants maintain symbiotic actinobacteria with antibiotic properties that help combat Escovopsis infection. This antibiotic symbiosis has persisted for over tens of millions of years, begging the questions of how antibiotic potency is maintained over these time scales. Our study tests the GMC in a bacterial defensive symbiosis and in a multi-partite symbiosis framework. Our results show that this multipartite symbiotic system conforms to the GMC and demonstrates that this theory is applicable in both microbes and indirect symbiont-symbiont interactions.

RevDate: 2019-11-04
CmpDate: 2019-11-04

Sharma C, NK Bhardwaj (2019)

Biotransformation of fermented black tea into bacterial nanocellulose via symbiotic interplay of microorganisms.

International journal of biological macromolecules, 132:166-177.

Bacterial nanocellulose (BNC), a natural origin biopolymer with multi-dimensional applications has captured a great deal of attention owing to its implausible properties. However, low yield of BNC accompanied with high production cost is challenging its usage in various technological applications. In this study, BNC production has been reported utilizing fermented black tea broth brewed from fresh tea leaves (FBTBF) as well as from used tea leaves (FBTBU) as a cost-effective and high-quality BNC yielding medium. The symbiotic combination of bacteria and yeasts (SCOBY) was exploited here to bring fermentation in tea broth. The production yields on dry weight basis were 13.3 g L-1 in FBTBF and 12.8 g L-1 in FBTBU, obtained with 60 g L-1 of glucose in 20 days. The conversion yields of 0.32 and 0.31 g BNC/g sugar were obtained with both the tea broths. The study of produced pellicle using ATR-FTIR, FE-SEM and XRD confirmed its structural, morphological and chemical nature similar to that of BNC. Thus, fermented black tea broth appears to be a potential medium for BNC production. The use of fermented tea broth for the industrial scale production of BNC might significantly reduce its production cost.

RevDate: 2019-11-04
CmpDate: 2019-11-04

Qu H, Zhang Y, Chai H, et al (2019)

Effects of microbiota-driven therapy on inflammatory responses in elderly individuals: A systematic review and meta-analysis.

PloS one, 14(2):e0211233 pii:PONE-D-18-25723.

Current evidence suggests that age-associated inflammation, a strong risk factor for the health status of elderly individuals, is closely associated with gut microbiota. Previous animal studies have demonstrated a benefit of microbiota-driven therapy in decreasing low-grade chronic inflammation in elderly individuals; however, it remains controversial in clinical studies. Therefore, the present systematic review and meta-analysis were designed to assess the effects of microbiota-driven therapy on inflammatory markers in elderly individuals. PubMed, EMBASE, and the Cochrane Library were searched with no language restrictions from the inception of the database to November 11th, 2018 to identify all existing literature. We calculated pooled standard mean difference (SMD) using fixed effect model or random effect model to assess the effects of microbiota-driven therapy on elderly individuals. The methodological quality of the studies was determined according to the Cochrane Handbook. The publication bias was evaluated by funnel plot and Egger regression test. Ten randomized controlled studies, with 689 elderly individuals (347 individuals in the microbiota-driven therapy group and 342 individuals in the placebo group), were included in the analysis. Compared with placebo, microbiota-driven therapy did not decrease the levels of tumor necrosis factor-α (SMD, -0.24; 95% CI, -0.69 to 0.21; p = 0.30; I2 = 82.7%), interleukin-6 (SMD, -0.13; 95% CI, -0.74 to 0.49; p = 0.69; I2 = 90.7%) and interleukin-10 (SMD, 1.00; 95% CI, -0.15 to 2.15; p = 0.09; I2 = 96.3%). In addition, the microbiota-driven therapy also did not decrease the levels of C reactive protein (SMD, -1.28; 95% CI, -2.62 to 0.06; p = 0.06; I2 = 96.2%), interleukin-1β (SMD, -0.22; 95% CI, -0.81 to 0.37; p = 0.46; I2 = 73.8%), interleukin-8 (SMD, -0.03; 95% CI, -0.67 to 0.61; p = 0.93; I2 = 88.0%) and monocyte chemoattractant protein-1 (SMD, -0.11; 95% CI, -0.41 to 0.20; p = 0.49; I2 = 0%) when compared with placebo. No obvious publication bias was observed (p>0.05). In conclusion, the present meta-analysis of available randomized controlled studies did not suggest any significant benefit of microbiota-driven therapy in decreasing the inflammatory responses of elderly individuals.

