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07 Dec 2019 at 01:45
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Bibliography on: Symbiosis


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RJR: Recommended Bibliography 07 Dec 2019 at 01:45 Created: 


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

Created with PubMed® Query: symbiosis NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-12-06

Su Y, Zhang K, Zhou Z, et al (2019)

Microplastic exposure represses the growth of endosymbiotic dinoflagellate Cladocopium goreaui in culture through affecting its apoptosis and metabolism.

Chemosphere, 244:125485 pii:S0045-6535(19)32725-0 [Epub ahead of print].

Microplastics are widespread emerging marine pollutants that have been found in the coral reef ecosystem. In the present study, using Cladocopium goreaui as a symbiont representative, we investigated cytological, physiological, and molecular responses of a Symbiodiniaceae species to weeklong microplastic exposure (Polystyrene, diameter 1.0 μm, 9.0 × 109 particles L-1). The density and size of algal cells decreased significantly at 7 d and 6-7 d of microplastic exposure, respectively. Chlorophyll a content increased significantly at 7 d of exposure, whereas Fv/Fm did not change significantly during the entire exposure period. We observed significant increases in superoxide dismutase activity and caspase3 activation level, significant decrease in glutathione S-transferase activity, but no change in catalase activity during the whole exposure period. Transcriptomic analysis revealed 191 significantly upregulated and 71 significantly downregulated genes at 7 d after microplastic exposure. Fifteen GO terms were overrepresented for these significantly upregulated genes, which were grouped into four categories including transmembrane ion transport, substrate-specific transmembrane transporter activity, calcium ion binding, and calcium-dependent cysteine-type endopeptidase activity. Thirteen of the significantly upregulated genes encode metal ion transporter and ammonium transporter, and five light-harvesting protein genes were among the significantly downregulated genes. These results demonstrate that microplastics can act as an exogenous stressor, suppress detoxification activity, nutrient uptake, and photosynthesis, elevate oxidative stress, and raise the apoptosis level through upregulating ion transport and apoptotic enzymes to repress the growth of C. goreaui. These effects have implications in negative impacts of microplastics on coral-Symbiodiniaceae symbiosis that involves C. goreaui.

RevDate: 2019-12-06

Varoquaux N, Cole B, Gao C, et al (2019)

Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses.

Proceedings of the National Academy of Sciences of the United States of America pii:1907500116 [Epub ahead of print].

Drought is the most important environmental stress limiting crop yields. The C4 cereal sorghum [Sorghum bicolor (L.) Moench] is a critical food, forage, and emerging bioenergy crop that is notably drought-tolerant. We conducted a large-scale field experiment, imposing preflowering and postflowering drought stress on 2 genotypes of sorghum across a tightly resolved time series, from plant emergence to postanthesis, resulting in a dataset of nearly 400 transcriptomes. We observed a fast and global transcriptomic response in leaf and root tissues with clear temporal patterns, including modulation of well-known drought pathways. We also identified genotypic differences in core photosynthesis and reactive oxygen species scavenging pathways, highlighting possible mechanisms of drought tolerance and of the delayed senescence, characteristic of the stay-green phenotype. Finally, we discovered a large-scale depletion in the expression of genes critical to arbuscular mycorrhizal (AM) symbiosis, with a corresponding drop in AM fungal mass in the plants' roots.

RevDate: 2019-12-06

Kimeklis AK, Chirak ER, Kuznetsova IG, et al (2019)

Rhizobia Isolated from the Relict Legume Vavilovia formosa Represent a Genetically Specific Group within Rhizobium leguminosarum biovar viciae.

Genes, 10(12): pii:genes10120991.

Twenty-two rhizobia strains isolated from three distinct populations (North Ossetia, Dagestan, and Armenia) of a relict legume Vavilovia formosa were analysed to determine their position within Rhizobium leguminosarum biovar viciae (Rlv). These bacteria are described as symbionts of four plant genera Pisum, Vicia, Lathyrus, and Lens from the Fabeae tribe, of which Vavilovia is considered to be closest to its last common ancestor (LCA). In contrast to biovar viciae, bacteria from Rhizobium leguminosarum biovar trifolii (Rlt) inoculate plants from the Trifolieae tribe. Comparison of house-keeping (hkg: 16S rRNA, glnII, gltA, and dnaK) and symbiotic (sym: nodA, nodC, nodD, and nifH) genes of the symbionts of V. formosa with those of other Rlv and Rlt strains reveals a significant group separation, which was most pronounced for sym genes. A remarkable feature of the strains isolated from V. formosa was the presence of the nodX gene, which was commonly found in Rlv strains isolated from Afghanistan pea genotypes. Tube testing of different strains on nine plant species, including all genera from the Fabeae tribe, demonstrated that the strains from V. formosa nodulated the same cross inoculation group as the other Rlv strains. Comparison of nucleotide similarity in sym genes suggested that their diversification within sym-biotypes of Rlv was elicited by host plants. Contrariwise, that of hkg genes could be caused by either local adaptation to soil niches or by genetic drift. Long-term ecological isolation, genetic separation, and the ancestral position of V. formosa suggested that symbionts of V. formosa could be responsible for preserving ancestral genotypes of the Rlv biovar.

RevDate: 2019-12-06

Chirak ER, Kimeklis AK, Karasev ES, et al (2019)

Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa.

Genes, 10(12): pii:genes10120990.

Vavilovia formosa is a relict leguminous plant growing in hard-to-reach habitats in the rocky highlands of the Caucasus and Middle East, and it is considered as the putative closest living relative of the last common ancestor (LCA) of the Fabeae tribe. Symbionts of Vavilovia belonging to Rhizobium leguminosarum bv. viciae compose a discrete group that differs from the other strains, especially in the nucleotide sequences of the symbiotically specialised (sym) genes. Comparison of the genomes of Vavilovia strains with the reference group composed of R. leguminosarum bv. viciae strains isolated from Pisum and Vicia demonstrated that the vavilovia strains have a set of genomic features, probably indicating the important stages of microevolution of the symbiotic system. Specifically, symbionts of Vavilovia (considered as an ancestral group) demonstrated a scattered arrangement of sym genes (>90 kb cluster on pSym), with the location of nodT gene outside of the other nod operons, the presence of nodX and fixW, and the absence of chromosomal fixNOPQ copies. In contrast, the reference (derived) group harboured sym genes as a compact cluster (<60 kb) on a single pSym, lacking nodX and fixW, with nodT between nodN and nodO, and possessing chromosomal fixNOPQ copies. The TOM strain, obtained from nodules of the primitive "Afghan" peas, occupied an intermediate position because it has the chromosomal fixNOPQ copy, while the other features, the most important of which is presence of nodX and fixW, were similar to the Vavilovia strains. We suggest that genome evolution from the ancestral to the derived R. leguminosarum bv. viciae groups follows the "gain-and-loss of sym genes" and the "compaction of sym cluster" strategies, which are common for the macro-evolutionary and micro-evolutionary processes. The revealed genomic features are in concordance with a relict status of the vavilovia strains, indicating that V. formosa coexists with ancestral microsymbionts, which are presumably close to the LCA of R. leguminosarum bv. viciae.

RevDate: 2019-12-05

Morard R, Füllberg A, Brummer GA, et al (2019)

Genetic and morphological divergence in the warm-water planktonic foraminifera genus Globigerinoides.

PloS one, 14(12):e0225246 pii:PONE-D-19-17658.

The planktonic foraminifera genus Globigerinoides provides a prime example of a species-rich genus in which genetic and morphological divergence are uncorrelated. To shed light on the evolutionary processes that lead to the present-day diversity of Globigerinoides, we investigated the genetic, ecological and morphological divergence of its constituent species. We assembled a global collection of single-cell barcode sequences and show that the genus consists of eight distinct genetic types organized in five extant morphospecies. Based on morphological evidence, we reassign the species Globoturborotalita tenella to Globigerinoides and amend Globigerinoides ruber by formally proposing two new subspecies, G. ruber albus n.subsp. and G. ruber ruber in order to express their subspecies level distinction and to replace the informal G. ruber "white" and G. ruber "pink", respectively. The genetic types within G. ruber and Globigerinoides elongatus show a combination of endemism and coexistence, with little evidence for ecological differentiation. CT-scanning and ontogeny analysis reveal that the diagnostic differences in adult morphologies could be explained by alterations of the ontogenetic trajectories towards final (reproductive) size. This indicates that heterochrony may have caused the observed decoupling between genetic and morphological diversification within the genus. We find little evidence for environmental forcing of either the genetic or the morphological diversification, which allude to biotic interactions such as symbiosis, as the driver of speciation in Globigerinoides.

RevDate: 2019-12-05

Joshee K, Abhang T, R Kulkarni (2019)

Fatty acid profiling of 75 Indian snack samples highlights overall low trans fatty acid content with high polyunsaturated fatty acid content in some samples.

PloS one, 14(12):e0225798 pii:PONE-D-19-21727.

Diet-derived fatty acids have well-proven varying effects on human health. In particular, trans fatty acids (TFA) are associated with high risk of cardiovascular diseases whereas, polyunsaturated fatty acids (PUFA) are considered to be beneficial to the human health. In this study, we report fatty acid profiling of 75 food samples from India belonging to three broad categories, viz., perishable deep-fried, non-perishable deep-fried and bakery. Lipids were extracted from the snacks and fatty acids converted into methyl esters and analysed by gas chromatography. Thirty-seven detected fatty acids were classified into four categories: saturated (SFA), monounsaturated (MUFA), PUFA, and TFA, of which SFA represented the most abundant class in two-third of the samples. The highest average proportions of TFA and SFA of 3.26% and 56.1%, respectively, in total fatty acids were found in the bakery products; whereas, that of PUFA (38%) in the perishable deep-fried products. Principal Component Analysis depicted clustering of many samples according to the above-mentioned categories and helped predict the oil usage. Lower TFA content in all the samples and high proportion of PUFA in a quarter of the samples is suggestive of a better trend as compared to earlier studies.

RevDate: 2019-12-05

Chen L, Li D, Shao Y, et al (2019)

Identifying Microbiota Signature and Functional Rules Associated With Bacterial Subtypes in Human Intestine.

Frontiers in genetics, 10:1146.

Gut microbiomes are integral microflora located in the human intestine with particular symbiosis. Among all microorganisms in the human intestine, bacteria are the most significant subgroup that contains many unique and functional species. The distribution patterns of bacteria in the human intestine not only reflect the different microenvironments in different sections of the intestine but also indicate that bacteria may have unique biological functions corresponding to their proper regions of the intestine. However, describing the functional differences between the bacterial subgroups and their distributions in different individuals is difficult using traditional computational approaches. Here, we first attempted to introduce four effective sets of bacterial features from independent databases. We then presented a novel computational approach to identify potential distinctive features among bacterial subgroups based on a systematic dataset on the gut microbiome from approximately 1,500 human gut bacterial strains. We also established a group of quantitative rules for explaining such distinctions. Results may reveal the microstructural characteristics of the intestinal flora and deepen our understanding on the regulatory role of bacterial subgroups in the human intestine.

RevDate: 2019-12-05

Xu S, Jiang L, Qiao G, et al (2019)

The Bacterial Flora Associated with the Polyphagous Aphid Aphis gossypii Glover (Hemiptera: Aphididae) Is Strongly Affected by Host Plants.

Microbial ecology pii:10.1007/s00248-019-01435-2 [Epub ahead of print].

Aphids live in symbiosis with a variety of bacteria, including the obligate symbiont Buchnera aphidicola and diverse facultative symbionts. The symbiotic associations for one aphid species, especially for polyphagous species, often differ across populations. In the present study, by using high-throughput 16S rRNA sequencing, we surveyed in detail the microbiota in natural populations of the cotton aphid Aphis gossypii in China and assessed differences in bacterial diversity with respect to host plant and geography. The microbial community of A. gossypii was dominated by a few heritable symbionts. Arsenophonus was the most dominant secondary symbiont, and Spiroplasma was detected for the first time. Statistical tests and ordination analyses showed that host plants rather than geography seemed to have shaped the associated symbiont composition. Special symbiont communities inhabited the Cucurbitaceae-feeding populations, which supported the ecological specialization of A. gossypii on cucurbits from the viewpoint of symbiotic bacteria. Correlation analysis suggested antagonistic interactions between Buchnera and coexisting secondary symbionts and more complicated interactions between different secondary symbionts. Our findings lend further support to an important role of the host plant in structuring symbiont communities of polyphagous aphids and will improve our understanding of the interactions among phytophagous insects, symbionts, and environments.

