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Bibliography on: Symbiosis

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


ESP: PubMed Auto Bibliography 09 Apr 2020 at 01:50 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: 2020-04-08

Chakravarti LJ, Buerger P, Levin RA, et al (2020)

Gene regulation underpinning increased thermal tolerance in a laboratory-evolved coral photosymbiont.

Molecular ecology [Epub ahead of print].

Small increases in ocean temperature can disrupt the obligate symbiosis between corals and dinoflagellate microalgae, resulting in coral bleaching. Little is known about the genes that drive the physiological and bleaching response of algal symbionts to elevated temperature. Moreover, many studies to-date have compared highly divergent strains, making it challenging to accredit specific genes to contrasting traits. Here we compare transcriptional responses at ambient (27°C) and bleaching-relevant (31°C) temperatures in a monoclonal, wild-type (WT) strain of Symbiodiniaceae to those of a selected-strain (SS), derived from the same monoclonal culture and experimentally evolved to elevated temperature over 80 generations (2.5 years). Thousands of genes were differentially expressed at a log fold-change of >8 between the WT and SS over a 35-day temperature treatment period. At 31 °C, WT cells exhibited a temporally unstable transcriptomic response upregulating genes involved in the universal stress response such as molecular chaperoning, protein repair, protein degradation and DNA repair. Comparatively, SS cells exhibited a temporally stable transcriptomic response and downregulated many stress response genes that were upregulated by the WT. Among the most highly upregulated genes in the SS at 31°C were algal transcription factors and a gene likely of bacterial origin that encodes a type II secretion system protein, suggesting interactions with bacteria may contribute to the increased thermal tolerance of the SS. Genes and functional pathways conferring thermal tolerance in the SS could be targeted in future genetic engineering experiments designed to develop thermally resilient algal symbionts for use in coral restoration and conservation.

RevDate: 2020-04-08

Boem F, Nannini G, A Amedei (2020)

Not just 'immunity': how the microbiota can reshape our approach to cancer immunotherapy.

Immunotherapy [Epub ahead of print].

Cancer immunotherapy refers to a set of approaches aiming at enhancing the immune system to fight cancer growth and spread. This variety of therapeutic approaches, especially those inhibiting immune checkpoints, have shown very promising results. Nevertheless, patients may respond differently to treatments and the efficacy of immunotherapy seems to be dependent on several factors that go beyond the molecular targeting of immune cells modulation. Here, we review how the activity of gut microbiota appears to be crucial in determining the effectiveness of some immunotherapeutic treatments, fostering or impeding the conditions under which treatments can work or not. Moreover, we discuss how these findings suggest not only extending the range of immunotherapeutic approaches but also reshaping our understanding of immunotherapy itself.

RevDate: 2020-04-08

Xiang QW, Bai J, Cai J, et al (2020)

NopD of Bradyrhizobium sp. XS1150 Possesses SUMO Protease Activity.

Frontiers in microbiology, 11:386.

Effectors secreted by the type III protein secretion system (T3SS) of rhizobia are host-specific determinants of the nodule symbiosis. Here, we have characterized NopD, a putative type III effector of Bradyrhizobium sp. XS1150. NopD was found to possess a functional N-terminal secretion signal sequence that could replace that of the NopL effector secreted by Sinorhizobium sp. NGR234. Recombinant NopD and the C-terminal domain of NopD alone can process small ubiquitin-related modifier (SUMO) proteins and cleave SUMO-conjugated proteins. Activity was abolished in a NopD variant with a cysteine-to-alanine substitution in the catalytic core (NopD-C972A). NopD recognizes specific plant SUMO proteins (AtSUMO1 and AtSUMO2 of Arabidopsis thaliana; GmSUMO of Glycine max; PvSUMO of Phaseolus vulgaris). Subcellular localization analysis with A. thaliana protoplasts showed that NopD accumulates in nuclear bodies. NopD, but not NopD-C972A, induces cell death when expressed in Nicotiana tabacum. Likewise, inoculation tests with constructed mutant strains of XS1150 indicated that nodulation of Tephrosia vogelii is negatively affected by the protease activity of NopD. In conclusion, our findings show that NopD is a symbiosis-related protein that can process specific SUMO proteins and desumoylate SUMO-conjugated proteins.

RevDate: 2020-04-08
CmpDate: 2020-04-06

Erban T, Klimov P, Molva V, et al (2020)

Whole genomic sequencing and sex-dependent abundance estimation of Cardinium sp., a common and hyperabundant bacterial endosymbiont of the American house dust mite, Dermatophagoides farinae.

Experimental & applied acarology, 80(3):363-380.

The two common species of house dust mites (HDMs), Dermatophagoides farinae and D. pteronyssinus, are major sources of allergens in human dwellings worldwide. Many allergens from HDMs have been described, but their extracts vary in immunogens. Mite strains may differ in their microbiomes, which affect mite allergen expression and contents of bacterial endotoxins. Some bacteria, such as the intracellular symbiont Cardinium, can affect both the sex ratio and biochemical pathways of mites, resulting in abundance variations of mite allergens/immunogens. Here, we investigated the bacterial microbiomes of D. farinae and D. pteronyssinus males and females using barcode 16S rDNA sequencing, qPCR, and genomic data analysis. We found a single species of Cardinium associated with D. farinae strains from the USA, China and Europe. Cardinium had high abundance relative to other bacterial taxa and represented 99% of all bacterial DNA reads from female mites from the USA. Cardinium was also abundant with respect to the number of host cells-we estimated 10.4-11.8 cells of Cardinium per single female mite cell. In a European D. farinae strain, Cardinium was more prevalent in females than in males (representing 92 and 67% of all bacterial taxa in females and males, respectively). In contrast, D. pteronyssinus lacked any Cardinium species, and the microbiomes of male and female mites were similar. We produced a Cardinium genome assembly (1.48 Mb; GenBank: PRJNA555788, GCA_007559345.1) associated with D. farinae. The ascertained ubiquity and abundance of Cardinium strongly suggest that this intracellular bacterium plays an important biological role in D. farinae.

RevDate: 2020-04-08
CmpDate: 2020-04-08

Leonard SP, Powell JE, Perutka J, et al (2020)

Engineered symbionts activate honey bee immunity and limit pathogens.

Science (New York, N.Y.), 367(6477):573-576.

Honey bees are essential pollinators threatened by colony losses linked to the spread of parasites and pathogens. Here, we report a new approach for manipulating bee gene expression and protecting bee health. We engineered a symbiotic bee gut bacterium, Snodgrassella alvi, to induce eukaryotic RNA interference (RNAi) immune responses. We show that engineered S. alvi can stably recolonize bees and produce double-stranded RNA to activate RNAi and repress host gene expression, thereby altering bee physiology, behavior, and growth. We used this approach to improve bee survival after a viral challenge, and we show that engineered S. alvi can kill parasitic Varroa mites by triggering the mite RNAi response. This symbiont-mediated RNAi approach is a tool for studying bee functional genomics and potentially for safeguarding bee health.

RevDate: 2020-04-08
CmpDate: 2020-04-06

Breusing C, Franke M, CR Young (2020)

Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region.

PloS one, 15(1):e0227053.