RevDate: 2019-11-04
CmpDate: 2019-11-04

Vacheron J, Péchy-Tarr M, Brochet S, et al (2019)

T6SS contributes to gut microbiome invasion and killing of an herbivorous pest insect by plant-beneficial Pseudomonas protegens.

The ISME journal, 13(5):1318-1329.

Pseudomonas protegens are multi-talented plant-colonizing bacteria that suppress plant pathogens and stimulate plant defenses. In addition, they are capable of invading and killing agriculturally important plant pest insects that makes them promising candidates for biocontrol applications. Here we assessed the role of type VI secretion system (T6SS) components of type strain CHA0 during interaction with larvae of the cabbage pest Pieris brassicae. We show that the T6SS core apparatus and two VgrG modules, encompassing the respective T6SS spikes (VgrG1a and VgrG1b) and associated effectors (RhsA and Ghh1), contribute significantly to insect pathogenicity of P. protegens in oral infection assays but not when bacteria are injected directly into the hemolymph. Monitoring of the colonization levels of P. protegens in the gut, hemolymph, and excrements of the insect larvae revealed that the invader relies on T6SS and VgrG1a module function to promote hemocoel invasion. A 16S metagenomic analysis demonstrated that T6SS-supported invasion by P. protegens induces significant changes in the insect gut microbiome affecting notably Enterobacteriaceae, a dominant group of the commensal gut bacteria. Our study supports the concept that pathogens deploy T6SS-based strategies to disrupt the commensal microbiota in order to promote host colonization and pathogenesis.

RevDate: 2019-11-04
CmpDate: 2019-11-04

He M, Wang J, Fan X, et al (2019)

Genetic basis for the establishment of endosymbiosis in Paramecium.

The ISME journal, 13(5):1360-1369.

The single-celled ciliate Paramecium bursaria is an indispensable model for investigating endosymbiosis between protists and green-algal symbionts. To elucidate the mechanism of this type of endosymbiosis, we combined PacBio and Illumina sequencing to assemble a high-quality and near-complete macronuclear genome of P. bursaria. The genomic characteristics and phylogenetic analyses indicate that P. bursaria is the basal clade of the Paramecium genus. Through comparative genomic analyses with its close relatives, we found that P. bursaria encodes more genes related to nitrogen metabolism and mineral absorption, but encodes fewer genes involved in oxygen binding and N-glycan biosynthesis. A comparison of the transcriptomic profiles between P. bursaria with and without endosymbiotic Chlorella showed differential expression of a wide range of metabolic genes. We selected 32 most differentially expressed genes to perform RNA interference experiment in P. bursaria, and found that P. bursaria can regulate the abundance of their symbionts through glutamine supply. This study provides novel insights into Paramecium evolution and will extend our knowledge of the molecular mechanism for the induction of endosymbiosis between P. bursaria and green algae.

RevDate: 2019-11-04
CmpDate: 2019-11-04

Crutcher FK, CM Kenerley (2019)

Analysis of a putative glycosylation site in the Trichoderma virens elicitor SM1 reveals no role in protein dimerization.

Biochemical and biophysical research communications, 509(3):817-821.

The biocontrol fungus Trichoderma virens is an avirulent symbiont with the ability to control plant disease through the production of antibiotic compounds, induction of plant resistance to pathogens, and mycoparasitism of other fungi. Previous research has shown that resistance to plant pathogens in maize is induced by the secretion of a member of the cerato-platanin family of proteins, sm1, and that only the monomer of this protein has this activity. It has been hypothesized that glycosylation of sm1 disrupts dimer formation and keeps sm1 in this active monomer form. To further understand the role of this putative glycosylation site as a mechanism to prevent dimerization and subsequent elicitor activity, a point mutation was created in sm1 and transformed into a sm1 deletion strain. Analysis of the behavior of the altered protein (PTM) demonstrates that the putative glycosylation site is not involved in protein dimerization and deletion of this site does not prevent the protein from testing positive for glycosylation. We propose that SM1 is not glycosylated but instead may interact with an oligosaccharide or other small molecule. However, the exact mechanism of dimerization in SM1 remains unknown.