RevDate: 2019-12-05

Alex A, A Antunes (2019)

Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses.

Microorganisms, 7(12): pii:microorganisms7120635.

The most recently described bacterial members of the genus Endozoicomonas have been found in association with a wide variety of marine invertebrates. Despite their ubiquity in the host holobiont, limited information is available on the molecular genomic signatures of the symbiotic association of Endozoicomonas with marine sponges. Here, we generated a draft genome of Endozoicomonas sp. OPT23 isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative genomics analyses. Genome-specific analysis and metabolic pathway comparison of the members of the genus Endozoicomonas revealed the presence of gene clusters encoding for unique metabolic features, such as the utilization of carbon sources through lactate, L-rhamnose metabolism, and a phenylacetic acid degradation pathway in Endozoicomonas sp. OPT23. Moreover, the genome harbors genes encoding for eukaryotic-like proteins, such as ankyrin repeats, tetratricopeptide repeats, and Sel1 repeats, which likely facilitate sponge-bacterium attachment. The genome also encodes major secretion systems and homologs of effector molecules that seem to enable the sponge-associated bacterium to interact with the sponge and deliver the virulence factors for successful colonization. In conclusion, the genome analysis of Endozoicomonas sp. OPT23 revealed the presence of adaptive genomic signatures that might favor their symbiotic lifestyle within the sponge host.

RevDate: 2019-12-04

Bratovanov EV, Ishida K, Heinze B, et al (2019)

Genome Mining and Heterologous Expression Reveal Two Distinct Families of Lasso Peptides Highly Conserved in Endofungal Bacteria.

ACS chemical biology [Epub ahead of print].

Genome mining identified the fungal-bacterial endosymbiosis Rhizopus microsporus-Mycetohabitans (previously: Burkholderia) rhizoxinica as a rich source of novel natural products. Yet, most of the predicted compounds have remained cryptic. In this study we employed heterologous expression to isolate and characterize three ribosomally-synthesized and post-translationally modified peptides (RiPPs) with lariat topology (lasso peptides) from the endosymbiont M. rhizoxinica: burhizin-23, mycetohabin-16 and mycetohabin-15. Through coexpression experiments it was shown that an orphan gene product results in mature mycetohabin-15, albeit encoded remotely from the core biosynthetic gene cluster. Comparative genomics revealed that mycetohabins are highly conserved trait among M. rhizoxinica and related endosymbiotic bacteria. Gene knockout and reinfection experiments indicated that the lasso peptides are not crucial for establishing the symbiosis; instead, the peptides are exported into the environment during endosymbiosis. This is the first report on lasso peptides from endosymbiontic bacteria.

RevDate: 2019-12-04

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

Genome sequence data announcement of Bifidobacterium bifidum strain ICIS-202 isolated from a healthy human intestine stimulating active nitrogen oxide production in macrophages.

Data in brief, 27:104761 pii:104761.

This report presents the data on the draft genome sequence of Bifidobacterium bifidum strain ICIS-202. The strain, isolated from the intestine of a young healthy woman, was deposited in the State Collection of Microorganisms of Normal Microbiota in Gabrichevsky Institute of Epidemiology and Microbiology, Moscow, Russian Federation as a prospective candidate for probiotic development. The size of the genome was 2,265,060 bp (62,4% G + C content). The annotation revealed 1771 coding sequences, including 1771 proteins, 5 rRNA, 52 tRNA, and 3 ncRNA genes. The draft genome sequence data of B. bifidum strain ICIS-202 is available in DBJ/EMBL/GenBank under the accession nos. SSMS00000000.1, PRJNA412271 and SAMN07709009 for Genome, Bioproject and Biosample databases, respectively.

RevDate: 2019-12-04

Zhang X, Li X, Wu C, et al (2019)

Exogenous Nitric Oxide and Phosphorus Stress Affect the Mycorrhization, Plant Growth, and Associated Microbes of Carya illinoinensis Seedlings Colonized by Tuber indicum.

Frontiers in microbiology, 10:2634.

In the artificial cultivation of truffles, ectomycorrhizal colonization level, host plant quality, and the associated microbes in the rhizosphere soil are vitally important. To explore the effects of nitric oxide (NO) and phosphorus (P) stress on the early symbiosis of truffles and host plants, different concentrations of exogenous NO donor sodium nitroprusside (SNP) and P were applied to Carya illinoinensis seedlings inoculated with the Chinese black truffle (Tuber indicum). The growth of T. indicum-mycorrhized seedlings and their mycorrhizal colonization rate were investigated. Additionally, the denitrifying bacterial community harboring NO reductase (norB) genes and the fungal community in the rhizosphere of the host were analyzed by high-throughput sequencing. The results showed that the colonization rate of T. indicum was significantly influenced by SNP treatments and P stress, with the highest level being obtained when the SNP was 100 μmol/L under low P stress (5 μmol/L). Treatment with 100 μmol/L SNP alone also increased the colonization rate of T. indicum and had positive effects on the plant height, stem circumference, biomass, root-shoot ratio and root POD activity of the seedlings at different times after inoculation. Under low P stress, the 100 μmol/L SNP increased the richness of the norB-type denitrifying bacterial community. Interestingly, the diversity and richness of norB-type denitrifying bacteria were significantly positively correlated with the colonization rate of T. indicum. SNP treatments under low P stress altered the abundance of some dominant taxa such as Alphaproteobacteria, Gammaproteobacteria, Pseudomonas, Ensifer, and Sulfitobacter. Evaluation of the fungal community in the rhizosphere revealed that 100 μmol/L SNP treatment alone had no noticeable effect on their richness and diversity, but it did shape the abundance of some fungi. Buellia, Podospora, Phaeoisaria, Ascotaiwania, and Lophiostoma were more abundant following exogenous NO application, while the abundance of Acremonium, Monographella, and Penicillium were decreased. Network analysis indicated that T. indicum was positively and negatively correlated with some fungal genera when treated with 100 μmol/L SNP. Overall, these results revealed how exogenous NO and P stress influence the symbiosis of truffles and host plants, and indicate that application of SNP treatments has the potential for ectomycorrhizal synthesis and truffle cultivation.

RevDate: 2019-12-04

Bauer E, Kaltenpoth M, H Salem (2019)

Minimal fermentative metabolism fuels extracellular symbiont in a leaf beetle.

The ISME journal pii:10.1038/s41396-019-0562-1 [Epub ahead of print].

While genome erosion is extensively studied in intracellular symbionts, the metabolic implications of reductive evolution in microbes subsisting extracellularly remain poorly understood. Stammera capleta-an extracellular symbiont in leaf beetles-possesses an extremely reduced genome (0.27 Mb), enabling the study of drastic reductive evolution in the absence of intracellularity. Here, we outline the genomic and transcriptomic profiles of Stammera and its host to elucidate host-symbiont metabolic interactions. Given the symbiont's substantial demands for nutrients and membrane components, the host's symbiotic organ shows repurposing of internal resources by upregulating nutrient transporters and cuticle-processing genes targeting epithelial chitin. Facilitated by this supplementation and its localization, Stammera exhibits a highly streamlined gene expression profile and a fermentation pathway for energy conversion, sharply contrasting the respiratory metabolism retained by most intracellular symbionts. Our results provide insights into a tightly regulated and metabolically integrated extracellular symbiosis, expanding our understanding of the minimal metabolism required to sustain life outside of a host cell.

RevDate: 2019-12-04

Chung M, Teigen LE, Libro S, et al (2019)

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics.

mSystems, 4(6): pii:4/6/e00596-19.

To better understand the transcriptomic interplay of organisms associated with lymphatic filariasis, we conducted multispecies transcriptome sequencing (RNA-Seq) on the filarial nematode Brugia malayi, its Wolbachia endosymbiont wBm, and its laboratory vector Aedes aegypti across the entire B. malayi life cycle. In wBm, transcription of the noncoding 6S RNA suggests that it may be a regulator of bacterial cell growth, as its transcript levels correlate with bacterial replication rates. For A. aegypti, the transcriptional response reflects the stress that B. malayi infection exerts on the mosquito with indicators of increased energy demand. In B. malayi, expression modules associated with adult female samples consistently contained an overrepresentation of genes involved in chromatin remodeling, such as the bromodomain-containing proteins. All bromodomain-containing proteins encoded by B. malayi were observed to be upregulated in the adult female, embryo, and microfilaria life stages, including 2 members of the bromodomain and extraterminal (BET) protein family. The BET inhibitor JQ1(+), originally developed as a cancer therapeutic, caused lethality of adult worms in vitro, suggesting that it may be a potential therapeutic that can be repurposed for treating lymphatic filariasis.IMPORTANCE The current treatment regimen for lymphatic filariasis is mostly microfilaricidal. In an effort to identify new drug candidates for lymphatic filariasis, we conducted a three-way transcriptomics/systems biology study of one of the causative agents of lymphatic filariasis, Brugia malayi, its Wolbachia endosymbiont wBm, and its vector host Aedes aegypti at 16 distinct B. malayi life stages. B. malayi upregulates the expression of bromodomain-containing proteins in the adult female, embryo, and microfilaria stages. In vitro, we find that the existing cancer therapeutic JQ1(+), which is a bromodomain and extraterminal protein inhibitor, has adulticidal activity in B. malayi.

RevDate: 2019-12-04

Pankievicz VCS, Irving TB, Maia LGS, et al (2019)

Are we there yet? The long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops.

BMC biology, 17(1):99 pii:10.1186/s12915-019-0710-0.

Nitrogen is an essential element of life, and nitrogen availability often limits crop yields. Since the Green Revolution, massive amounts of synthetic nitrogen fertilizers have been produced from atmospheric nitrogen and natural gas, threatening the sustainability of global food production and degrading the environment. There is a need for alternative means of bringing nitrogen to crops, and taking greater advantage of biological nitrogen fixation seems a logical option. Legumes are used in most cropping systems around the world because of the nitrogen-fixing symbiosis with rhizobia. However, the world's three major cereal crops-rice, wheat, and maize-do not associate with rhizobia. In this review, we will survey how genetic approaches in rhizobia and their legume hosts allowed tremendous progress in understanding the molecular mechanisms controlling root nodule symbioses, and how this knowledge paves the way for engineering such associations in non-legume crops. We will also discuss challenges in bringing these systems into the field and how they can be surmounted by interdisciplinary collaborations between synthetic biologists, microbiologists, plant biologists, breeders, agronomists, and policymakers.

RevDate: 2019-12-04

Vergnes S, Gayrard D, Veyssière M, et al (2019)

Phyllosphere Colonization by a Soil Streptomyces sp. Promotes Plant Defense Responses Against Fungal Infection.

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

Streptomycetes are soil-dwelling, filamentous actinobacteria and represent a prominent bacterial clade inside the plant root microbiota. The ability of streptomycetes to produce a broad spectrum of antifungal metabolites suggests that these bacteria could be used to manage plant diseases. Here, we describe the identification of a soil Streptomyces strain named AgN23 which strongly activates a large array of defense responses when applied on Arabidopsis thaliana leaves. AgN23 increased the biosynthesis of salicylic acid, leading to the development of salicylic acid induction deficient 2 (SID2)-dependent necrotic lesions. Size exclusion fractionation of plant elicitors secreted by AgN23 showed that these signals are tethered into high molecular weight complexes. AgN23 mycelium was able to colonize the leaf surface, leading to plant resistance against Alternaria brassicicola infection in wild-type Arabidopsis plants. AgN23-induced resistance was found partially compromised in salicylate, jasmonate, and ethylene mutants. Our data show that Streptomyces soil bacteria can develop at the surface of plant leaves to induce defense responses and protection against foliar fungal pathogens, extending their potential use to manage plant diseases.

RevDate: 2019-12-03

Kalayeh MM, M Shah (2019)

On Symbiosis of Attribute Prediction and Semantic Segmentation.

IEEE transactions on pattern analysis and machine intelligence [Epub ahead of print].