Vestimentiferan tubeworms are key taxa in deep-sea chemosynthetic habitats worldwide. As adults they obtain their nutrition through their sulfide-oxidizing bacterial endosymbionts, which are acquired from the environment. Although horizontal transmission should favor infections by various symbiotic microbes, the current paradigm holds that every tubeworm harbors only one endosymbiotic 16S rRNA phylotype. Although previous studies based on traditional Sanger sequencing have questioned these findings, population level high-throughput analyses of the symbiont 16S diversity are still missing. To get further insights into the symbiont genetic variation and uncover hitherto hidden diversity we applied state-of-the-art 16S-V4 amplicon sequencing to populations of the co-occurring tubeworm species Lamellibrachia barhami and Escarpia spicata that were collected during E/V Nautilus and R/V Western Flyer cruises to cold seeps in the eastern Pacific Ocean. In agreement with earlier work our sequence data indicated that L. barhami and E. spicata share one monomorphic symbiont phylotype. However, complementary CARD-FISH analyses targeting the 16S-V6 region implied the existence of an additional phylotype in L. barhami. Our results suggest that the V4 region might not be sufficiently variable to investigate diversity in the intra-host symbiont population at least in the analyzed sample set. This is an important finding given that this region has become the standard molecular marker for high-throughput microbiome analyses. Further metagenomic research will be necessary to solve these issues and to uncover symbiont diversity that is hidden below the 16S rRNA level.

RevDate: 2020-04-08
CmpDate: 2020-04-06

Albuquerque-Martins R, Carvalho P, Miranda D, et al (2019)

Edible ectomycorrhizal fungi and Cistaceae. A study on compatibility and fungal ecological strategies.

PloS one, 14(12):e0226849.

Wild edible mycorrhizal mushrooms are among the most appreciated and prized mushrooms in the world. Despite the cultivation of ectomycorrhizal (ECM) mushrooms has been a growing subject of study worldwide, it has been hampered by the mutualistic lifestyle of the fungi. Although not being obligate symbionts, most of the species of ECM mushrooms only produce fruit bodies in association with trees or shrubs. In the present study, we aimed at understanding certain aspects of the ecology of four different edible ECM fungi: Lactarius deliciosus, Tricholoma equestre, T. portentosum and Boletus fragrans. Despite having a broad distribution worldwide, these fungi inhabit also Mediterranean habitats with understories typically dominated by rockroses (Cistaceae). Studying the ecology of these mutualistic fungi as well as the interaction with these species of shrubs is not only scientifically relevant but also pivotal for the discovery of profitable cultivation protocols. We evaluated the compatibility of these ECM species with five species within Cistaceae family - Cistus ladanifer, C. psilosepalus, C. salviifolius, Halimium halimifolium and Tuberaria lignosa. Each species of fungi proved to be able to establish mycorrhizas with at least 2 different plants species but varied in their host range of the tested Cistaceae. The dissimilarity in terms of host specificity between some fungal species seemed to be connected with the phylogenetic distances of the fungi. A correlation between the colonization percentage of the root systems and the mycelial growth rates in pure culture was found. The connection of these traits might be an important key to understanding the ecological competitor-colonizer tradeoffs of these ECM fungal species. Altogether, our study reports unknown plant-fungi combinations with economical relevance and also adds new insights about the ecology of these species of ECM fungi.

RevDate: 2020-04-08
CmpDate: 2020-04-06

Pernice M, Raina JB, Rädecker N, et al (2020)

Down to the bone: the role of overlooked endolithic microbiomes in reef coral health.

The ISME journal, 14(2):325-334.

Reef-building corals harbour an astonishing diversity of microorganisms, including endosymbiotic microalgae, bacteria, archaea, and fungi. The metabolic interactions within this symbiotic consortium are fundamental to the ecological success of corals and the unique productivity of coral reef ecosystems. Over the last two decades, scientific efforts have been primarily channelled into dissecting the symbioses occurring in coral tissues. Although easily accessible, this compartment is only 2-3 mm thick, whereas the underlying calcium carbonate skeleton occupies the vast internal volume of corals. Far from being devoid of life, the skeleton harbours a wide array of algae, endolithic fungi, heterotrophic bacteria, and other boring eukaryotes, often forming distinct bands visible to the bare eye. Some of the critical functions of these endolithic microorganisms in coral health, such as nutrient cycling and metabolite transfer, which could enable the survival of corals during thermal stress, have long been demonstrated. In addition, some of these microorganisms can dissolve calcium carbonate, weakening the coral skeleton and therefore may play a major role in reef erosion. Yet, experimental data are wanting due to methodological limitations. Recent technological and conceptual advances now allow us to tease apart the complex physical, ecological, and chemical interactions at the heart of coral endolithic microbial communities. These new capabilities have resulted in an excellent body of research and provide an exciting outlook to further address the functional microbial ecology of the "overlooked" coral skeleton.

RevDate: 2020-04-08
CmpDate: 2020-04-06

Zavarzina DG, Gavrilov SN, Chistyakova NI, et al (2020)

Syntrophic growth of alkaliphilic anaerobes controlled by ferric and ferrous minerals transformation coupled to acetogenesis.

The ISME journal, 14(2):425-436.

Redox-active iron minerals can act as energy sources or electron-transferring mediators in microbial syntrophic associations, being important means of interspecies metabolic cooperation in sedimentary environments. Alkaline conditions alter the thermodynamic stability of iron minerals, influencing their availability for interspecies syntrophic interactions. We have modeled anaerobic alkaliphilic microbial associations in ethanol-oxidizing co-culture of an obligate syntroph Candidatus "Contubernalis alkalaceticum" and a facultative lithotroph Geoalkalibacter ferrihydriticus, which is capable of dissimilatory Fe(III) reduction and homoacetogenic oxidation of Fe(II) with CO2. The co-cultures were cultivated with thermodynamically metastable ferric-containing ferrihydrite, or ferrous-containing siderite, or without minerals. Mössbauer spectral analysis revealed the transformation of both minerals to the stable magnetite. In the presence of ferrihydrite, G. ferrihydriticus firstly reduced Fe(III) with ethanol and then switched to syntrophic homoacetogenesis, providing the growth of obligate syntroph on ethanol. The ability of G. ferrihydriticus to accept hydrogen from its syntrophic partner and produce extra acetate from carbonate during ethanol oxidation was confirmed by co-culture growth without minerals. In the presence of siderite, G. ferrihydriticus performed homoacetogenesis using two electron donors simultaneously- siderite and hydrogen. Pieces of evidence for direct and indirect hydrogen-mediated electron exchange between partner organisms were obtained. Relative abundancies of partner organisms and the rate of acetate production by their co-cultures were strongly determined by thermodynamic benefits, which G. ferrihydriticus got from redox transformations of iron minerals. Even the minor growth of G. ferrihydriticus sustained the growth of the syntroph. Accordingly, microbe-to-mineral interactions could represent underestimated drivers of syntrophic interactions in alkaline sedimentary environments.

RevDate: 2020-04-08
CmpDate: 2020-04-06

Schnorr SL, Hofman CA, Netshifhefhe SR, et al (2019)

Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa.

BMC microbiology, 19(1):164.

BACKGROUND: Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming 'higher' termite members of Macrotermitinae are also consumed by modern great apes and are implicated as critical dietary resources for early hominins. While the chemical nutritional composition of edible termites is well known, their microbiomes are unexplored in the context of human health. Here we sequenced the V4 region of the 16S rRNA gene of gut microbiota extracted from the whole intestinal tract of two Macrotermes sp. soldiers collected from the Limpopo region of South Africa.