RevDate: 2019-11-04
CmpDate: 2019-11-04

Morioka E, Oida M, Tsuchida T, et al (2018)

Nighttime activities and peripheral clock oscillations depend on Wolbachia endosymbionts in flies.

Scientific reports, 8(1):15432.

Wolbachia are ubiquitous bacterial endosymbionts of arthropods and affect host gene expression. Although Wolbachia infections were suggested to modulate sleep in flies, their influence on the circadian clock remained obscure. Here, we screened bacterial symbionts in a laboratory Drosophila melanogaster colony, and observed widespread infections of wMel strain Wolbachia. We established a Wolbachia-free strain from a clock gene reporter strain, period-luciferase (per-luc). Temperature (19-29 °C)-compensated free-running periods were detected regardless of infections which may reflect the lack of wMel infections in central circadian pacemaker neurons. However, locomotor activity levels during the night or subjective night were significantly amplified in uninfected flies. Moreover, the behavioral phenotype of F1 offspring of an uninfected female and infected male resembled that of uninfected flies. This trait is consistent with maternal transmission of Wolbachia infection. Interestingly, per-luc activities in headless bodies, as an index of peripheral circadian oscillators, were severely damped in uninfected flies. Additionally, circadian amplitudes of PER immunoreactivities in Malpighian tubules were reduced in uninfected flies. These results demonstrate that Wolbachia boost fly peripheral clock oscillations and diurnal behavioral patterns. Genetic mechanisms underlying behavioral rhythms have been widely analyzed using mutant flies whereas screening of Wolbachia will be necessary for future studies.

RevDate: 2019-11-04
CmpDate: 2019-11-04

Alleman A, Hertweck KL, S Kambhampati (2018)

Random Genetic Drift and Selective Pressures Shaping the Blattabacterium Genome.

Scientific reports, 8(1):13427.

Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium - providing nutritional augmentation to its host in the form of amino acid synthesis - displays radical genome alterations when compared to its most recent free-living relative Flavobacterium. To date, eight Blattabacterium genomes have been published, affording an unparalleled opportunity to examine the direction and magnitude of selective forces acting upon this group of symbionts. Here, we find that the Blattabacterium genome is experiencing a 10-fold increase in selection rate compared to Flavobacteria. Additionally, the proportion of selection events is largely negative in direction, with only a handful of loci exhibiting signatures of positive selection. These findings suggest that the Blattabacterium genome will continue to erode, potentially resulting in an endosymbiont with an even further reduced genome, as seen in other insect groups such as Hemiptera.

RevDate: 2019-11-01

Brody AK, Waterman B, Ricketts TH, et al (2019)

Genotype-specific effects of ericoid mycorrhizae on floral traits and reproduction in Vaccinium corymbosum.

American journal of botany [Epub ahead of print].

PREMISE: Most plants interact with mycorrhizal fungi and animal pollinators simultaneously. Yet, whether mycorrhizae affect traits important to pollination remains poorly understood and may depend on the match between host and fungal genotypes. Here, we examined how ericoid mycorrhizal fungi affected flowering phenology, floral traits, and reproductive success, among eight genotypes of highbush blueberry, Vaccinium corymbosum (Ericaceae). We asked three overarching questions: (1) Do genotypes differ in response to inoculation? (2) How does inoculation affect floral and flowering traits? (3) Are inoculated plants more attractive to pollinators and less pollen limited than non-inoculated plants of the same genotype?

METHODS: To examine these questions, we experimentally inoculated plants with ericoid mycorrhizal fungi, grew the plants in the field, and measured flowering and floral traits over 2 years. In year 2, we conducted a hand-pollination experiment to test whether plants differed in pollen limitation.

RESULTS: Inoculated plants had significantly higher levels of colonization for some genotypes, and there were significant floral trait changes in inoculated plants for some genotypes as well. On average, inoculated plants produced significantly larger floral displays, more fruits per inflorescence, and heavier fruits with lower sugar content, than non-inoculated, control plants. Hand pollination enhanced the production of fruits, and fruit mass, for non-inoculated plants but not for those that were inoculated.

CONCLUSIONS: Our results demonstrate that inoculation with ericoid mycorrhizal fungi enhanced flowering and altered investment in reproduction in genotype-specific ways. These findings underscore the importance of examining belowground symbionts and genotype-specific responses in their hosts to fully understand the drivers of aboveground interactions.