Attributes are semantically meaningful characteristics whose applicability widely crosses category boundaries. They are particularly important in describing and recognizing concepts for which no explicit training example is given, e.g., zero-shot learning. Additionally, since attributes are human describable, they can be used for efficient human-computer interaction. In this paper, we propose to employ semantic segmentation to improve person-related attribute prediction. The core idea lies in the fact that many attributes describe local properties. In other words, the probability of an attribute to appear in an image is far from being uniform in the spatial domain. We build our attribute prediction model jointly with a deep semantic segmentation network. This harnesses the localization cues learned by the semantic segmentation to guide the attention of the attribute prediction to the regions where different attributes naturally show up. As a result of this approach, in addition to prediction, we are able to localize the attributes despite merely having access to image-level labels (weak supervision) during training. We first propose semantic segmentation-based pooling and gating, respectively denoted as SSP and SSG. In the former, the estimated segmentation masks are used to pool the final activations of the attribute prediction network, from multiple semantically homogeneous regions. This is in contrast to global average pooling which is agnostic with respect to where in the spatial domain activations occur. In SSG, the same idea is applied to the intermediate layers of the network. Specifically, we create multiple copies of the internal activations. In each copy, only values that fall within a certain semantic region are preserved while outside of that, activations are suppressed. This mechanism allows us to prevent pooling operation from blending activations that are associated with semantically different regions. SSP and SSG, while effective, impose heavy memory utilization since each channel of the activations is pooled/gated with all the semantic segmentation masks. To circumvent this, we propose Symbiotic Augmentation (SA), where we learn only one mask per activation channel. SA allows the model to either pick one, or combine (weighted superposition) multiple semantic maps, in order to generate the proper mask for each channel. SA simultaneously applies the same mechanism to the reverse problem by leveraging output logits of attribute prediction to guide the semantic segmentation task. We evaluate our proposed methods for facial attributes on CelebA and LFWA datasets, while benchmarking WIDER Attribute and Berkeley Attributes of People for whole body attributes. Our proposed methods achieve superior results compared to the previous works. Furthermore, we show that in the reverse problem, semantic face parsing significantly improves when its associated task is jointly learned, through our proposed Symbiotic Augmentation, with facial attribute prediction. We confirm that when few training instances are available, indeed image-level facial attribute labels can serve as an effective source of weak supervision to improve semantic face parsing. That reaffirms the need to jointly model these two interconnected tasks.

RevDate: 2019-12-03

Anhê FF, Barra NG, JD Schertzer (2019)

Glucose alters symbiotic relationships between gut microbiota and host physiology.

Bacteria and mammals exhibit all aspects of symbiosis. Metabolic flux in bacteria and in specific host cells can influence host-microbe symbiotic relationships and tip the balance between mutualism, commensalism, and parasitism. The relationship between microbes and host metabolism is bidirectional: microbes can influence host blood glucose, but glucose levels can influence the microbiota and host response and outcomes to specific bacteria. A key consideration determining symbiotic relationships is compartmentalization of bacterial niches by mucosal, chemical, and physical barriers of the gut. We propose that compartmentalization of glucose levels in the blood versus the intestinal lumen is another important factor dictating host-microbe symbiosis. Host glucose and specific bacteria can modify the intestinal barrier, immune function, and antimicrobial defences, which can break down compartmentalization of microbes, alter glucose levels and impact symbiosis. Determining how glucose metabolism promotes mutualistic, commensal, and parasitic relationships within the entire microbiota community is relevant to glucose control in diabetes and enteric infections, which occur more often and have worse outcomes in diabetics.

RevDate: 2019-12-02

Tominaga T, Miura C, Takeda N, et al (2019)

Gibberellin Promotes Fungal Entry and Colonization during Paris-type Arbuscular Mycorrhizal Symbiosis in Eustoma grandiflorum.

Plant & cell physiology pii:5650413 [Epub ahead of print].

Arbuscular mycorrhizas (AMs) are divided into two types according to morphology: Arum- and Paris-type AMs. Gibberellins (GAs) mainly inhibit the establishment of Arum-type AM symbiosis in most of model plants, whereas the effects of GAs on Paris-type AM symbiosis are unclear. To provide insights into the mechanism underlying this type of symbiosis, the roles of GAs on Paris-type AM symbiosis were investigated in Eustoma grandiflorum used as the host plant for Paris-type AM establishment. E. grandiflorum seedlings were inoculated with the model AM fungus, Rhizophagus irregularis, and then the effects of GA and the GA-biosynthesis inhibitor uniconazole-P on the symbiosis were quantitatively evaluated. Exogenous GA significantly increased hyphopodium formation at the epidermis, thus leading to the promotion of fungal colonization and arbuscule formation in the root cortex. By contrast, the suppression of GA biosynthesis and signaling attenuated fungal entry to E. grandiflorum roots. Moreover, the exudates from GA-treated roots strongly induced the hyphal branching of R. irregularis. Our results show that GA has an opposite effect on Paris-type AM symbiosis in E. grandiflorum compared with Arum-type AM symbiosis. This finding could be explained by the differential regulation of the early colonization stage, where fungal hyphae make contact with and penetrate the epidermis.

RevDate: 2019-12-02

Fackelmann G, S Sommer (2019)

Microplastics and the gut microbiome: How chronically exposed species may suffer from gut dysbiosis.

Marine pollution bulletin, 143:193-203.

As small pieces of plastics known as microplastics pollute even the remotest parts of Earth, research currently focuses on unveiling how this pollution may affect biota. Despite increasing awareness, one potentially major consequence of chronic exposure to microplastics has been largely neglected: the impact of the disruption of the symbiosis between host and the natural community and abundance pattern of the gut microbiota. This so-called dysbiosis might be caused by the consumption of microplastics, associated mechanical disruption within the gastrointestinal tract, the ingestion of foreign and potentially pathogenic bacteria, as well as chemicals, which make-up or adhere to microplastics. Dysbiosis may interfere with the host immune system and trigger the onset of (chronic) diseases, promote pathogenic infections, and alter the gene capacity and expression of gut microbiota. We summarize how chronically exposed species may suffer from microplastics-induced gut dysbiosis, deteriorating host health, and highlight corresponding future directions of research.

RevDate: 2019-12-02

Liu W, Li Y, Bai X, et al (2019)

LuxR-type regulator AclR1 of Azorhizobium caulinodans regulates cyclic di-GMP and numerous phenotypes in free-living and symbiotic states.

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

LuxR-type regulators play important roles in transcriptional regulation in bacteria and control various biological processes. A genome sequence analysis showed the existence of seven LuxR-type regulators in Azorhizobium caulinodans ORS571, an important nitrogen-fixing bacterium in both its free-living state and its symbiosis with its host, Sesbania rostrata. However, the functional mechanisms of these regulators remain unclear. In this study, we identified a LuxR-type regulator that contains a REC domain in its N-terminus and designated it AclR1. Interestingly, phylogenetic analysis revealed that AclR1 exhibited relatively close evolutionary relationships with MalT/GerE/FixJ/NarL family proteins. Functional analysis of an aclR1 deletion mutant (ΔaclR1) in the free-living state showed that AclR1 positively regulated cell motility and flocculation but negatively regulated exopolysaccharide production, biofilm formation, and second messenger cyclic diguanylate (c-di-GMP)-related gene expression. In the symbiotic state, the ΔaclR1 mutant was defective in competitive colonization and nodulation on host plants. These results suggested that AclR1 could provide bacteria with the ability to compete effectively for symbiotic nodulation. Overall, our results show that the REC-LuxR-type regulator AclR1 regulates numerous phenotypes both in the free-living state and during host plant symbiosis.

RevDate: 2019-12-02

Karaivazoglou K, Konstantakis C, Assimakopoulos SF, et al (2019)

Neonate gut colonization: The rise of a social brain.

Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society [Epub ahead of print].

BACKGROUND: The human gut microbiota constitutes an integral part of human physiology, playing an important role in maintaining health, and compositional or functional changes in intestinal microbiota may be associated with the emergence of several chronic diseases. Animal and human studies have shown that there is a dynamic cross-talk between intestinal microorganisms and brain networks which has an impact on neurodevelopment and may be extremely critical in shaping human social behavior.

PURPOSE: The aim of the current review is to appraise and present in a concise manner all findings linking the evolution of neonate and infant gut colonization with early social development and to formulate scientifically informed hypotheses which could guide future research on this field.

RevDate: 2019-12-02

Michaud C, Hervé V, Dupont S, et al (2019)

Efficient but occasionally imperfect vertical transmission of gut mutualistic protists in a wood-feeding termite.

Molecular ecology [Epub ahead of print].

Although mutualistic associations between animals and microbial symbionts are widespread in nature, the mechanisms that have promoted their evolutionary persistence remain poorly understood. A vertical mode of symbiont transmission (from parents to offspring) is thought to ensure partner fidelity and stabilisation, although the efficiency of vertical transmission has rarely been investigated, especially in cases where hosts harbour a diverse microbial community. Here we evaluated vertical transmission rates of cellulolytic gut oxymonad and parabasalid protists in the wood-feeding termite Reticulitermes grassei. We sequenced amplicons of the 18S rRNA gene of protists from 24 colonies of R. grassei collected in two populations. For each colony, the protist community was characterised from the gut of 14 swarming reproductives and from a pool of 10 worker guts. A total of 98 OTUs belonging to 13 species-level taxa were found. The vertical transmission rate was estimated for each protist present in a colony by its frequency among the reproductives. Results revealed that transmission rates were high, with an average of 0.897 (±0.164) per protist species. Overall, the protist community did not differ between reproductive sexes, suggesting that both the queen and king could contribute to the gut microbiota of the offspring. A positive relationship between the transmission rate of protists and their prevalence within populations was also detected. However, transmission rates alone did not explain protist prevalence. In conclusion, these findings reveal key forces behind a conserved, multi-species mutualism, raising further questions on the roles of horizontal transfer and negative selection in shaping symbiont prevalence.

RevDate: 2019-12-02

McIlroy SE, Cunning R, Baker AC, et al (2019)

Competition and succession among coral endosymbionts.

Ecology and evolution, 9(22):12767-12778 pii:ECE35749.

Host species often support a genetically diverse guild of symbionts, the identity and performance of which can determine holobiont fitness under particular environmental conditions. These symbiont communities are structured by a complex set of potential interactions, both positive and negative, between the host and symbionts and among symbionts. In reef-building corals, stable associations with specific symbiont species are common, and we hypothesize that this is partly due to ecological mechanisms, such as succession and competition, which drive patterns of symbiont winnowing in the initial colonization of new generations of coral recruits. We tested this hypothesis using the experimental framework of the de Wit replacement series and found that competitive interactions occurred among symbionts which were characterized by unique ecological strategies. Aposymbiotic octocoral recruits within high- and low-light environments were inoculated with one of three Symbiodiniaceae species as monocultures or with cross-paired mixtures, and we tracked symbiont uptake using quantitative genetic assays. Priority effects, in which early colonizers excluded competitive dominants, were evidenced under low light, but these early opportunistic species were later succeeded by competitive dominants. Under high light, a more consistent competitive hierarchy was established in which competitive dominants outgrew and limited the abundance of others. These findings provide insight into mechanisms of microbial community organization and symbiosis breakdown and recovery. Furthermore, transitions in competitive outcomes across spatial and temporal environmental variation may improve lifetime host fitness.

RevDate: 2019-12-03
CmpDate: 2019-12-03

Hause B (2019)

Elevated CO2 -induced improvement of mycorrhization - which players lie in-between?.

The New phytologist, 224(1):5-7.

RevDate: 2019-12-02
CmpDate: 2019-12-02

Michalska-Smith MJ, S Allesina (2019)

Telling ecological networks apart by their structure: A computational challenge.

PLoS computational biology, 15(6):e1007076 pii:PCOMPBIOL-D-18-01703.

Ecologists have been compiling ecological networks for over a century, detailing the interactions between species in a variety of ecosystems. To this end, they have built networks for mutualistic (e.g., pollination, seed dispersal) as well as antagonistic (e.g., herbivory, parasitism) interactions. The type of interaction being represented is believed to be reflected in the structure of the network, which would differ substantially between mutualistic and antagonistic networks. Here, we put this notion to the test by attempting to determine the type of interaction represented in a network based solely on its structure. We find that, although it is easy to separate different kinds of nonecological networks, ecological networks display much structural variation, making it difficult to distinguish between mutualistic and antagonistic interactions. We therefore frame the problem as a challenge for the community of scientists interested in computational biology and machine learning. We discuss the features a good solution to this problem should possess and the obstacles that need to be overcome to achieve this goal.