RESULTS: Major and minor soldier subcastes of M. falciger exhibit consistent differences in taxonomic representation, and are variable in microbial presence and abundance patterns when compared to another edible but less preferred species, M. natalensis. Subcaste differences include alternate patterns in sulfate-reducing bacteria and methanogenic Euryarchaeota abundance, and differences in abundance between Alistipes and Ruminococcaceae. M. falciger minor soldiers and M. natalensis soldiers have similar microbial profiles, likely from close proximity to the termite worker castes, particularly during foraging and fungus garden cultivation. Compared with previously published termite and cockroach gut microbiome data, the taxonomic representation was generally split between termites that directly digest lignocellulose and humic substrates and those that consume a more distilled form of nutrition as with the omnivorous cockroaches and fungus-farming termites. Lastly, to determine if edible termites may point to a shared reservoir for rare bacterial taxa found in the gut microbiome of humans, we focused on the genus Treponema. The majority of Treponema sequences from edible termite gut microbiota most closely relate to species recovered from other termites or from environmental samples, except for one novel OTU strain, which clustered separately with Treponema found in hunter-gatherer human groups.

CONCLUSIONS: Macrotermes consumed by humans display special gut microbial arrangements that are atypical for a lignocellulose digesting invertebrate, but are instead suited to the simplified nutrition in the fungus-farmer diet. Our work brings to light the particular termite microbiome features that should be explored further as avenues in human health, agricultural sustainability, and evolutionary research.

RevDate: 2020-04-08
CmpDate: 2020-04-06

Igiehon NO, Babalola OO, BR Aremu (2019)

Genomic insights into plant growth promoting rhizobia capable of enhancing soybean germination under drought stress.

BMC microbiology, 19(1):159.

BACKGROUND: The role of soil microorganisms in plant growth, nutrient utilization, drought tolerance as well as biocontrol activity cannot be over-emphasized, especially in this era when food crisis is a global challenge. This research was therefore designed to gain genomic insights into plant growth promoting (PGP) Rhizobium species capable of enhancing soybean (Glycine max L.) seeds germination under drought condition.

RESULTS: Rhizobium sp. strain R1, Rhizobium tropici strain R2, Rhizobium cellulosilyticum strain R3, Rhizobium taibaishanense strain R4 and Ensifer meliloti strain R5 were found to possess the entire PGP traits tested. Specifically, these rhizobial strains were able to solubilize phosphate, produce exopolysaccharide (EPS), 1-aminocyclopropane-1-carboxylate (ACC), siderophore and indole-acetic-acid (IAA). These strains also survived and grew at a temperature of 45 °C and in an acidic condition with a pH 4. Consequently, all the Rhizobium strains enhanced the germination of soybean seeds (PAN 1532 R) under drought condition imposed by 4% poly-ethylene glycol (PEG); nevertheless, Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 inoculations were able to improve seeds germination more than R2, R4 and R5 strains. Thus, genomic insights into Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 revealed the presence of some genes with their respective proteins involved in symbiotic establishment, nitrogen fixation, drought tolerance and plant growth promotion. In particular, exoX, htrA, Nif, nodA, eptA, IAA and siderophore-producing genes were found in the two rhizobial strains.

CONCLUSIONS: Therefore, the availability of the whole genome sequences of R1 and R3 strains may further be exploited to comprehend the interaction of drought tolerant rhizobia with soybean and other legumes and the PGP ability of these rhizobial strains can also be harnessed for biotechnological application in the field especially in semiarid and arid regions of the globe.

RevDate: 2020-04-07

Baltazar F, Afonso J, Costa M, et al (2020)

Lactate Beyond a Waste Metabolite: Metabolic Affairs and Signaling in Malignancy.

Frontiers in oncology, 10:231.

To sustain their high proliferation rates, most cancer cells rely on glycolytic metabolism, with production of lactic acid. For many years, lactate was seen as a metabolic waste of glycolytic metabolism; however, recent evidence has revealed new roles of lactate in the tumor microenvironment, either as metabolic fuel or as a signaling molecule. Lactate plays a key role in the different models of metabolic crosstalk proposed in malignant tumors: among cancer cells displaying complementary metabolic phenotypes and between cancer cells and other tumor microenvironment associated cells, including endothelial cells, fibroblasts, and diverse immune cells. This cell metabolic symbiosis/slavery supports several cancer aggressiveness features, including increased angiogenesis, immunological escape, invasion, metastasis, and resistance to therapy. Lactate transport is mediated by the monocarboxylate transporter (MCT) family, while another large family of G protein-coupled receptors (GPCRs), not yet fully characterized in the cancer context, is involved in lactate/acidosis signaling. In this mini-review, we will focus on the role of lactate in the tumor microenvironment, from metabolic affairs to signaling, including the function of lactate in the cancer-cancer and cancer-stromal shuttles, as well as a signaling oncometabolite. We will also review the prognostic value of lactate metabolism and therapeutic approaches designed to target lactate production and transport.

RevDate: 2020-04-07

Krug L, Morauf C, Donat C, et al (2020)

Plant Growth-Promoting Methylobacteria Selectively Increase the Biomass of Biotechnologically Relevant Microalgae.

Frontiers in microbiology, 11:427.

Microalgae, a diverse group of single-celled organisms exhibiting versatile traits, find broad applications in industry. However, high production costs require further efforts to optimize their production and to enhance biomass yields. In the present study, co-occurrence of algae and methylobacteria was observed when naturally occurring microalgae biofilms were subjected to 16S rRNA gene fragment amplicon sequencing. This bacterial group is so far less explored than other microalgae-associated bacteria in terms of mutualistic relationships that might be exploitable for biotechnological applications. In order to assess the potential of four plant growth-promoting strains from the genus Methylobacterium for increased algae biomass production, co-cultivation experiments were conducted with three industrially relevant microalgae (Chlorella vulgaris, Scenedesmus vacuolatus, and Haematococcus lacustris). For S. vacuolatus and H. lacustris, a significant increase in algal biomass formation of 1.3-fold to up to 14-fold was observed after 7 days of co-incubation. Visualization of mixed cultures using confocal laser scanning microscopy revealed a high abundance of methylobacteria in the phycosphere of H. lacustris and S. vacuolatus, visually attached to the algae's surface forming a biofilm-like assemblage. Genome analyses revealed that features attributable to enhanced algal growth include genes involved in the synthesis of vitamins, siderophores and plant hormones. Our results provide evidence for the constructability of novel symbiotic algae-bacteria relationships with inter-kingdom supportive capacities, underlining the potential of microbial consortia as promising tool for sustainable biotechnology and agriculture.

RevDate: 2020-04-07

Yu B, Yu B, L Yu (2020)

Commentary: Reconciling Hygiene and Cleanliness: A New Perspective from Human Microbiome.

Indian journal of microbiology, 60(2):259-261.

Human beings have co-evolved with the microorganisms in our environment for millions of years, and have developed into a symbiosis in a mutually beneficial/defensive way. Human beings have significant multifaceted relationships with the diverse microbial community. Apart from the important protective role of microbial community exposure in development of early immunity, millions of inimitable bacterial genes of the diverse microbial community are the indispensable source of essential nutrients like essential amino acids and essential fatty acids for human body. The essential nutrition from microbiome is harvested through xenophagy. As an immune effector, xenophagy will capture any microorganisms that touch the epithelial cells of our gastrointestinal tract, degrade them and turn them into nutrients for the use of our body.

RevDate: 2020-04-07

Vaelli PM, Theis KR, Williams JE, et al (2020)

The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts.

eLife, 9: pii:53898.

Rough-skinned newts (Taricha granulosa) use tetrodotoxin (TTX) to block voltage-gated sodium (Nav) channels as a chemical defense against predation. Interestingly, newts exhibit extreme population-level variation in toxicity attributed to a coevolutionary arms race with TTX-resistant predatory snakes, but the source of TTX in newts is unknown. Here, we investigated whether symbiotic bacteria isolated from toxic newts could produce TTX. We characterized the skin-associated microbiota from a toxic and non-toxic population of newts and established pure cultures of isolated bacterial symbionts from toxic newts. We then screened bacterial culture media for TTX using LC-MS/MS and identified TTX-producing bacterial strains from four genera, including Aeromonas, Pseudomonas, Shewanella, and Sphingopyxis. Additionally, we sequenced the Nav channel gene family in toxic newts and found that newts expressed Nav channels with modified TTX binding sites, conferring extreme physiological resistance to TTX. This study highlights the complex interactions among adaptive physiology, animal-bacterial symbiosis, and ecological context.