RevDate: 2019-11-01

Durkin ES, Proctor H, LT Luong (2019)

Life history of Macrocheles muscaedomesticae (Parasitiformes: Macrochelidae): new insights on life history and evidence of facultative parasitism on Drosophila.

Experimental & applied acarology pii:10.1007/s10493-019-00431-y [Epub ahead of print].

Macrocheles muscaedomesticae is a cosmopolitan macrochelid mite whose populations have likely diverged considering the many locations they inhabit, but most of the work published on this mite species has been on the basis of their association with the house fly, Musca domestica. Here, we studied several aspects of the biology of M. muscaedomesticae associated with drosophilid flies collected in Alberta, Canada. We assessed the degree of divergence of our populations from others, compared their life history to other published populations and experimentally tested whether M. muscaedomesticae feeds on Drosophila hydei hosts by comparing the body mass of mites that attached to hosts to those that did not. There was no strong phylogenetic differentiation among any of the M. muscaedomesticae specimens, suggesting multiple recent introductions of this species to Canada. Compared to other populations, our mites exhibited lower fecundity, which may have been a result of the temperature or nematode-only diet in which they were maintained. Finally, mites that attached to hosts for 4 h weighed significantly more than those that did not. Without direct evidence for host tissue transfer to the mites, it is difficult to determine whether the mites are indeed feeding on their hosts while attached. However, the existing evidence for the costs fly hosts endure at the expense of these mites makes this relationship antagonistic.

RevDate: 2019-11-01

Clark DW, Okada Y, Moore KHS, et al (2019)

Associations of autozygosity with a broad range of human phenotypes.

Nature communications, 10(1):4957 pii:10.1038/s41467-019-12283-6.

In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44-66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding.

RevDate: 2019-11-01

Bukharin OV, Perunova NB, Andryuschenko SV, et al (2019)

Genome Sequence Announcement of Bacillus paranthracis Strain ICIS-279, Isolated from Human Intestine.

Microbiology resource announcements, 8(44): pii:8/44/e00662-19.

This report describes the genome sequence of Bacillus paranthracis strain ICIS-279, isolated from human feces. It demonstrates a tumor necrosis factor alpha (TNF-α) inhibitory activity up to 0.1 ng/ml. The genome size is 5,180,499 bp, with a G+C content of 35.4%. Annotation revealed 5,168 coding sequences, including 5,168 proteins and 43 rRNA, 102 tRNA, and 5 noncoding RNA (ncRNA) genes.

RevDate: 2019-11-01

Dhas Y, Banerjee J, Damle G, et al (2019)

Serum 25(OH)D concentration and its association with inflammation and oxidative stress in the middle-aged Indian healthy and diabetic subjects.

Steroids pii:S0039-128X(19)30222-3 [Epub ahead of print].

BACKGROUND: Vitamin D deficiency is associated with inflammation and oxidative stress. We have studied the association of 25-hydroxyvitamin D [25(OH)D] with markers of inflammation and oxidative stress.

METHODS: We have recruited total 180 male and female subjects aged between 30-50 years and divided them into two groups as control (n=90) and T2DM (n=90). We have measured 25(OH)D concentration, markers of inflammation including interleukin (IL)-6, IL-1β, and tumor necrosis factor-α (TNF-α) and markers of oxidative stress including malondialdehyde (MDA) and oxidized low-density lipoprotein (Ox-LDL) by using standard methods.

RESULTS: We stratified control and T2DM groups by 25(OH)D concentration and it indicates that in severe deficiency and sufficiency category IL-6, IL-1β, TNF-α, and Ox-LDL were significantly different while in moderate deficiency category only MDA was significantly different, among control and T2DM groups. In an insufficiency category, IL-6, IL-1β, TNF-α, MDA, and Ox-LDL were significantly different among control and T2DM groups. Correlation analysis indicates a negative correlation of 25(OH)D with IL-6, IL-1β, TNF-α, and Ox-LDL among total subjects. Further, logistics regression analysis demonstrated a significant association of different categories of 25(OH)D with IL-6, IL-1β, TNF-α, and Ox-LDL before and after adjustment to body mass index and waist to hip ratio.

CONCLUSION: This study suggest that vitamin D may have significant implications in the prevention of inflammation and oxidative stress.