RevDate: 2019-12-02
CmpDate: 2019-12-02

Coykendall DK, Cornman RS, Prouty NG, et al (2019)

Molecular characterization of Bathymodiolus mussels and gill symbionts associated with chemosynthetic habitats from the U.S. Atlantic margin.

PloS one, 14(3):e0211616 pii:PONE-D-18-08567.

Mussels of the genus Bathymodiolus are among the most widespread colonizers of hydrothermal vent and cold seep environments, sustained by endosymbiosis with chemosynthetic bacteria. Presumed species of Bathymodiolus are abundant at newly discovered cold seeps on the Mid-Atlantic continental slope, however morphological taxonomy is challenging, and their phylogenetic affinities remain unestablished. Here we used mitochondrial sequence to classify species found at three seep sites (Baltimore Canyon seep (BCS; ~400m); Norfolk Canyon seep (NCS; ~1520m); and Chincoteague Island seep (CTS; ~1000m)). Mitochondrial COI (N = 162) and ND4 (N = 39) data suggest that Bathymodiolus childressi predominates at these sites, although single B. mauritanicus and B. heckerae individuals were detected. As previous work had suggested that methanotrophic and thiotrophic interactions can both occur at a site, and within an individual mussel, we investigated the symbiont communities in gill tissues of a subset of mussels from BCS and NCS. We constructed metabarcode libraries with four different primer sets spanning the 16S gene. A methanotrophic phylotype dominated all gill microbial samples from BCS, but sulfur-oxidizing Campylobacterota were represented by a notable minority of sequences from NCS. The methanotroph phylotype shared a clade with globally distributed Bathymodiolus spp. symbionts from methane seeps and hydrothermal vents. Two distinct Campylobacterota phylotypes were prevalent in NCS samples, one of which shares a clade with Campylobacterota associated with B. childressi from the Gulf of Mexico and the other with Campylobacterota associated with other deep-sea fauna. Variation in chemosynthetic symbiont communities among sites and individuals has important ecological and geochemical implications and suggests shifting reliance on methanotrophy. Continued characterization of symbionts from cold seeps will provide a greater understanding of the ecology of these unique environments as well and their geochemical footprint in elemental cycling and energy flux.

RevDate: 2019-12-03
CmpDate: 2019-12-03

Tsyganova AV, Seliverstova EV, Brewin NJ, et al (2019)

Comparative analysis of remodelling of the plant-microbe interface in Pisum sativum and Medicago truncatula symbiotic nodules.

Protoplasma, 256(4):983-996.

Infection of host cells by nitrogen-fixing soil bacteria, known as rhizobia, involves the progressive remodelling of the plant-microbe interface. This process was examined by using monoclonal antibodies to study the subcellular localisation of pectins and arabinogalactan proteins (AGPs) in wild-type and ineffective nodules of Pisum sativum and Medicago truncatula. The highly methylesterified homogalacturonan (HG), detected by monoclonal antibody JIM7, showed a uniform localisation in the cell wall, regardless of the cell type in nodules of P. sativum and M. truncatula. Low methylesterified HG, recognised by JIM5, was detected mainly in the walls of infection threads in nodules of both species. The galactan side chain of rhamnogalacturonan I (RG-I), recognised by LM5, was present in the nodule meristem in both species and in the infection thread walls in P. sativum, but not in M. truncatula. The membrane-anchored AGP recognised by JIM1 was observed on the plasma membrane in nodules of P. sativum and M. truncatula. In P. sativum, the AGP epitope recognised by JIM1 was present on mature symbiosome membranes of wild-type nodules, but JIM1 labelling was absent from symbiosome membranes in the mutant Sprint-2Fix- (sym31) with undifferentiated bacteroids, suggesting a possible involvement of AGP in the maturation of symbiosomes. Thus, the common and species-specific traits of cell wall remodelling during nodule differentiation were demonstrated.

RevDate: 2019-12-01

António N (2019)

Combining mesenchymal stem cell therapy and exercise training in myocardial infarction: The perfect symbiosis?.

Revista portuguesa de cardiologia : orgao oficial da Sociedade Portuguesa de Cardiologia = Portuguese journal of cardiology : an official journal of the Portuguese Society of Cardiology pii:S0870-2551(19)30524-4 [Epub ahead of print].

RevDate: 2019-11-29

Zeng W, Liu B, Zhong J, et al (2019)

A Natural High-Sugar Diet Has Different Effects on the Prokaryotic Community Structures of Lower and Higher Termites (Blattaria).

Environmental entomology pii:5648023 [Epub ahead of print].

The lignocellulosic digestive symbiosis in termites is a dynamic survival adaptation system. While the contribution of hereditary and habitat factors to the development of the symbiotic bacterial community of termites had been confirmed, the manner in which these factors affect functional synergism among different bacterial lineages has still not been fully elucidated. Therefore, the 16S rRNA gene libraries of Odontotermes formosanus Shiraki (Blattodea: Termitidae) and Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) sampled from sugarcane fields (high sugar) or pine tree forests (no free sugar) were sequenced. The results verify that the prokaryotic community structures of termites could be significantly reshaped by native dietary isolation within a species. Although the most dominant phyla are convergent in all samples, their relative abundances in these two termite species exhibited a reverse variation pattern when the termite hosts were fed on the high-sugar diet. Furthermore, we showed that the taxonomic composition of the dominant phyla at the family or genus level differentiate depending on the diet and the host phylogeny. We hypothesize that the flexible bacterial assemblages at low taxonomic level might exert variable functional collaboration to accommodate to high-sugar diet. In addition, the functional predictions of Tax4Fun suggest a stable metabolic functional structure of the microbial communities of the termites in both different diet habitats and taxonomy. We propose that the symbiotic bacterial community in different host termites developed a different functional synergistic pattern, which may be essential to maintain the stability of the overall metabolic function for the survival of termites.

RevDate: 2019-11-29

Maillet F, Fournier J, Mendis HC, et al (2019)

Sinorhizobium meliloti succinylated high molecular weight succinoglycan and the Medicago truncatula LysM receptor-like kinase MtLYK10 participate independently in symbiotic infection.

The Plant journal : for cell and molecular biology [Epub ahead of print].

The formation of nitrogen-fixing nodules on legume hosts is a finely-tuned process involving many components of both symbiotic partners. Production of the exopolysaccharide succinoglycan by the nitrogen-fixing bacterium Sinorhizobium meliloti 1021 is needed for an effective symbiosis with Medicago spp, and the succinyl modification to this polysaccharide is critical. However, it is not known when succinoglycan intervenes in the symbiotic process, and it is not known whether the plant lysin-motif receptor-like kinase MtLYK10 intervenes in recognition of succinoglycan, as might be inferred from work on the Lotus japonicus MtLYK10 ortholog, LjEPR3. We studied the symbiotic infection phenotypes of S. meliloti mutants deficient in succinoglycan production or producing modified succinoglycan, in wild-type Medicago truncatula plants and in Mtlyk10 mutant plants. On wild-type plants, S. meliloti strains producing no succinoglycan or only unsuccinylated succinoglycan still induced nodule primordia and epidermal infections, but further progression of the symbiotic process was blocked. These S. meliloti mutants induced a more severe infection phenotype on Mtlyk10 mutant plants. Nodulation by succinoglycan-defective strains was achieved by in trans rescue with a Nod factor-deficient S. meliloti mutant. While the Nod factor-deficient strain was always more abundant inside nodules, the succinoglycan-deficient strain was more efficient than the strain producing only unsuccinylated succinoglycan. Together, these data show that succinylated succinoglycan is essential for infection thread formation in M. truncatula, and that MtLYK10 plays an important, but different role in this symbiotic process. These data also suggest that succinoglycan is more important than Nod factors for bacterial survival inside nodules.

RevDate: 2019-11-29

Quagliariello A, Di Paola M, De Fanti S, et al (2019)

Gut microbiota composition in Himalayan and Andean populations and its relationship with diet, lifestyle and adaptation to the high-altitude environment.

Journal of anthropological sciences = Rivista di antropologia : JASS, 97: [Epub ahead of print].

Human populations living at high altitude evolved a number of biological adjustments to cope with a challenging environment characterised especially by reduced oxygen availability and limited nutritional resources. This condition may also affect their gut microbiota composition. Here, we explored the impact of exposure to such selective pressures on human gut microbiota by considering different ethnic groups living at variable degrees of altitude: the high-altitude Sherpa and low-altitude Tamang populations from Nepal, the high-altitude Aymara population from Bolivia, as well as a low-altitude cohort of European ancestry, used as control. We thus observed microbial profiles common to the Sherpa and Aymara, but absent in the low-altitude cohorts, which may contribute to the achievement of adaptation to high-altitude lifestyle and nutritional conditions. The collected evidences suggest that microbial signatures associated to these rural populations may enhance metabolic functions able to supply essential compounds useful for the host to cope with high altitude-related physiological changes and energy demand. Therefore, these results add another valuable piece of the puzzle to the understanding of the beneficial effects of symbiosis between microbes and their human host even from an evolutionary perspective.

RevDate: 2019-11-29

Huang L, Chen D, Zhang H, et al (2019)

Funneliformis mosseae Enhances Root Development and Pb Phytostabilization in Robinia pseudoacacia in Pb-Contaminated Soil.

Frontiers in microbiology, 10:2591.

It is possible that arbuscular mycorrhizal fungi play a pivotal role in root development and Pb phytostabilization in plants grown in Pb-contaminated soil. In this study, a pot experiment was conducted over 4 months to evaluate the effects of Funneliformis mosseae strain BGCXJ01A on root characteristics of black locust (Robinia pseudoacacia L.) seedlings in Pb-contaminated soil. Four Pb treatments (0, 90, 900, and 3,000 mg kg-1) were applied to soil in the presence and absence of F. mosseae. Inoculation with F. mosseae prominently improved root length, surface area, volume, and tip number in the plants across all Pb treatments. The F. mosseae inoculation also increased root diameter and fork number, especially under high Pb treatments. The presence of F. mosseae significantly increased the root activity and root tolerance index. However, there was little difference in specific root length between inoculated and non-inoculated plants. The biomass of roots, stems, and leaves all increased following inoculation with F. mosseae. Inoculated plants had greater accumulation and translocation capacities for Pb in the roots and stems, but lower capacities were found in the leaves when compared with those in non-inoculated plants. These results highlight that F. mosseae can alleviate the toxic effects of Pb on root development and can immobilize Pb in the roots and stems of R. pseudoacacia grown in Pb-contaminated soil. This study provides a model system for phytoremediation of Pb-contaminated soil via reciprocal symbiosis between arbuscular mycorrhizal fungi and woody legumes.

RevDate: 2019-11-29

Fukatsu T (2019)

Grand Challenges to Launching an Ideal Platform for Publishing Microbe-Insect Symbiosis Studies.

Frontiers in microbiology, 10:2542.

RevDate: 2019-11-28

Safai A, Prasad S, Chougule T, et al (2019)

Microstructural abnormalities of substantia nigra in Parkinson's disease: A neuromelanin sensitive MRI atlas based study.

Human brain mapping [Epub ahead of print].

Microstructural changes associated with degeneration of dopaminergic neurons of the substantia nigra pars compacta (SNc) in Parkinson's disease (PD) have been studied using Diffusion Tensor Imaging (DTI). However, these studies show inconsistent results, mainly due to methodological variations in delineation of SNc. To mitigate this, our work aims to construct a probabilistic atlas of SNc based on a 3D Neuromelanin Sensitive MRI (NMS-MRI) sequence and demonstrate its applicability to investigate microstructural changes on a large dataset of PD. Using manual segmentation and deformable registration we created a novel SNc atlas in the MNI space using NMS-MRI sequences of 27 healthy controls (HC). We first quantitatively evaluated this atlas and then employed it to investigate the micro-structural abnormalities in SNc using diffusion MRI from 133 patients with PD and 99 HCs. Our results demonstrated significant increase in diffusivity with no changes in anisotropy. In addition, we also observed an asymmetry of the diffusion metrics with a higher diffusivity and lower anisotropy in the left SNc than the right. Finally, a multivariate classifier based on SNc diffusion features could delineate patients with PD with an average accuracy of 71.7%. Overall, from this work we establish a normative baseline for the SNc region of interest using NMS-MRI while the application on PD data emphasizes on the contribution of diffusivity measures rather than anisotropy of white matter in PD.