RevDate: 2020-04-07

Hu Y, B Chen (2020)

Arbuscular mycorrhiza induced putrescine degradation into γ-aminobutyric acid, malic acid accumulation, and improvement of nitrogen assimilation in roots of water-stressed maize plants.

Mycorrhiza pii:10.1007/s00572-020-00952-0 [Epub ahead of print].

Water shortage limits plant growth and development by inducing physiological and metabolic disorders, while arbuscular mycorrhizal (AM) symbiosis can improve plant adaptation to drought stress by altering some metabolic and signaling pathways. In this study, root growth and levels of some metabolites (polyamines, amino acids, and malic acid [MA]) and key enzymes were examined in AM-inoculated and non-inoculated (NM) maize seedlings under different water conditions. The results showed that AM symbiosis stimulated root growth and the accumulation of putrescine (Put) during initial plant growth. Root Put concentration significantly decreased in AM compared with NM plants under water stress; correspondingly, Put degradation via diamine oxidase into γ-aminobutyric acid (GABA) occurred. Moreover, glutamine concentration and the activity of N assimilation enzymes (nitrate reductase and glutamine synthetase) were higher in roots of AM than NM plants under moderate water stress. The activity of GABA transaminase and malic enzyme, and MA concentration were also higher in roots of AM than NM plants under moderate water stress. Our results indicated that Put catabolism along with improved N assimilation and the accumulation of GABA and MA were the key metabolic processes in roots of AM maize plants in response to water stress.

RevDate: 2020-04-07

Püschel D, Bitterlich M, Rydlová J, et al (2020)

Facilitation of plant water uptake by an arbuscular mycorrhizal fungus: a Gordian knot of roots and hyphae.

Mycorrhiza pii:10.1007/s00572-020-00949-9 [Epub ahead of print].

Arbuscular mycorrhizal (AM) fungi play a positive role in plant water relations, and the AM symbiosis is often cited as beneficial for overcoming drought stress of host plants. Nevertheless, water uptake via mycorrhizal hyphal networks has been little addressed experimentally, especially so through isotope tracing. In a greenhouse study conducted in two-compartment rhizoboxes, Medicago truncatula was planted in the primary compartment (PC), either inoculated with Rhizophagus irregularis or left uninoculated. Plant roots were either allowed to enter the secondary compartment (SC) or were restricted to the PC by root-excluding mesh. Substrate moisture was manipulated in the PC such that the plants were grown either in high moisture (15% of gravimetric water content, GWC) or low moisture (8% GWC). Meanwhile, the SC was maintained at 15% GWC throughout and served as a water source accessible (or not) by roots and/or hyphae. Water in the SC was labeled with deuterium (D) to quantify water uptake by the plants from the SC. Significantly, increased D incorporation into plants indicated higher water uptake by mycorrhizal plants when roots had access to the D source, but this was mainly explained by generally larger mycorrhizal root systems in proximity to the D source. On the other hand, AM fungal hyphae with access to the D source increased D incorporation into plants more than twofold compared to non-mycorrhizal plants. Despite this strong effect, water transport via AM fungal hyphae was low compared to the transpiration demand of the plants.

RevDate: 2020-04-07

Mesquita GBA, Silva WLP, Fecchio A, et al (2020)

Amblyomma ticks consumed by a giant cowbird, Molothrus oryzivorus.

Ticks and tick-borne diseases pii:S1877-959X(19)30470-4 [Epub ahead of print].

The removal of ectoparasites is a common behavior found across animal taxa and is a determinant to avoid the negative effects of parasites' presence. Eventually, the elimination of ectoparasites is associated with mutualistic interactions. Cleaner birds remove ectoparasites, providing benefits to its mutualistic host by reducing parasite burden while they obtain a protein food source. Here we report some evidence that giant cowbirds (Molothrus oryzivorus) may have an important role as a cleaner bird. We found 74 adult ticks inside the ventriculus of one male giant cowbird. The ticks belonged to three different species: Amblyomma dubitatum, A. sculptum and A. triste. We found that the sex-ratio of the consumed adult ticks was not different from 1:1. Although additional data are necessary, the large number of ticks found suggests that the giant cowbird may have developed a mutualistic association with large, social mammals such as capybaras (Hydrochoerus hydrochaeris), since this animal is an important host species for the three tick species found in the present study.

RevDate: 2020-04-06

Lockwood MB, SJ Green (2020)

Clinical care is evolving: The microbiome for advanced practice nurses.

Journal of the American Association of Nurse Practitioners, 32(4):290-292.

Over the course of four billion years, humans have developed an intimate relationship with the more than 37 trillion microbes that inhabit our bodies. This relationship runs the gamut from symbiosis to pathogenesis. The number of microbial cells is roughly equivalent to that of mammalian cells in the body. However, due to substantial microbial diversity in host-associated communities, the genetic content of the microbiome is roughly 150 times greater than that of the human genome. Microbial genes encode for proteins capable of producing a wide variety of molecules essential for our health and survival. Many factors such as mode of birth, diet, chlorination of water, and medications significantly affect the richness and diversity of the microbiome. Advanced practice nurses have important roles to play as clinicians, scientists, educators, and patient advocates as our understanding of the microbiome's effects on health becomes better articulated. An understanding of how the microbiome can affect an individual's health or the efficacy of treatment will soon be essential in the clinical setting, and nurses should be encouraged to educate themselves on the relationship between our microbial partners, the environment, and human health.

RevDate: 2020-04-06

Rosic N, Rémond C, MA Mello-Athayde (2020)

Differential impact of heat stress on reef-building corals under different light conditions.

Marine environmental research, 158:104947 pii:S0141-1136(19)30825-6 [Epub ahead of print].

Heat stress is an environmental factor that regularly challenges the well-being of living organisms. This study aims to examine the physiological changes happening in two reef-building coral species exposed to thermal stress under various light conditions. The two ecologically relevant heatwave scenarios were applied under ambient lights (high irradiance) and reduced light conditions (250 and < 10 μmol photons m-2 s-1). Corals were exposed to elevated temperatures of 32°C (plus 6°) for a period of 1 up to 5 days corresponding to heatwaves reported on the Great Barrier Reef (GBR) that were associated with coral bleaching. We monitored changes in the physiological performance of these two coral species by measuring symbionts and corals' physiological parameters including symbiont density, levels of multiple algal pigments (chlorophyll a and peridinin), as well as the changes in the host protein concentration. During the short-term heat stress, both species were with stable physiological performance with the only exception of Stylophora pistillata under ambient lights. These results show that S. pistillata was negatively influenced by a synergistic effect of temperature and high irradiance resulting in the first signs of bleaching after only 24h of thermal stress. Exposure to prolonged thermal stress, characterised with a slower rate of temperature increase, affected both coral species investigated and resulted in bleaching mainly by day 5. Interestingly, severe light reduction (<10 μmol photons m-2 s-1) made Acropora millepora corals more thermally sensitive and resulted in earlier signs of bleaching (on day 3). These findings indicate that there was a synergistic effect of very low lights and thermal stress that caused higher levels of bleaching in A. millepora. Our results revealed differential thermal sensitivity for two branching corals exposed to different thermal stress scenarios under various light irradiance conditions, naturally found in their existing habitats. Consequently, global warming may have a differential impact on coral reef biodiversity depending on light availability.