RevDate: 2019-10-31

Quigley KM, Alvarez Roa C, Torda G, et al (2019)

Co-dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles.

MicrobiologyOpen [Epub ahead of print].

Interactions between corals and their associated microbial communities (Symbiodiniaceae and prokaryotes) are key to understanding corals' potential for and rate of acclimatory and adaptive responses. However, the establishment of microalgal and bacterial communities is poorly understood during coral ontogeny in the wild. We examined the establishment and co-occurrence between multiple microbial communities using 16S rRNA (bacterial) and ITS2 rDNA (Symbiodiniaceae) gene amplicon sequencing in juveniles of the common coral, Acropora tenuis, across the first year of development. Symbiodiniaceae communities in juveniles were dominated by Durusdinium trenchii and glynnii (D1 and D1a), with lower abundances of Cladocopium (C1, C1d, C50, and Cspc). Bacterial communities were more diverse and dominated by taxa within Proteobacteria, Cyanobacteria, and Planctomycetes. Both communities were characterized by significant changes in relative abundance and diversity of taxa throughout the year. D1, D1a, and C1 were significantly correlated with multiple bacterial taxa, including Alpha-, Deltra-, and Gammaproteobacteria, Planctomycetacia, Oxyphotobacteria, Phycisphaerae, and Rhizobiales. Specifically, D1a tended to associate with Oxyphotobacteria and D1 with Alphaproteobacteria, although these associations may represent correlational and not causal relationships. Bioenergetic modeling combined with physiological measurements of coral juveniles (surface area and Symbiodiniaceae cell densities) identified key periods of carbon limitation and nitrogen assimilation, potentially coinciding with shifts in microbial community composition. These results demonstrate that Symbiodiniaceae and bacterial communities are dynamic throughout the first year of ontology and may vary in tandem, with important fitness effects on host juveniles.

RevDate: 2019-10-31

Ormeño-Orrillo E, Martínez-Romero E, D Zúñiga-Dávila (2019)

Identification of the symbiosis island of Bradyrhizobium paxllaeri LMTR 21T.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] pii:10.1007/s42770-019-00164-5 [Epub ahead of print].

The complete symbiosis island (SI) of Bradyrhizobium paxllaeri LMTR 21T, a mutualistic symbiont of the legume Phaseolus lunatus, was identified and analyzed. The SI was 646 kb in size, had lower G+C content than the genome average, and encoded not only nodulation and nitrogen fixation functions but also those for hydrogen uptake, vitamin and phytohormone biosynthesis, molybdenum transport, nonribosomal peptide synthesis, and type III secretion. Additionally, two divergent nodA genes were encoded in the SI.

RevDate: 2019-10-31

Aschtgen MS, Brennan CA, Nikolakakis K, et al (2019)

Insights into flagellar function and mechanism from the squid-vibrio symbiosis.

NPJ biofilms and microbiomes, 5:32 pii:106.

Flagella are essential and multifunctional nanomachines that not only move symbionts towards their tissue colonization site, but also play multiple roles in communicating with the host. Thus, untangling the activities of flagella in reaching, interacting, and signaling the host, as well as in biofilm formation and the establishment of a persistent colonization, is a complex problem. The squid-vibrio system offers a unique model to study the many ways that bacterial flagella can influence a beneficial association and, generally, other bacteria-host interactions. Vibrio fischeri is a bioluminescent bacterium that colonizes the Hawaiian bobtail squid, Euprymna scolopes. Over the last 15 years, the structure, assembly, and functions of V. fischeri flagella, including not only motility and chemotaxis, but also biofilm formation and symbiotic signaling, have been revealed. Here we discuss these discoveries in the perspective of other host-bacteria interactions.

RevDate: 2019-10-31

Lampert N, Mikaelyan A, A Brune (2019)

Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches.

BMC microbiology, 19(1):238 pii:10.1186/s12866-019-1601-9.

BACKGROUND: Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter.

RESULTS: The physicochemical conditions determined with microsensors in the guts of Ergaula capucina, Pycnoscelus surinamensis, and Byrsotria rothi were similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop of B. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites.

CONCLUSION: Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.

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ESP Quick Facts

ESP Origins

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

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

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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.

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

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

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

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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.

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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

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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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Selected Bibliographies

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