RevDate: 2019-11-28

Ramoneda J, Le Roux J, Frossard E, et al (2019)

Insights from invasion ecology: Can consideration of eco-evolutionary experience promote benefits from root mutualisms in plant production?.

AoB PLANTS, 11(6):plz060 pii:plz060.

Mutualistic plant-microbial functioning relies on co-adapted symbiotic partners as well as conducive environmental conditions. Choosing particular plant genotypes for domestication and subsequent cultivar selection can narrow the gene pools of crop plants to a degree that they are no longer able to benefit from microbial mutualists. Elevated mineral nutrient levels in cultivated soils also reduce the dependence of crops on nutritional support by mutualists such as mycorrhizal fungi and rhizobia. Thus, current ways of crop production are predestined to compromise the propagation and function of microbial symbionts, limiting their long-term benefits for plant yield stability. The influence of mutualists on non-native plant establishment and spread, i.e. biological invasions, provides an unexplored analogue to contemporary crop production that accounts for mutualistic services from symbionts like rhizobia and mycorrhizae. The historical exposure of organisms to biotic interactions over evolutionary timescales, or so-called eco-evolutionary experience (EEE), has been used to explain the success of such invasions. In this paper, we stress that consideration of the EEE concept can shed light on how to overcome the loss of microbial mutualist functions following crop domestication and breeding. We propose specific experimental approaches to utilize the wild ancestors of crops to determine whether crop domestication compromised the benefits derived from root microbial symbioses or not. This can predict the potential for success of mutualistic symbiosis manipulation in modern crops and the maintenance of effective microbial mutualisms over the long term.

RevDate: 2019-11-28

Nibbering B, NDJ Ubags (2019)

Microbial interactions in the atopic march.

Clinical and experimental immunology [Epub ahead of print].

The human body is populated by a large number of microorganisms and exist in symbiosis with these immensely diverse communities, which are suggested to influence health and disease. The microbiota plays an essential role in the maturation and function of the immune system. The prevalence of atopic diseases has increased drastically over the past decades, and the co-occurrence of multiple allergic diseases and allergic sensitization starting in early life has gained a great deal of attention. Immune responses in different organs affected by allergic diseases (e.g. skin, intestine and lung) may be linked to microbial changes in peripheral tissues. In the current review, we provide an overview of the current understanding of microbial interactions in allergic diseases and their potential role in the atopic march.

RevDate: 2019-11-28

Zheng H, Perreau J, Powell JE, et al (2019)

Division of labor in honey bee gut microbiota for plant polysaccharide digestion.

Proceedings of the National Academy of Sciences of the United States of America pii:1916224116 [Epub ahead of print].

Bees acquire carbohydrates from nectar and lipids; and amino acids from pollen, which also contains polysaccharides including cellulose, hemicellulose, and pectin. These potential energy sources could be degraded and fermented through microbial enzymatic activity, resulting in short chain fatty acids available to hosts. However, the contributions of individual microbiota members to polysaccharide digestion have remained unclear. Through analysis of bacterial isolate genomes and a metagenome of the honey bee gut microbiota, we identify that Bifidobacterium and Gilliamella are the principal degraders of hemicellulose and pectin. Both Bifidobacterium and Gilliamella show extensive strain-level diversity in gene repertoires linked to polysaccharide digestion. Strains from honey bees possess more such genes than strains from bumble bees. In Bifidobacterium, genes encoding carbohydrate-active enzymes are colocated within loci devoted to polysaccharide utilization, as in Bacteroides from the human gut. Carbohydrate-active enzyme-encoding gene expressions are up-regulated in response to particular hemicelluloses both in vitro and in vivo. Metabolomic analyses document that bees experimentally colonized by different strains generate distinctive gut metabolomic profiles, with enrichment for specific monosaccharides, corresponding to predictions from genomic data. The other 3 core gut species clusters (Snodgrassella and 2 Lactobacillus clusters) possess few or no genes for polysaccharide digestion. Together, these findings indicate that strain composition within individual hosts determines the metabolic capabilities and potentially affects host nutrition. Furthermore, the niche specialization revealed by our study may promote overall community stability in the gut microbiomes of bees.

RevDate: 2019-11-28

Metwally RA, SM Al-Amri (2019)

Individual and interactive role of Trichoderma viride and arbuscular mycorrhizal fungi on growth and pigment content of onion plants.

Letters in applied microbiology [Epub ahead of print].

The study of interactions between beneficial micro-organisms associated with plant roots is important, because such interactions might either enhance or inhibit the beneficial effects of individual species. The effect of the combined inoculation of arbuscular mycorrhizal (AM) fungi and a biocontrol fungus (Trichoderma viride) on different growth parameters and chlorophyll a,b, carotenoids, total chlorophyll and total pigments of onion (Allium cepa) plants was studied under glasshouse conditions. The results proved that AM fungi and T. viride are compatible with each other and their combined use was effective not only in improving onion growth parameters such as fresh and dry weights, root and shoot lengths and leaf area but also increasing total chlorophyll, carotenoids and total pigments content in onion leaves. Where, inoculation of onion plants by AM fungi and T. viride alone or in combination significantly increased bulb diameters of onion plants 20, 12·5 and 17·5% increase; respectively, when compared with control ones. Also percentage of AM fungal colonization increased greatly with T. viride inoculation. Therefore, AM fungi and T. viride could be a good alternate of chemical fertilizer for improving the growth of onion. SIGNIFICANCE AND IMPACT OF THE STUDY: Significance and Impact of the Study: The need for increasing agricultural productivity and quality has led to an excessive use of chemical fertilizers; creating serious threats to human health and the environment. The use of biofertilizers is an alternative for sustaining high production with low ecological impact. Thus the goal of this study was to propose a biological technique using arbuscular mycorrhizal symbiosis and Trichoderma viride (plant-microbe interaction) for increasing plant growth that represent a great opportunities for recent agricultural practices. This may be an indication displaying the AM and Trichoderma significance for plant progress and growth.

RevDate: 2019-11-26

Fabricius KE, G De'ath (2008)


Ecology, 89(11):3163-3173.

Many coral reef organisms live in symbiotic relationships with photosynthetic microalgae. This symbiosis extends the energy resources available to reef organisms, thereby potentially influencing biodiversity. In octocorals, about one-half of the taxa contain photosynthetic symbionts while the rest do not, and thus octocorals are an ideal model to assess the relationships between biodiversity, spatial and environmental factors, and photosynthetic symbionts. Data collected from 1106 sites on the Great Barrier Reef, Australia, between 12° and 24° S showed that taxa with photosynthetic symbionts (phototrophs) had higher abundances, wider ranges, and a wider spread of locations than taxa without symbionts (heterotrophs). In phototrophic assemblages, spatial turnover comprised both exchange and loss of taxa, and their richness was high across a broad range of environmental conditions. In contrast, heterotrophs were uncommon, had short ranges, and were located where energy supply was highest and disturbance lowest. Turnover between heterotrophic assemblages comprised taxonomic loss rather than exchange of taxa. The biodiversity patterns and differences between phototrophic and heterotrophic octocorals are similar to those recorded in more spatially limited studies of phototrophic sponges and hard corals, and heterotrophic sponges. This study therefore suggests that the association, or not, with photosynthetic symbionts, and spatial and environmental factors related to energy supply and disturbance are principal drivers of biodiversity, community composition, and ranges of coral reef benthos.

RevDate: 2019-11-27
CmpDate: 2019-11-27

Bishopp A, MJ Bennett (2019)

Turning lateral roots into nodules.

Science (New York, N.Y.), 366(6468):953-954.

RevDate: 2019-11-27
CmpDate: 2019-11-27

Gazdag O, Kovács R, Parádi I, et al (2019)

Density and Diversity of Microbial Symbionts under Organic and Conventional Agricultural Management.

Microbes and environments, 34(3):234-243.

The influence of organic and conventional farming and agroecology on the diversity and functioning of indigenous soil microbial communities was examined using a multifactorial analysis based on an extended minimum data set of classical status and functional tests. Main soil physicochemical properties and selected microbiological indicators, the quantity of heterotrophic or aerobic spore-forming bacteria, basal and substrate-induced respiration, catabolic activity with MicroResp™, and fluorescein diacetate enzyme activity were characterized. A pot experiment applying the most probable number method was designed with soil dilution series using Pisum sativum L. and Triticum spelta L. to assess the symbiotic infectivity and genetic diversity of key indicator groups of the plant microbiome, e.g. nitrogen-fixing bacteria (rhizobia) and arbuscular mycorrhizal fungi. Soil pH, humus content, CFU, enzyme activity, and soil respiration were significantly higher in organic soils. The activity of soil microorganisms was mainly related to clay, humus, calcium, and magnesium parameters. A redundancy analysis test of catabolic activities showed that samples were grouped according to different substrate utilization patterns and land uses were also clearly separated from each other. Farming practice influenced the abundance and diversity of microbial populations. Dark septate endophytic fungi were only found in conventional soils. In addition to confirming soil health improvements by organic management, our results highlight the importance of a complex evaluation including both classical status and functional parameters of soil microbiota, which may more reliably indicate a shift in the quality status of soils.

RevDate: 2019-11-27
CmpDate: 2019-11-27

Chatzivasileiou P, TA Vyzantiadis (2019)

Vaginal yeast colonisation: From a potential harmless condition to clinical implications and management approaches-A literature review.

Mycoses, 62(8):638-650.

Vaginal yeast colonisation is a common clinical condition in premenopausal women. The potential pathogenicity and the circumstances under which it could evolve into infection are not fully clarified. Extensive review the literature regarding the definition of the vaginal yeast colonisation, its demographic features and causes as well as the risk factors favouring infection along with the necessity of treatment. Databases, namely PubMed-MEDLINE, Google Scholar, the University College London databases, e-journals, e-books and official Health Organisations websites were extensively searched in English, French, German and Greek language with no restriction in the type of publications during the last thirty years. In healthy women, vaginal yeast colonisation is an asymptomatic state with Candida albicans being the most prevalent species. Pregnant, HIV-positive and diabetic hosts are at higher risk. Other risk factors include oral contraceptives, hormonal replacement therapy and previous antibiotic use. Colonisation does not necessitate therapeutic intervention when asymptomatic. Prophylactic therapy during the third trimester of pregnancy is often recommended for reducing the risk of neonatal candidiasis. The distinction between commensalism and vaginitis is often complicated. Clinicians should be aware of the clinical context in order to decide the indicated therapeutic approach.

RevDate: 2019-11-27
CmpDate: 2019-11-27

Studivan MS, Milstein G, JD Voss (2019)

Montastraea cavernosa corallite structure demonstrates distinct morphotypes across shallow and mesophotic depth zones in the Gulf of Mexico.

PloS one, 14(3):e0203732 pii:PONE-D-18-24780.

This study assessed morphological variation of the depth-generalist coral Montastraea cavernosa across shallow and mesophotic coral ecosystems in the Gulf of Mexico (GOM) using thirteen corallite metrics. While corallite structure differed significantly across sites, we observed that mean corallite diameters were smaller and spacing was greater in mesophotic corals as compared to shallow corals. Additional corallite variation, including greater mean corallite height of mesophotic samples, are hypothesized to be photoadaptive responses to low light environments. Multivariate analyses also revealed two distinct morphotypes identified by significant variation in corallite spacing with >90% accuracy. A 'shallow' morphotype was characterized by larger, more closely-spaced corallites, while a 'depth-generalist' type exhibited smaller, further-spaced corallites. Variable presence of morphotypes within some sites suggests genotypic influence on corallite morphology as there was a slight, but significant, impact of morphotype on genetic structure within shallow zones in the Flower Garden Banks. Patterns of increased algal symbiont (Symbiodiniaceae) density and chlorophyll concentration were retained in the depth-generalist morphotype even in shallow zones, identifying multiple photoadaptive strategies between morphotypes. The results of this study suggest that morphological variation among M. cavernosa represents a combination of genotypic variation and phenotypic plasticity rather than responses to environmental stimuli alone.

RevDate: 2019-11-27
CmpDate: 2019-11-27

Peng F, Campos EO, Sullivan JG, et al (2019)

Morphospace exploration reveals divergent fitness optima between plants and pollinators.