RevDate: 2020-04-05

Šmilauer P, Šmilauerová M, Kotilínek M, et al (2020)

Foraging speed and precision of arbuscular mycorrhizal fungi under field conditions - an experimental approach.

Molecular ecology [Epub ahead of print].

To better understand the ecology of arbuscular mycorrhizal (AM) symbiosis, we need to measure functional traits of individual fungal virtual taxa under field conditions. The efficiency of AM fungi in locating nutrient-rich patches in soil space is one of their central traits in this symbiotic relationship. We used plots of a long-term field experiment in grassland with manipulated functional group composition of host plant community to establish ingrowth patches with substrate free of roots and fungi and with varying nutrient availability. Comparison of the original AM fungal community before patch creation with that present 9 weeks after patch establishment enabled us to estimate relative hyphal foraging speed for 41 fungal taxa, and a comparison of the fungal community in neighbouring patches differing in nutrient availability provided estimates of hyphal foraging precision for 22 taxa. Members of two dominant fungal families, Glomeraceae and Claroideoglomeraceae, differed in their foraging speed and precision. Glomeraceae taxa responded more slowly, but with a higher focus on enriched patches. We further demonstrated the usefulness of obtained fungal functional traits by testing the differences between grass and dicotyledonous plant hosts using a dataset obtained in another experiment at the same plots. Grass species hosted AM fungal communities with higher foraging speed, but lower foraging precision than the dicotyledonous species. Our study results support the use of field experiments for measuring comparative characteristics of AM fungi, which are highly elusive (or mis-represented) under controlled conditions.

RevDate: 2020-04-04

Comerlato CB, Zhang X, Walker K, et al (2020)

Comparative proteomic analysis reveals metabolic variability of probiotic Enterococcus durans during aerobic and anaerobic cultivation.

Journal of proteomics pii:S1874-3919(20)30132-9 [Epub ahead of print].

The variation in the bioavailability of oxygen constitutes the environmental conditions found by bacteria in their passage through the host gastro-intestinal tract. Given the importance of oxygen in the defense mechanism of bacteria, it is important to understand how bacteria respond to this stress at a metabolic level. The probiotic strain Enterococcus durans LAB18S was cultivated under aerobic and anaerobic conditions using prebiotic oligosaccharides as carbon source. The whole cell proteome and secretome were analyzed through label-free quantitative proteomics approach. The results showed that the LAB18S isolate when grown with fructo-oligosacchrides (FOS) showed a higher number of differentially expressed proteins compared to samples with galacto-oligosaccharides (GOS) or glucose. Clinically important enzymes for the treatment of cancer, L-asparaginase and arginine deiminase, were overexpressed when the isolate was cultured in FOS. In addition, the absence of oxygen induced the strain to produce proteins related to cell multiplication, cell wall integrity and resistance, and H2O2 detoxification. This study showed that E. durans LAB18S growing on FOS was stimulated to produce clinically important biomolecules, including proteins that have been investigated as potential antineoplastic agents. Significance: The probiotic strain E. durans LAB18S produce clinically relevant enzymes for the treatment of cancer when cultivated in symbiosis with fructo-oligosacchrides (FOS). In addition, proteins associated with cellular multiplication, cell wall integrity and resistance, and H2O2 detoxification were induced under anaerobic growth. These characteristics could be relevant to support maintenance of intestinal health.

RevDate: 2020-04-04

Cristaldi A, Oliveri Conti G, Cosentino SL, et al (2020)

Phytoremediation potential of Arundo donax (Giant Reed) in contaminated soil by heavy metals.

Environmental research, 185:109427 pii:S0013-9351(20)30320-0 [Epub ahead of print].

Soil pollution from heavy metals poses a serious risk for environment and public health. Phytoremediation is an eco-friendly and cheaper alternative compared to chemical-physical techniques. We carried out in vitro tests where three microorganisms Trichoderma harzianum, Saccharomyces cerevisiae and Wickerhamomyces anomalus were exposed to eight different heavy metals (one metal at a time) in order to evaluate resistance, growth and bioaccumulation capability for each metal (Ni, Cd, Cu, V, Zn, As, Pb, Hg). Taking into account the natural characteristics of T. harzianum, (resistance to environmental stress, resistance to pathogenic fungi, ability to establish symbiotic relationships with superior green plants) and the good bioaccumulation capacity for V, As, Cd, Hg, Pb shown after in vitro tests, it was chosen as a microorganism to be used in greenhouse tests. Controlled exposure tests were performed in greenhouse, where Arundo donax and mycorrhized Arundo donax with T. harzianum were exposed for 7 months at two different doses (L1 and L2) of a heavy metal mix, so as to assess whether the symbiotic association could improve the bioaccumulation capability of the superior green plant A. donax. Heavy metals were determined with ICP-MS. The average bioaccumulation percentage values of A. donax for L1 and L2 were, respectively: Ni (31%, 26%); Cd (35%, 50%); Cu (30%, 35%); As (19%, 27%); Pb (18%, 14%); Hg (42%, 45%); V (39%, 26%); Zn (23%, 9%). The average bioaccumulation percentage values of mycorrhized A. donax with T. harzianum for L1 and L2 were, respectively: Ni (27%, 38%); Cd (44%, 42%); Cu (36%, 29%); As (17%, 23%); Pb (37%, 54%); Hg (44%, 60%); V (16%, 20%); Zn (14%, 7%). A. donax showed the highest BAF (bioaccumulation factor) for Cd (0.50), Cu (0.35), As (0.27) and Hg (0.45) after exposure to L2; mycorrhized A. donax with T. harzianum showed the highest BAF for Ni (0.38), Cd (0.42), Pb (0.54) and Hg (0.60) after exposure to L2. A. donax showed the highest TF (translocation factor) values for Cd (0.28) and Hg (0.26) after exposition at L1 and L2 respectively; A. donax mycorrhized with T. harzianum showed the highest TF values for Cd (0.70), As (0.56), V (0.24), Pb (0.18) after exposition at L2, and Zn (0.30) after exposition at L1. Our study showed a good growth capability in contaminated soils and a good bioaccumulation capability of heavy metals, both for A. donax and mycorrhized A. donax with T. harzianum. Furthermore, for three metals (Ni, Pb and Hg) the bioaccumulation capability was improved by the symbiosis of T. harzianum with A. donax. So, these results proved the suitability both for A. donax and mycorrhized A. donax with T. harzianum for phytoremediation processes.

RevDate: 2020-04-04

Si Y, Guo D, Deng S, et al (2020)

Ohr and OhrR Are Critical for Organic Peroxide Resistance and Symbiosis in Azorhizobium caulinodans ORS571.

Genes, 11(3): pii:genes11030335.

Azorhizobium caulinodans is a symbiotic nitrogen-fixing bacterium that forms both root and stem nodules on Sesbania rostrata. During nodule formation, bacteria have to withstand organic peroxides that are produced by plant. Previous studies have elaborated on resistance to these oxygen radicals in several bacteria; however, to the best of our knowledge, none have investigated this process in A. caulinodans. In this study, we identified and characterised the organic hydroperoxide resistance gene ohr (AZC_2977) and its regulator ohrR (AZC_3555) in A. caulinodans ORS571. Hypersensitivity to organic hydroperoxide was observed in an ohr mutant. While using a lacZ-based reporter system, we revealed that OhrR repressed the expression of ohr. Moreover, electrophoretic mobility shift assays demonstrated that OhrR regulated ohr by direct binding to its promoter region. We showed that this binding was prevented by OhrR oxidation under aerobic conditions, which promoted OhrR dimerization and the activation of ohr. Furthermore, we showed that one of the two conserved cysteine residues in OhrR, Cys11, was critical for the sensitivity to organic hydroperoxides. Plant assays revealed that the inactivation of Ohr decreased the number of stem nodules and nitrogenase activity. Our data demonstrated that Ohr and OhrR are required for protecting A. caulinodans from organic hydroperoxide stress and play an important role in the interaction of the bacterium with plants. The results that were obtained in our study suggested that a thiol-based switch in A. caulinodans might sense host organic peroxide signals and enhance symbiosis.