PloS one, 14(3):e0213029 pii:PONE-D-18-31052.

The obligate mutualism and exquisite specificity of many plant-pollinator interactions lead to the expectation that flower phenotypes (e.g., corolla tube length) and corresponding pollinator traits (e.g., hawkmoth proboscis length) are congruent as a result of coevolution by natural selection. However, the effect of variation in flower morphology on the fitness of plants and their pollinators has not been quantified systematically. In this study, we employed the theoretical morphospace paradigm using a combination of 3D printing, electronic sensing, and machine vision technologies to determine the influence of two flower morphological features (corolla curvature and nectary diameter) on the fitness of both parties: the artificial flower and its hawkmoth pollinator. Contrary to the expectation that the same flower morphology maximizes the fitness of both plant and pollinator, we found that the two parties have divergent optima for corolla curvature, with non-overlapping fitness peaks in flower morphospace. The divergent fitness optima between plants and pollinators could lead to evolutionary diversification in both groups.

RevDate: 2019-11-26

Kipp MA, Stüeken EE, Gehringer MM, et al (2019)

Exploring cycad foliage as an archive of the isotopic composition of atmospheric nitrogen.

Geobiology [Epub ahead of print].

Molecular nitrogen (N2) constitutes the majority of Earth's modern atmosphere, contributing ~0.79 bar of partial pressure (pN2). However, fluctuations in pN2 may have occurred on 107 -109 year timescales in Earth's past, perhaps altering the isotopic composition of atmospheric nitrogen. Here, we explore an archive that may record the isotopic composition of atmospheric N2 in deep time: the foliage of cycads. Cycads are ancient gymnosperms that host symbiotic N2 -fixing cyanobacteria in modified root structures known as coralloid roots. All extant species of cycads are known to host symbionts, suggesting that this N2 -fixing capacity is perhaps ancestral, reaching back to the early history of cycads in the late Paleozoic. Therefore, if the process of microbial N2 fixation records the δ15 N value of atmospheric N2 in cycad foliage, the fossil record of cycads may provide an archive of atmospheric δ15 N values. To explore this potential proxy, we conducted a survey of wild cycads growing in a range of modern environments to determine whether cycad foliage reliably records the isotopic composition of atmospheric N2 . We find that neither biological nor environmental factors significantly influence the δ15 N values of cycad foliage, suggesting that they provide a reasonably robust record of the δ15 N of atmospheric N2 . Application of this proxy to the record of carbonaceous cycad fossils may not only help to constrain changes in atmospheric nitrogen isotope ratios since the late Paleozoic, but also could shed light on the antiquity of the N2 -fixing symbiosis between cycads and cyanobacteria.

RevDate: 2019-11-26

Gerasimova EA, Plotnikov AO, Khlopko YA, et al (2019)

Multiple Euryhaline Lineages of Centrohelids (Haptista: Centroplasthelida) in Inland Saline Waters Revealed with Metabarcoding.

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

The diversity of centrohelids in inland saline waters was studied with metabarcoding for the first time. The fragment of V6-V7 regions of 18S rDNA was sequenced with newly designed primers. Obtained OTUs were identified with molecular phylogenetic analysis and comparison of the signatures in 39es9 hairpin of V7. The obtained data included some OTUs, which could be attributed to four described species, but the majority belonged to previously established or novel environmental clades. Along with some presumably marine/brackish clades and freshwater/low salinity (0-2 ppt) clades, seven presumable species demonstrating broad (from 1-2 up to 78 ppt) salinity tolerance were detected. A number of OTUs belonged to Raphidocystis contractilis, which is known from three independent findings in brackish habitats only. Thus, it was assumed that this species is stenohaline and specifically adapted to salinity 5-15 ppt. The high level of salinity tolerance was suggested for centrohelids before based on morphology, which was used to justify their cosmopolitan distribution. Later these views were criticized based on environmental sequencing, but the results of the current survey indicate, that at least some species are present at salinities from almost freshwater (1-2 ppt) to twice oceanic (78 ppt) and are presumably capable of overcoming oceanic salinity barriers for their distribution.

RevDate: 2019-11-26

Sulima AS, Zhukov VA, Kulaeva OA, et al (2019)

New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX.

PeerJ, 7:e8070 pii:8070.

At the onset of legume-rhizobial symbiosis, the mutual recognition of partners occurs based on a complicated interaction between signal molecules and receptors. Bacterial signal molecules named Nod factors ("nodulation factors") are perceived by the plant LysM-containing receptor-like kinases (LysM-RLKs) that recognize details of its structure (i.e., unique substitutions), thus providing the conditions particular to symbiosis. In the garden pea (Pisum sativum L.), the allelic state of Sym2 gene has long been reported to regulate the symbiotic specificity: for infection to be successful, plants with the Sym2A allele (for "Sym2 Afghan", as these genotypes originate mostly from Afghanistan) require an additional acetylation of the Nod factor which is irrelevant for genotypes with the Sym2E allele (for "Sym2 European"). Despite being described about 90 years ago, Sym2 has not yet been cloned, though phenotypic analysis suggests it probably encodes a receptor for the Nod factor. Recently, we described a novel pea gene LykX (PsLykX) from the LysM-RLK gene family that demonstrates a perfect correlation between its allelic state and the symbiotic specificity of the Sym2A-type. Here we report on a series of Middle-Eastern pea genotypes exhibiting the phenotype of narrow symbiotic specificity discovered in the VIR plant genetic resources gene bank (Saint-Petersburg, Russia). These genotypes are new sources of Sym2A, as has been confirmed by an allelism test with Sym2A pea cv. Afghanistan. Within these genotypes, LykX is present either in the allelic state characteristic for cv. Afghanistan, or in another, minor allelic state found in two genotypes from Tajikistan and Turkmenistan. Plants carrying the second allele demonstrate the same block of rhizobial infection as cv. Afghanistan when inoculated with an incompatible strain. Intriguingly, this "Tajik" allele of LykX differs from the "European" one by a single nucleotide polymorphism leading to an R75P change in the receptor part of the putative protein. Thus, our new data are in agreement with the hypothesis concerning the identity of LykX and the elusive Sym2 gene.

RevDate: 2019-11-26

Ramírez-Bahena MH, Flores-Félix JD, Velázquez E, et al (2019)

The Mimosoid tree Leucaena leucocephala can be nodulated by the symbiovar genistearum of Bradyrhizobium canariense.

Systematic and applied microbiology pii:S0723-2020(19)30336-4 [Epub ahead of print].

Leucaena leucocephala is a Mimosoid legume tree indigenous to America that has spread to other continents, although it is not still present in some European countries such as Portugal. Nevertheless, we found that this legume can be nodulated in this country by slow-growing rhizobial strains which were identified as Bradyrhizobium canariense trough the analysis of the core genes recA and glnII. The analysis of the symbiotic gene nodC showed that these strains belong to the symbiovar genistearum, which commonly nodulates Genistoid legumes. Although two strains nodulating L. leucocephala in China and Brazil were classified within the genus Bradyrhizobium, they belong to undescribed species and to the symbiovars glycinearum and tropici, respectively. Therefore, we report here for the first time the ability of L. leucocephala to establish symbiosis with strains of B. canariense sv genistearum confirming the high promiscuity of L. leucocephala, that allows it to establish symbiosis with rhizobia native to different continents increasing its invasiveness potential.

RevDate: 2019-11-25

Radek R, Meuser K, Altinay S, et al (2019)

Novel Lineages of Oxymonad Flagellates from the Termite Porotermes adamsoni (Stolotermitidae): the Genera Oxynympha and Termitimonas.

Protist, 170(6):125683 pii:S1434-4610(19)30002-1 [Epub ahead of print].

The symbiotic gut flagellates of lower termites form host-specific consortia composed of Parabasalia and Oxymonadida. The analysis of their coevolution with termites is hampered by a lack of information, particularly on the flagellates colonizing the basal host lineages. To date, there are no reports on the presence of oxymonads in termites of the family Stolotermitidae. We discovered three novel, deep-branching lineages of oxymonads in a member of this family, the damp-wood termite Porotermes adamsoni. One tiny species (6-10μm), Termitimonas travisi, morphologically resembles members of the genus Monocercomonoides, but its SSU rRNA genes are highly dissimilar to recently published sequences of Polymastigidae from cockroaches and vertebrates. A second small species (9-13μm), Oxynympha loricata, has a slight phylogenetic affinity to members of the Saccinobaculidae, which are found exclusively in wood-feeding cockroaches of the genus Cryptocercus, the closest relatives of termites, but shows a combination of morphological features that is unprecedented in any oxymonad family. The third, very rare species is larger and possesses a contractile axostyle; it represents a phylogenetic sister group to the Oxymonadidae. These findings significantly advance our understanding of the diversity of oxymonads in termite guts and the evolutionary history of symbiotic digestion.

RevDate: 2019-11-25

Bednarz VN, Grover R, C Ferrier-Pagès (2019)

Elevated ammonium delays the impairment of the coral-dinoflagellate symbiosis during labile carbon pollution.

Aquatic toxicology (Amsterdam, Netherlands), 218:105360 pii:S0166-445X(19)30719-2 [Epub ahead of print].

Labile dissolved organic carbon (DOC) is a major pollutant in coastal marine environments affected by anthropogenic impacts, and may significantly contribute to coral bleaching and subsequent mortality on coastal reefs. DOC can cause bleaching indirectly through the rapid proliferation of copiotrophic and pathogenic bacteria. Here we demonstrate that labile DOC compounds can also impair the coral-dinoflagellate symbiosis by directly affecting coral physiology on both the host and algal symbiont level. In a controlled aquarium experiment, we monitored over several weeks key physiological parameters of the tropical coral Stylophora pistillata exposed to ambient and elevated labile DOC levels (0.1 and 1.0 mM) in combination with low and high nitrogen (i.e. ammonium) conditions (0.2 and 4.0 μM). At the symbiont level, DOC exposure under low ammonium availability decreased the photosynthetic efficiency accompanied by ∼75 % Chl a and ∼50 % symbiont cell reduction. The photosynthetic functioning of the symbionts recovered once the DOC enrichment ceased indicating a reversible shift between autotrophic and heterotrophic metabolism. At the host level, the assimilation of exogenous DOC sustained the tissue carbon reserves, but induced a depletion of the nitrogen reserves, indicated by ∼35 % decreased protein levels. This suggests an imbalanced exogenous carbon to nitrogen supply with nitrogen potentially limiting host metabolism on the long-term. We also demonstrate that increased ammonium availability delayed DOC-induced bleaching likely by keeping symbionts in a photosynthetically competent state, which is crucial for symbiosis maintenance and coral survival. Overall, the present study provides further insights into how coastal pollution can de-stabilize the coral-algal symbiosis and cause coral bleaching. Therefore, reducing coastal pollution and sustaining ecological integrity are critical to strengthen the resilience of coral reefs facing climate change.

RevDate: 2019-11-25

Rassati D, Marini L, A Malacrinò (2019)

Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion.

PeerJ, 7:e8103 pii:8103.

Microbial symbionts can play critical roles when their host attempts to colonize a new habitat. The lack of symbiont adaptation can in fact hinder the invasion process of their host. This scenario could change if the exotic species are able to acquire microorganisms from the invaded environment. Understanding the ecological factors that influence the take-up of new microorganisms is thus essential to clarify the mechanisms behind biological invasions. In this study, we tested whether different forest habitats influence the structure of the fungal communities associated with ambrosia beetles. We collected individuals of the most widespread exotic (Xylosandrus germanus) and native (Xyleborinus saxesenii) ambrosia beetle species in Europe in several old-growth and restored forests. We characterized the fungal communities associated with both species via metabarcoding. We showed that forest habitat shaped the community of fungi associated with both species, but the effect was stronger for the exotic X. germanus. Our results support the hypothesis that the direct contact with the mycobiome of the invaded environment might lead an exotic species to acquire native fungi. This process is likely favored by the occurrence of a bottleneck effect at the mycobiome level and/or the disruption of the mechanisms sustaining co-evolved insect-fungi symbiosis. Our study contributes to the understanding of the factors affecting insect-microbes interactions, helping to clarify the mechanisms behind biological invasions.

RevDate: 2019-11-25

Solomon GM, Dodangoda H, McCarthy-Walker T, et al (2019)

The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster.

PeerJ, 7:e8097 pii:8097.

Microorganisms play a central role in the biology of vinegar flies such as Drosophila suzukii and Drosophila melanogaster: serving as a food source to both adults and larvae, and influencing a range of traits including nutrition, behavior, and development. The niches utilized by the fly species partially overlap, as do the microbiota that sustain them, and interactions among these players may drive the development of crop diseases. To learn more about how the microbiota of one species may affect the other, we isolated and identified microbes from field-caught D. suzukii, and then characterized their effects on D. melanogaster larval development time in the laboratory. We found that the D. suzukii microbiota consistently included both yeasts and bacteria. It was dominated by yeasts of the genus Hanseniaspora, and bacteria from the families Acetobacteraceae and Enterobacteriaceae. Raising D. melanogaster under gnotobiotic conditions with each microbial isolate individually, we found that some bacteria promoted larval development relative to axenic conditions, but most did not have a significant effect. In contrast, nearly all the yeasts tested significantly accelerated larval development. The one exception was Starmerella bacillaris, which had the opposite effect: significantly slowing larval developmental rate. We investigated the basis for this effect by examining whether S. bacillaris cells could sustain larval growth, and measuring the survival of S. bacillaris and other yeasts in the larval gut. Our results suggest S. bacillaris is not digested by D. melanogaster and therefore cannot serve as a source of nutrition. These findings have interesting implications for possible interactions between the two Drosophilia species and their microbiota in nature. Overall, we found that microbes isolated from D. suzukii promote D. melanogaster larval development, which is consistent with the model that infestation of fruit by D. suzukii can open up habitat for D. melanogaster. We propose that the microbiome is an important dimension of the ecological interactions between Drosophila species.

RevDate: 2019-11-23

Potkay A, Ten Veldhuis MC, Fan Y, et al (2019)

Water and Vapor Transport in Algal-Fungal Lichen: Modeling constrained by Laboratory Experiments, an application for Flavoparmelia caperata.

Plant, cell & environment [Epub ahead of print].

Algal-fungal symbionts share water, nutrients and gases via an architecture unique to lichens. Because lichen activity is controlled by moisture dynamics, understanding water transport is prerequisite to understanding their fundamental biology. We propose a model of water distributions within foliose lichens governed by laws of fluid motion. Our model differentiates between water stored in symbionts, on extracellular surfaces, and in distinct morphological layers. We parameterize our model with hydraulic properties inverted from laboratory measurements of Flavoparmelia caperata and validate for wetting and drying. We ask: (1) Where is the bottleneck to water transport? (2) How do hydration and dehydration dynamics differ, and (3) what causes these differences? Resistance to vapor flow is concentrated at thallus surfaces and acts as the bottleneck for equilibrium, while internal resistances are small. The model captures hysteresis in hydration and desiccation, which are shown to be controlled by nonlinearities in hydraulic capacitance. Muting existing nonlinearities slowed drying and accelerated wetting, while exaggerating nonlinearities accelerated drying and slowed wetting. The hydraulic nonlinearity of Flavoparmelia caperata is considerable, which may reflect its preference for humid and stable environments. The model establishes the physical foundation for future investigations of transport of water, gas, and sugar between symbionts.

RevDate: 2019-11-23

Missbah El Idrissi M, Lamin H, ElFaik S, et al (2019)

Microvirga sp. symbiovar mediterranense nodulates Lupinus cosentinii grown wild in Morocco.

Journal of applied microbiology [Epub ahead of print].

AIM: To analyze the diversity of nodule-forming bacteria isolated from Lupinus cosentinii naturally-grown in the Maamora cork oak forest (Rabat, Morocco).

METHODS AND RESULTS: Out of a total of thirty one bacterial strains, four were selected based on their REP-PCR fingerprinting that were studied by sequencing and phylogenetic analysis of their 16S rRNA, gyrB, dnaK, recA and rpoB housekeeping genes as well as the nodC symbiotic gene. The nearly complete 16S rRNA gene sequence of the four representative strains showed that they are related to Tunisian strains of genus Microvirga isolated from L. micranthus with nucleotide identity values ranging from 98.67% to 97.13%. The single and concatenated sequences of the16S rRNA, gyrB, dnaK, recA and rpoB housekeeping genes indicated that the L. cosentinii-isolated strains had 99.2 to 99.9% similarities with the Tunisian L. micranthus microsymbionts. The nodC gene phylogeny revealed that the Moroccan strains clustered in the newly described mediterranense symbiovar, and nodulation tests showed that they nodulated not only L. cosentinii but also L. angustifolius, L. luteus and L. albus.

CONCLUSIONS: To our knowledge, this is the first report concerning the isolation, molecular identification and phylogenetic diversity of L. cosentinii nodule-forming endosymbionts and of their description as members of the Microvirga genus.

In this work, we show that Microvirga sp. can be isolated from root nodules of wild-grown L. cosentinii in Northeast Africa, that selected strains also nodulate L. angustifolius, L. luteus and L. albus, and that they belong to symbiovar mediterranense. In addition, our data support that the ability of Microvirga to nodulate lupines could be related to the soil pH, its geographical distribution being more widespread than expected.

RevDate: 2019-11-23

Herrera H, Soto J, de Bashan LE, et al (2019)

Root-Associated Fungal Communities in Two Populations of the Fully Mycoheterotrophic Plant Arachnitis uniflora Phil. (Corsiaceae) in Southern Chile.

Microorganisms, 7(12): pii:microorganisms7120586.

The microbiological interactions of the roots of non-photosynthetic plants in South America have been scarcely explored. This study analyzes culturable fungal diversity associated with the mycoheterotrophic plant Arachnitis uniflora Phil. (Corsiaceae) in southern Chile, growing in two different understoreys of native (Nothofagus-dominated) and mixed forest (native, Cupressussempervirens, and Pinusradiata). Rhizospheric and endophytic fungi were isolated, cultured, and purified to identify microorganisms associated with A. uniflora roots. We showed the different fungi associated with the plant, and that these distributions are influenced by the sampling site. We isolated 410 fungal strains (144 endophytic and 266 from the rhizosphere). We identified 13 operative taxonomical units from plants sampled in the mixed forest, while 15 were from the native forest. Rhizospheric microorganisms were mainly related to Penicillium spp., whereas some pathogenic and saprophytic strains were more frequent inside the roots. Our results have also shown that the fungal strains are weak for phosphate solubilization, but other pathways such as organic acid exudation and indole acetic acid production can be considered as major mechanisms to stimulate plant growth. Our results point to new fungal associates of A. uniflora plants reported in Andean ecosystems, identifying new beneficial endophytic fungi associated with roots of this fully mycoheterotrophic plant.

RevDate: 2019-11-26

Patel BN, Rosenberg L, Willcox G, et al (2019)

Human-machine partnership with artificial intelligence for chest radiograph diagnosis.

NPJ digital medicine, 2:111.

Human-in-the-loop (HITL) AI may enable an ideal symbiosis of human experts and AI models, harnessing the advantages of both while at the same time overcoming their respective limitations. The purpose of this study was to investigate a novel collective intelligence technology designed to amplify the diagnostic accuracy of networked human groups by forming real-time systems modeled on biological swarms. Using small groups of radiologists, the swarm-based technology was applied to the diagnosis of pneumonia on chest radiographs and compared against human experts alone, as well as two state-of-the-art deep learning AI models. Our work demonstrates that both the swarm-based technology and deep-learning technology achieved superior diagnostic accuracy than the human experts alone. Our work further demonstrates that when used in combination, the swarm-based technology and deep-learning technology outperformed either method alone. The superior diagnostic accuracy of the combined HITL AI solution compared to radiologists and AI alone has broad implications for the surging clinical AI deployment and implementation strategies in future practice.

RevDate: 2019-11-26

Soyano T, Shimoda Y, Kawaguchi M, et al (2019)

A shared gene drives lateral root development and root nodule symbiosis pathways in Lotus.

Science (New York, N.Y.), 366(6468):1021-1023.

Legumes develop root nodules in symbiosis with nitrogen-fixing rhizobial bacteria. Rhizobia evoke cell division of differentiated cortical cells into root nodule primordia for accommodating bacterial symbionts. In this study, we show that NODULE INCEPTION (NIN), a transcription factor in Lotus japonicus that is essential for initiating cortical cell divisions during nodulation, regulates the gene ASYMMETRIC LEAVES 2-LIKE18/LATERAL ORGAN BOUNDARIES DOMAIN16a (ASL18/LBD16a). Orthologs of ASL18/LBD16a in nonlegume plants are required for lateral root development. Coexpression of ASL18a and the CCAAT box-binding protein Nuclear Factor-Y (NF-Y) subunits, which are also directly targeted by NIN, partially suppressed the nodulation-defective phenotype of L. japonicusdaphne mutants, in which cortical expression of NIN was attenuated. Our results demonstrate that ASL18a and NF-Y together regulate nodule organogenesis. Thus, a lateral root developmental pathway is incorporated downstream of NIN to drive nodule symbiosis.

RevDate: 2019-11-22

Monteil CL, CT Lefevre (2019)

Magnetoreception in Microorganisms.

Trends in microbiology pii:S0966-842X(19)30267-7 [Epub ahead of print].

Magnetoreception is the sense whereby organisms geolocate and navigate in response to the Earth's magnetic field lines. For decades, magnetotactic bacteria have been the only known magnetoreceptive microorganisms. The magnetotactic behaviour of these aquatic prokaryotes is due to the biomineralization of magnetic crystals. While an old report alleged the existence of microbial algae with similar behaviour, recent discoveries have demonstrated the existence of unicellular eukaryotes able to sense the geomagnetic field, and have revealed different mechanisms and strategies involved in such a sensing. Some ciliates can be magnetically guided after predation of magnetotactic bacteria, while some flagellates acquired this sense through symbiosis with magnetic bacteria. A report has even suggested that some magnetotactic protists could biomineralize magnetic crystals.

RevDate: 2019-11-21

Xiang Q, Wang J, Qin P, et al (2019)

Effect of common bean seed exudates on growth, lipopolysaccharide and lipopolysaccharide transport gene expression of Rhizobium anhuiense.

Canadian journal of microbiology [Epub ahead of print].

Lipopolysaccharide (LPS) is essential for successful nodulation during the symbiosis of rhizobia and legumes. However, the detailed mechanism of the LPS in this process has not yet been clearly elucidated. In this study, the effects of exudates the common bean seeds on the growth, lipopolysaccharide production and lipopolysaccharide transport genes expression (lpt) of Rhizobium anhuiense were investigated. R. anhuiense exposed to exudates showed changes in LPS electrophoretic profiles and content, where the LPS band was wider and the LPS content was higher in R. anhuiense treated with seeds exudates. Exudates enhanced cell growth of R. anhuiense in a concentration dependent manner; R. anhuiense exposed to higher doses of the exudate showed faster growth. Seven ltp genes of R. anhuiense were amplified and sequenced. Sequences of six lpt genes, except for lptE, were the same as found in previously analyzed R. anhuiense strains, while lptE shared low sequence similarity with other strains. Exposure to the exudates strongly stimulated the expression of all lpt genes. An approximately 6.7- (lptG) to 301-fold (lptE) increase in the transcriptional levels were observed after only 15 min of exposure to exudates. These results indicate that seed exudates affect the LPS by making the cell wall structure more conducive to symbiotic nodulation.

RevDate: 2019-11-21

López-Madrigal S, EH Duarte (2019)

Titer regulation in arthropod-Wolbachia symbioses.

FEMS microbiology letters pii:5637388 [Epub ahead of print].

Symbiosis between intracellular bacteria (endosymbionts) and animals are widespread. The alphaproteobacterium Wolbachia pipientis is known to maintain a variety of symbiotic associations, ranging from mutualism to parasitism, with a wide range of invertebrates. Wolbachia infection might deeply affect host fitness (e.g. reproductive manipulation, antiviral protection), which is thought to explain its high prevalence in nature. Bacterial loads significantly influence both the infection dynamics and the extent of bacteria-induced host phenotypes. Hence, fine regulation of bacterial titers is considered as a milestone in host-endosymbiont interplay. Here we review both environmental and biological factors modulating Wolbachia titers in arthropods.

RevDate: 2019-11-26

Friel CA, ML Friesen (2019)

Legumes Modulate Allocation to Rhizobial Nitrogen Fixation in Response to Factorial Light and Nitrogen Manipulation.