RevDate: 2020-04-03

Monnin D, Jackson R, Kiers ET, et al (2020)

Parallel Evolution in the Integration of a Co-obligate Aphid Symbiosis.

Current biology : CB pii:S0960-9822(20)30349-3 [Epub ahead of print].

Insects evolve dependence-often extreme-on microbes for nutrition. This includes cases in which insects harbor multiple endosymbionts that function collectively as a metabolic unit [1-5]. How do these dependences originate [6], and is there a predictable sequence of events leading to the integration of new symbionts? While co-obligate symbioses, in which hosts rely on multiple nutrient-provisioning symbionts, have evolved numerous times across sap-feeding insects, there is only one known case in aphids, involving Buchnera aphidicola and Serratia symbiotica in the Lachninae subfamily [7-9]. Here, we identify three additional independent transitions to the same co-obligate symbiosis in different aphids. Comparing recent and ancient associations allow us to investigate intermediate stages of metabolic and anatomical integration of Serratia. We find that these uniquely replicated evolutionary events support the idea that co-obligate associations initiate in a predictable manner-through parallel evolutionary processes. Specifically, we show how the repeated losses of the riboflavin and peptidoglycan pathways in Buchnera lead to dependence on Serratia. We then provide evidence of a stepwise process of symbiont integration, whereby dependence evolves first. Then, essential amino acid pathways are lost (at ∼30-60 mya), which coincides with the increased anatomical integration of the companion symbiont. Finally, we demonstrate that dependence can evolve ahead of specialized structures (e.g., bacteriocytes), and in one case with no direct nutritional basis. More generally, our results suggest the energetic costs of synthesizing nutrients may provide a unified explanation for the sequence of gene losses that occur during the evolution of co-obligate symbiosis.

RevDate: 2020-04-03

Su SY, Lu IH, Cheng WC, et al (2020)

EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis.

BMC genomics, 21(Suppl 3):163 pii:10.1186/s12864-019-6404-8.

BACKGROUND: DNA methylation is a crucial epigenomic mechanism in various biological processes. Using whole-genome bisulfite sequencing (WGBS) technology, methylated cytosine sites can be revealed at the single nucleotide level. However, the WGBS data analysis process is usually complicated and challenging.

RESULTS: To alleviate the associated difficulties, we integrated the WGBS data processing steps and downstream analysis into a two-phase approach. First, we set up the required tools in Galaxy and developed workflows to calculate the methylation level from raw WGBS data and generate a methylation status summary, the mtable. This computation environment is wrapped into the Docker container image DocMethyl, which allows users to rapidly deploy an executable environment without tedious software installation and library dependency problems. Next, the mtable files were uploaded to the web server EpiMOLAS_web to link with the gene annotation databases that enable rapid data retrieval and analyses.

CONCLUSION: To our knowledge, the EpiMOLAS framework, consisting of DocMethyl and EpiMOLAS_web, is the first approach to include containerization technology and a web-based system for WGBS data analysis from raw data processing to downstream analysis. EpiMOLAS will help users cope with their WGBS data and also conduct reproducible analyses of publicly available data, thereby gaining insights into the mechanisms underlying complex biological phenomenon. The Galaxy Docker image DocMethyl is available at EpiMOLAS_web is publicly accessible at

RevDate: 2020-04-03
CmpDate: 2020-04-03

van Vliet S, M Doebeli (2019)

The role of multilevel selection in host microbiome evolution.

Proceedings of the National Academy of Sciences of the United States of America, 116(41):20591-20597.

Animals are associated with a microbiome that can affect their reproductive success. It is, therefore, important to understand how a host and its microbiome coevolve. According to the hologenome concept, hosts and their microbiome form an integrated evolutionary entity, a holobiont, on which selection can potentially act directly. However, this view is controversial, and there is an active debate on whether the association between hosts and their microbiomes is strong enough to allow for selection at the holobiont level. Much of this debate is based on verbal arguments, but a quantitative framework is needed to investigate the conditions under which selection can act at the holobiont level. Here, we use multilevel selection theory to develop such a framework. We found that selection at the holobiont level can in principle favor a trait that is costly to the microbes but that provides a benefit to the host. However, such scenarios require rather stringent conditions. The degree to which microbiome composition is heritable decays with time, and selection can only act at the holobiont level when this decay is slow enough, which occurs when vertical transmission is stronger than horizontal transmission. Moreover, the host generation time has to be short enough compared with the timescale of the evolutionary dynamics at the microbe level. Our framework thus allows us to quantitatively predict for what kind of systems selection could act at the holobiont level.

RevDate: 2020-04-03
CmpDate: 2020-04-03

Flakus A, Etayo J, Pérez-Ortega S, et al (2019)

A new genus, Zhurbenkoa, and a novel nutritional mode revealed in the family Malmideaceae (Lecanoromycetes, Ascomycota).

Mycologia, 111(4):593-611.

Lichen-inhabiting fungi are highly specialized mycoparasites, commensals or rarely saprotrophs, that are common components of almost every ecosystem, where they develop obligate associations with lichens. Their relevance, however, contrasts with the relatively small number of these fungi described so far. Recent estimates and ongoing studies indicate that a significant fraction of their diversity remains undiscovered and may be expected in tropical regions, in particular in hyperdiverse fog-exposed montane forests. Here, we introduce the new genus Zhurbenkoa, from South America and Europe, for three lichenicolous fungi growing on thalli of the widespread lichen genus Cladonia (Lecanorales). Phylogenetic analyses based on combined sequence data of mt and nuc rDNA obtained from Andean populations (Bolivia) placed Zhurbenkoa as a member of Malmideaceae, a recently introduced family of lichen-forming fungi in the class Lecanoromycetes. Zhurbenkoa is closely related to the genera Savoronala and Sprucidea. The new genus is characterized by the development of grayish brown to almost black apothecia lacking an evident margin, an epihymenium interspersed with crystals (often seen as pruina), a strongly conglutinated hymenium made of noncapitate and sparsely branched paraphyses, a colorless exciple composed of radially arranged hyphae, a Lecanora/Micarea-like ascus type, and aseptate or 1-septate ellipsoidal colorless ascospores. Zhurbenkoa includes two Neotropical (Z. cladoniarum, Z. latispora) and one widespread (Z. epicladonia) species. The lichenicolous trophic mode is documented for the first time in the Malmideaceae, which until now included only lichen-forming associations between fungi and green algae.

RevDate: 2020-04-03
CmpDate: 2020-04-03

Goh CH, Nicotra AB, U Mathesius (2019)

Genes controlling legume nodule numbers affect phenotypic plasticity responses to nitrogen in the presence and absence of rhizobia.

Plant, cell & environment, 42(5):1747-1757.