Frontiers in plant science, 10:1316.

The costs and benefits that define gain from trade in resource mutualisms depend on resource availability. Optimal partitioning theory predicts that allocation to direct uptake versus trade will be determined by both the relative benefit of the resource acquired through trade and the relative cost of the resource being traded away. While the costs and benefits of carbon:nitrogen exchange in the legume-rhizobia symbiosis have been examined in depth with regards to mineral nitrogen availability, the effects of varying carbon costs are rarely considered. Using a growth chamber experiment, we measured plant growth and symbiosis investment in the model legume Medicago truncatula and its symbiont Ensifer medicae across varying nitrogen and light environments. We demonstrate that plants modulate their allocation to roots and nodules as their return on investment varies according to external nitrogen and carbon availabilities. We find empirical evidence that plant allocation to nodules responds to carbon availability, but that this depends upon the nitrogen environment. In particular, at low nitrogen-where rhizobia provided the majority of nitrogen for plant growth-relative nodule allocation increased when carbon limitation was alleviated with high light levels. Legumes' context-dependent modulation of resource allocation to rhizobia thus prevents this interaction from becoming parasitic even in low-light, high-nitrogen environments where carbon is costly and nitrogen is readily available.

RevDate: 2019-11-26

Chien HL, Huang WZ, Tsai MY, et al (2019)

Overexpression of the Chromosome Partitioning Gene parA in Azorhizobium caulinodans ORS571 Alters the Bacteroid Morphotype in Sesbania rostrata Stem Nodules.

Frontiers in microbiology, 10:2422.

Azorhizobium caulinodans ORS571 is a diazotroph that forms N2-fixing nodules on the roots and stems of the tropical legume Sesbania rostrata. Deletion of the parA gene of this bacterium results in cell cycle defects, pleiomorphic cell shape, and formation of immature stem nodules on its host plant. In this study, we constructed a parA overexpression mutant (PnptII-parA) to complement a previous study and provide new insights into bacteroid formation. We found that overproduction of ParA did not affect growth, cell morphology, chromosome partitioning, or vegetative nitrogen fixation in the free-living state. Under symbiosis, however, distinctive features, such as a single swollen bacteroid in one symbiosome, relatively narrow symbiosome space, and polyploid cells were observed. The morphotype of the PnptII-parA bacteroid is reminiscent of terminal differentiation in some IRLC indeterminate nodules, but S. rostrata is not thought to produce the NCR peptides that induce terminal differentiation in rhizobia. In addition, the transcript patterns of many symbiosis-related genes elicited by PnptII-parA were different from those elicited by the wild type. Accordingly, we propose that the particular symbiosome formation in PnptII-parA stem-nodules is due to cell cycle disruption caused by excess ParA protein in the symbiotic cells during nodulation.

RevDate: 2019-11-26

Slaughter LC, Nelson JA, Carlisle AE, et al (2019)

Tall Fescue and E. coenophiala Genetics Influence Root-Associated Soil Fungi in a Temperate Grassland.

Frontiers in microbiology, 10:2380.

A constitutive, host-specific symbiosis exists between the aboveground fungal endophyte Epichloë coenophiala (Morgan-Jones & W. Gams) and the cool-season grass tall fescue (Lolium arundinaceum (Schreb.) Darbysh.), which is a common forage grass in the United States, Australia, New Zealand, and temperate European grasslands. New cultivars of tall fescue are continually developed to improve pasture productivity and animal health by manipulating both grass and E. coenophiala genetics, yet how these selected grass-endophyte combinations impact other microbial symbionts such as mycorrhizal and dark septate fungi remains unclear. Without better characterizing how genetically distinct grass-endophyte combinations interact with belowground microorganisms, we cannot determine how adoption of new E. coenophiala-symbiotic cultivars in pasture systems will influence long-term soil characteristics and ecosystem function. Here, we examined how E. coenophiala presence and host × endophyte genetic combinations control root colonization by belowground symbiotic fungi and associated plant nutrient concentrations and soil properties in a 2-year manipulative field experiment. We used four vegetative clone pairs of tall fescue that consisted of one endophyte-free (E-) and one E. coenophiala-symbiotic (E+) clone each, where E+ clones within each pair contained one of four endophyte genotypes: CTE14, CTE45, NTE16, or NTE19. After 2 years of growth in field plots, we measured root colonization of arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE), extraradical AMF hyphae in soil, total C, N, and P in root and shoot samples, as well as C and N in associated soils. Although we observed no effects of E. coenophiala presence or symbiotic genotype on total AMF or DSE colonization rates in roots, different grass-endophyte combinations altered AMF arbuscule presence and extraradical hyphal length in soil. The CTE45 genotype hosted the fewest AMF arbuscules regardless of endophyte presence, and E+ clones within NTE19 supported significantly greater soil extraradical hyphae compared to E- clones. Because AMF are often associated with improved soil physical characteristics and C sequestration, our results suggest that development and use of unique grass-endophyte combinations may cause divergent effects on long-term ecosystem properties.

RevDate: 2019-11-26

Aphale D, Natu A, Laldas S, et al (2019)

Administration of Streptococcus bovis isolated from sheep rumen digesta on rumen function and physiology as evaluated in a rumen simulation technique system.

Veterinary world, 12(9):1362-1371.

Background and Aim: Little information about the stability and changes of sheep ruminal microbiota due to pathogen intervention in the rumen simulation technique (RUSITEC) is available. This study aimed to investigate the effect of administration of a novel isolated Streptococcus bovis strain on rumen microbiology and physiology. In addition, the isolation of pigment-producing Streptococcus lutetiensis is described.

Materials and Methods: Microbial strains were isolated from sheep rumen digesta. An isolated strain of S. bovis was evaluated in the RUSITEC system fed with mixed cattle feed and compared with an in-house developed probiotic formulation (PF), PF 1, containing Bacillus amyloliquifaciens, Bacillus subtilis, and Propionibacterium freudenreichii. The parameters of volatile fatty acid, lactic acid, pH profiling, and the coliform anti-pathogenicity were evaluated to determine the effect of S. bovis on rumen function and physiology.

Results: Administration of S. bovis reduced the coliform count by 31.20% from 7.2×1010 colony-forming units (CFU)/mLto 1.7×106 CFU/mL. Agar diffusion assays revealed the extracellular antimicrobial activity of S. bovis against coliforms; Escherichia coli and Salmonella enterica with 12 and 14 mm zones of inhibition, respectively. Simultaneously, an increase of 61.62% in the rumen yeast count was noted. The physiological changes resulted in a 5% reduction in acetic acid concentration from 431 to 405 mg/L.

Conclusion: The present research indicates that S. bovis is highly capable of altering rumen physiology and function on colonization and is a key transition microbe to be studied during rumen intervention studies. A decrease in the coliform count could be attributed to extracellular production of a bacteriocin-like substance, as illustrated through agar diffusion assays.

RevDate: 2019-11-21

Traubenik S, Reynoso MA, Hobecker KV, et al (2019)

Reprogramming of root cells during nitrogen-fixing symbiosis involves dynamic polysome association of coding and non-coding RNAs.

The Plant cell pii:tpc.19.00647 [Epub ahead of print].

Translational control is a widespread mechanism that allows the cell to rapidly modulate gene expression in order to provide flexibility and adaptability to eukaryotic organisms. We applied TRAP (Translating Ribosome Affinity Purification) combined with RNA sequencing to characterize translational regulation of mRNAs at early stages of the nitrogen-fixing symbiosis established between Medicago truncatula and Sinorhizobium meliloti. Our analysis revealed a poor correlation between transcriptional and translational changes and identified hundreds of regulated protein-coding and long non-coding RNAs (lncRNAs), some of which are regulated in specific cell-types. We demonstrated that a short variant of the lncRNA TAS3 increased its association to the translational machinery in response to rhizobia. Functional analysis revealed that this short variant of TAS3 might act as a target mimic that capture miR390, contributing to reduce tasiARFs production and modulating nodule formation and rhizobial infection. The analysis of alternative transcript variants identified a translationally up-regulated mRNA encoding the subunit 3 of the SUPERKILLER complex (SKI3), which participates in mRNA decay. Knock-down of SKI3 decreased nodule initiation and development, as well as the survival of bacteria within nodules. Our results highlight the importance of translational control and mRNA decay pathways for the successful establishment of the nitrogen-fixing symbiosis.

RevDate: 2019-11-20

García JM, Pozo MJ, JA López-Ráez (2020)

Histochemical and Molecular Quantification of Arbuscular Mycorrhiza Symbiosis.

Methods in molecular biology (Clifton, N.J.), 2083:293-299.

Arbuscular mycorrhizae (AM) are one of the most widespread and studied plant associations with beneficial microorganisms. Indeed, more than 80% of land plants, including most agricultural and horticultural crop species, are able to establish this mutualistic symbiosis with AM fungi. Through this association the fungus helps the plant in the acquisition of water and mineral nutrients, especially under stress conditions. AM symbiosis affects other ecologically and economically important traits such as plant architecture, flowering, and fruit quality but also tolerance against biotic and abiotic stresses. As a consequence, AM fungi have a great potential as biofertilizers and bioprotection agents in sustainable agriculture. However, in order to take advantage of all these benefits, a good and functional symbiosis is required. Here we present methods for reliable quantification of colonization levels which should be useful not only for research but also from the agronomic point of view.

RevDate: 2019-11-20

Wang R, Clarke BB, FC Belanger (2019)

Transcriptome Analysis of Choke Stroma and Asymptomatic Inflorescence Tissues Reveals Changes in Gene Expression in Both Epichloëfestucae and Its Host Plant Festuca rubra subsp. rubra.

Microorganisms, 7(11): pii:microorganisms7110567.

Many cool-season grasses have symbiotic relationships with Epichloë (Ascomycota, Clavicipitaceae) fungal endophytes that inhabit the intercellular spaces of the above-ground parts of the host plants. The presence of the Epichloë endophytes is generally beneficial to the hosts due to enhanced tolerance to biotic and abiotic stresses conferred by the endophytes. Many Epichloë spp. are asexual, and those infections always remain asymptomatic. However, some Epichloë spp. have a sexual stage and produce a macroscopic fruiting body, a stroma, that envelops the developing inflorescence causing a syndrome termed "choke disease". Here, we report a fungal and plant gene expression analysis of choke stroma tissue and asymptomatic inflorescence tissue of Epichloëfestucae-infected strong creeping red fescue (Festuca rubra subsp. rubra). Hundreds of fungal genes and over 10% of the plant genes were differentially expressed when comparing the two tissue types. The differentially expressed fungal genes in the choke stroma tissue indicated a change in carbohydrate and lipid metabolism, as well as a change in expression of numerous genes for candidate effector proteins. Plant stress-related genes were up-regulated in the stroma tissue, suggesting the plant host was responding to the epiphytic stage of E. festucae as a pathogen.

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: 2019-11-21

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: 2019-11-17

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: 2019-11-22
CmpDate: 2019-11-22

Miller DP, RJ Lamont (2019)

Signaling Systems in Oral Bacteria.

Advances in experimental medicine and biology, 1197:27-43.

The supra- and subgingival plaque biofilm communities of plaque are composed of hundreds of different microbes. These communities are spatially and temporally structured, largely due to cell-cell communications that coordinate synergistic interactions, and intracellular signaling systems to sense changes in the surrounding environment. Homeostasis is maintained through metabolic communication, mutualistic cross-feeding, and cross-respiration. These nutritional symbioses can reciprocally influence the local microenvironments by altering the pH and by detoxifying oxidative compounds. Signal transduction mechanisms include two-component systems, tyrosine phosphorelays, quorum sensing systems, and cyclic nucleotide secondary messengers. Signaling converges on transcriptional programs and can result in synergistic or antagonistic interbacterial interactions that sculpt community development. The sum of all these interactions can be a well-organized polymicrobial community that remains in homeostasis with the host, or a dysbiotic community that provokes pathogenic responses in the host.

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: 2019-11-17

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.

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: 2019-11-18
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: 2019-11-26

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

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

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

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

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

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: 2019-11-18
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: 2019-11-20

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.

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: 2019-11-17

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.

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: 2019-11-10

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.


RJR Experience and Expertise


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


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


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


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


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


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


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


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

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

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

Research Gate page for R J Robbins

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

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

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