We investigated the role of three autoregulation of nodulation (AON) genes in regulating of root and shoot phenotypes when responding to changing nitrogen availability in the model legume, Medicago truncatula. These genes, RDN1-1 (ROOT DETERMINED NODULATION1-1), SUNN (SUPER NUMERIC NODULES), and LSS (LIKE SUNN SUPERNODULAOR), act in a systemic signalling pathway that limits nodule numbers. This pathway is also influenced by nitrogen availability, but it is not well known if AON genes control root and shoot phenotypes other than nodule numbers in response to nitrogen. We conducted a controlled glasshouse experiment to compare root and shoot phenotypes of mutants and wild type plants treated with four nitrate concentrations. All AON mutants showed altered rhizobia-independent phenotypes, including biomass allocation, lateral root length, lateral root density, and root length ratio. In response to nitrogen, uninoculated AON mutants were less plastic than the wild type in controlling root mass ratio, root length ratio, and lateral root length. This suggests that AON genes control nodulation-independent root architecture phenotypes in response to nitrogen. The phenotypic differences between wild type and AON mutants were exacerbated by the presence of nodules, pointing to resource competition as an additional mechanism affecting root and shoot responses to nitrogen.

RevDate: 2020-04-02

Duan Y, Petzold M, Saleem-Batcha R, et al (2020)

Bacterial tropone natural products and derivatives: Overview on the biosynthesis, bioactivities, ecological role and biotechnological potential.

Chembiochem : a European journal of chemical biology [Epub ahead of print].

Tropone natural products are non-benzene aromatic compounds of significant ecological and pharmaceutical interest. Here we highlight current knowledge on bacterial tropones and derivatives such as tropolones, tropodithietic acid, and roseobacticides. Their unusual biosynthesis depends on a universal CoA-bound precursor featuring a seven-membered carbon ring as backbone, which is generated by a side reaction of the phenylacetic acid catabolic pathway. Then, enzymes encoded by separate gene clusters further modify this key intermediate, which may comprise oxidation, CoA-release, or incorporation of sulfur among other reactions. Tropones adopt important roles in the terrestrial and marine environment where they act as antibiotics, algaecides, or quorum sensing signals, while their bacterial producers are often involved in symbiotic interactions with plants and marine invertebrates (e.g., algae, corals, sponges, or mollusks). Because of their potent bioactivities and of slowly developing bacterial resistance, tropones and derivatives hold great promise for biomedical or biotechnological applications, for instance as antibiotics in (shell)fish aquaculture.

RevDate: 2020-04-02

Lundy SD, Vij SC, Rezk AH, et al (2020)

The microbiome of the infertile male.

Current opinion in urology, 30(3):355-362.

PURPOSE OF REVIEW: Contrary to historic dogma, many tissues and organs in the human body contain a resident population of bacteria, fungi, and viruses collectively known as the microbiome. The microbiome plays a role in both homeostatic symbiosis and also pathogenic dysbiosis in a wide array of diseases. Our understanding of the relationship between the microbiome and male factor infertility is in its infancy but is slowly evolving.

RECENT FINDINGS: Recent literature indicates that semen (and likely the testis) is not sterile and contains a distinct microbiome, and these changes in its composition are associated with alterations in semen quality and fertility status. Preliminary investigation indicates that manipulating the human microbiome may have implications in improving semen parameters and fertility.

SUMMARY: In this review, we describe relationships between the microbiome and the genitourinary system, discuss the prior work on the relationship among bacteriospermia, leukocytospermia and male factor infertility, and summarize the current literature utilizing 16s rRNA-based next-generation sequencing on the seminal and testicular microbiome. We explore the specific microbial taxa implicated in various aspects of spermatic dysfunction and introduce preliminary evidence for therapeutic approaches to alter the microbiome and improve fertility status.

RevDate: 2020-04-02

Zhang H, Gong W, Zeng W, et al (2020)

Organic carbon promotes algae proliferation in membrane-aeration based bacteria-algae symbiosis system (MA-BA).

Water research, 176:115736 pii:S0043-1354(20)30273-6 [Epub ahead of print].

In the bacteria-algae (BA) system, the amount of oxygen produced by the algae is always insufficient for the organic carbon degradation, resulting in less inorganic carbon (IC) production. Meanwhile, the conventional extra aeration method always causes CO2 stripping and IC loss. Both two reasons limited the algae boosting. Membrane aeration (MA) has the excellent capability of organic carbon thorough degradation and gas blown-off control. In this study, MA-BA was employed to investigate the effect of organic carbon on the algae growth. Results showed that COD had a positive correlation with Chlorophyll-a (Chl-a) and algae proliferation in MA-BA system according to the redundancy analysis (RDA). The biggest Chl-a concentration (20.95 mg/cm2) occurred in R4 (COD = 400 mg/L). Stimulated algal population changed nutrient removal pathway from bacterial action to algae action. Meantime, Soared algae accumulation would selectively excite the abundance of bacteria that supported the algae growth, such as Acinetobacter, which exhibited a growing trend as the increase of influent COD, especially in the inner biofilm. This paper provided new insight into the effect of organic carbon on the algae in a novel MA-BA system, which will be helpful for future research.

RevDate: 2020-04-02

Wang Y, Liu L, Yu M, et al (2020)

Carideicomes alvinocaridis gen. nov., sp. nov., a marine bacterium isolated from shrimp gill in a hydrothermal field of Okinawa Trough.

International journal of systematic and evolutionary microbiology, 70(3):1777-1784.

A Gram-stain-negative, strictly aerobic, oval-shaped, non-motile bacterium with no flagella, designated strain SCR17T, was isolated from a shrimp gill habitat in Tangyin hydrothermal field of Okinawa Trough. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SCR17T formed a lineage within the family 'Rhodobacteraceae', and shared 16S rRNA gene sequence similarity of 93.2-96.2 % to the related genera Aquicoccus and Roseivivax. Strain SCR17T was able to grow with 0-14 % (w/v) NaCl (optimum, 9-10 %). The sole respiratory quinone was ubiquinone-10. The major polar lipids of strain SCR17T comprised phosphatidylcholine (PC), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unidentified aminolipid (AL), an unidentified phospholipid (PL) and an unidentified lipid (L). The predominant fatty acids (more than 10 % of the total fatty acids) were C18 : 1ω7c or/and C18 : 1ω6c, anteiso-C15 : 0, C16 : 0 and C19 : 0 cyclo ω8c . The genomic DNA G+C content of strain SCR17T was 67.7 mol%. Based on polyphasic taxonomic analyses, strain SCR17T is considered to represent a novel species in a new genus of the family 'Rhodobacteraceae', for which the name Carideicomes alvinocaridis gen. nov., sp. nov. is proposed. The type strain of Carideicomes alvinocaridis is SCR17T (=JCM 33426T=MCCC 1K03732T). The discovery of a novel host-associated bacterium in hydrothermal fields provides an opportunity for the study of host-bacterial symbiosis in extreme environments.

RevDate: 2020-04-02

Coffman KA, Harrell TC, GR Burke (2020)

A Mutualistic Poxvirus Exhibits Convergent Evolution with Other Heritable Viruses in Parasitoid Wasps.

Journal of virology, 94(8): pii:JVI.02059-19.

For insects known as parasitoid wasps, successful development as a parasite results in the death of the host insect. As a result of this lethal interaction, wasps and their hosts have coevolved strategies to gain an advantage in this evolutionary arms race. Although normally considered to be strict pathogens, some viruses have established persistent infections within parasitoid wasp lineages and are beneficial to wasps during parasitism. Heritable associations between viruses and parasitoid wasps have evolved independently multiple times, but most of these systems remain largely understudied with respect to viral origin, transmission and replication strategies of the virus, and interactions between the virus and host insects. Here, we report a detailed characterization of Diachasmimorpha longicaudata entomopoxvirus (DlEPV), a poxvirus found within the venom gland of Diachasmimorpha longicaudata wasps. Our results show that DlEPV exhibits similar but distinct transmission and replication dynamics compared to those of other parasitoid viral elements, including vertical transmission of the virus within wasps, as well as virus replication in both female wasps and fruit fly hosts. Functional assays demonstrate that DlEPV is highly virulent within fly hosts, and wasps without DlEPV have severely reduced parasitism success compared to those with a typical viral load. Taken together, the data presented in this study illustrate a novel case of beneficial virus evolution, in which a virus of unique origin has undergone convergent evolution with other viral elements associated with parasitoid wasps to provide an analogous function throughout parasitism.IMPORTANCE Viruses are generally considered to be disease-causing agents, but several instances of beneficial viral elements have been identified in insects called parasitoid wasps. These virus-derived entities are passed on through wasp generations and enhance the success of the wasps' parasitic life cycle. Many parasitoid-virus partnerships studied to date exhibit common features among independent cases of this phenomenon, including a mother-to-offspring route of virus transmission, a restricted time and location for virus replication, and a positive effect of virus activity on wasp survival. Our characterization of Diachasmimorpha longicaudata entomopoxvirus (DlEPV), a poxvirus found in Diachasmimorpha longicaudata parasitoid wasps, represents a novel example of beneficial virus evolution. Here, we show that DlEPV exhibits functional similarities to known parasitoid viral elements that support its comparable role during parasitism. Our results also demonstrate unique differences that suggest DlEPV is more autonomous than other long-term viral associations described in parasitoid wasps.

RevDate: 2020-04-02
CmpDate: 2020-04-02

Zhou Y, Jackson D, Bacharier LB, et al (2019)

The upper-airway microbiota and loss of asthma control among asthmatic children.

Nature communications, 10(1):5714.

The airway microbiome has an important role in asthma pathophysiology. However, little is known on the relationships between the airway microbiome of asthmatic children, loss of asthma control, and severe exacerbations. Here we report that the microbiota's dynamic patterns and compositions are related to asthma exacerbations. We collected nasal blow samples (n = 319) longitudinally during a clinical trial at 2 time-points within one year: randomization when asthma is under control, and at time of early loss of asthma control (yellow zone (YZ)). We report that participants whose microbiota was dominated by the commensal Corynebacterium + Dolosigranulum cluster at RD experience the lowest rates of YZs (p = 0.005) and have longer time to develop at least 2 episodes of YZ (p = 0.03). The airway microbiota have changed from randomization to YZ. A switch from the Corynebacterium + Dolosigranulum cluster at randomization to the Moraxella- cluster at YZ poses the highest risk of severe asthma exacerbation (p = 0.04). Corynebacterium's relative abundance at YZ is inversely associated with severe exacerbation (p = 0.002).

RevDate: 2020-04-02
CmpDate: 2020-04-02

Wang X, Yu Y, Ge J, et al (2019)

Effects of α-pinene on the pinewood nematode (Bursaphelenchus xylophilus) and its symbiotic bacteria.

PloS one, 14(8):e0221099.

The pinewood nematode (PWN), Bursaphelenchus xylophilus, is an important plant-parasitic nematode that can cause severe mortality of pine trees. This PWN-induced harm to plants may be closely related to the abundance and diversity of the symbiotic microorganisms of the parasitic nematode. In this study, nematodes were divided into untreated and antibiotic-treated groups. Nematodes were treated by fumigation with different amounts of α-pinene, and the resultant mortality rates were analyzed statistically. Concentrations of symbiotic bacteria were calculated as colony-forming units per nematode. High-throughput sequencing was used to investigate the bacterial community structure. The results showed that the mortality of nematodes increased slightly with an increasing concentration of α-pinene, and nematodes untreated with antibiotics were more sensitive to α-pinene than those treated with antibiotics. The highest abundance of symbiotic bacteria was obtained via medium and low levels of α-pinene, but for which community diversity was the lowest (Shannon and Simpson indexes). The proportion of Pseudomonas spp. in the symbiotic bacteria of nematodes without antibiotics was relatively high (more than 70%), while that of Stenotrophomonas spp. was low (6%-20%). However, the proportion of Stenotrophomonas spp. was larger than that of Pseudomonas spp in the symbiotic bacteria associated with the antibiotic-treated nematodes. Pseudomonas sp. increased after pinene treatment, whereas Stenotrophomonas spp. decreased. These results indicate that although α-pinene has low toxicity to PWNs over a short time period, α-pinene ultimately influences the abundance and community diversity of the symbiotic bacteria of these nematodes; this influence may potentially disturb the development and reproduction of nematodes in the process of infecting pine trees.

RevDate: 2020-04-02
CmpDate: 2020-04-02

Madhusoodanan J (2019)

News Feature: Do hosts and their microbes evolve as a unit?.

Proceedings of the National Academy of Sciences of the United States of America, 116(29):14391-14394.

RevDate: 2020-04-02
CmpDate: 2020-04-02

Hamm JN, Erdmann S, Eloe-Fadrosh EA, et al (2019)

Unexpected host dependency of Antarctic Nanohaloarchaeota.

Proceedings of the National Academy of Sciences of the United States of America, 116(29):14661-14670.

In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lacusprofundi for growth. By performing growth using enrichments and fluorescence-activated cell sorting, we demonstrated successful cultivation of Candidatus Nanohaloarchaeum antarcticus, purification of Ca. Nha. antarcticus away from other species, and growth and verification of Ca. Nha. antarcticus with Hrr. lacusprofundi; these findings are analogous to those required for fulfilling Koch's postulates. We use fluorescent in situ hybridization and transmission electron microscopy to assess cell structures and interactions; metagenomics to characterize enrichment taxa, generate metagenome assembled genomes, and interrogate Antarctic communities; and proteomics to assess metabolic pathways and speculate about the roles of certain proteins. Metagenome analysis indicates the presence of a single species, which is endemic to Antarctic hypersaline systems that support the growth of haloarchaea. The presence of unusually large proteins predicted to function in attachment and invasion of hosts plus the absence of key biosynthetic pathways (e.g., lipids) in metagenome assembled genomes of globally distributed Nanohaloarchaeota indicate that all members of the lineage have evolved as symbionts. Our work expands the range of archaeal symbiotic lifestyles and provides a genetically tractable model system for advancing understanding of the factors controlling microbial symbiotic relationships.

RevDate: 2020-04-02
CmpDate: 2020-04-02

Fox M, Knorr DA, KM Haptonstall (2019)

Alzheimer's disease and symbiotic microbiota: an evolutionary medicine perspective.

Annals of the New York Academy of Sciences, 1449(1):3-24.

Microorganisms resident in our bodies participate in a variety of regulatory and pathogenic processes. Here, we describe how etiological pathways implicated in Alzheimer's disease (AD) may be regulated or disturbed by symbiotic microbial activity. Furthermore, the composition of symbiotic microbes has changed dramatically across human history alongside the rise of agriculturalism, industrialization, and globalization. We postulate that each of these lifestyle transitions engendered progressive depletion of microbial diversity and enhancement of virulence, thereby enhancing AD risk pathways. It is likely that the human life span extended into the eighth decade tens of thousands of years ago, yet little is known about premodern geriatric epidemiology. We propose that microbiota of the gut, oral cavity, nasal cavity, and brain may modulate AD pathogenesis, and that changes in the microbial composition of these body regions across history suggest escalation of AD risk. Dysbiosis may promote immunoregulatory dysfunction due to inadequate education of the immune system, chronic inflammation, and epithelial barrier permeability. Subsequently, proinflammatory agents-and occasionally microbes-may infiltrate the brain and promote AD pathogenic processes. APOE genotypes appear to moderate the effect of dysbiosis on AD risk. Elucidating the effect of symbiotic microbiota on AD pathogenesis could contribute to basic and translational research.

RevDate: 2020-04-01

Doré J (2019)

[Role and integration of the intestinal microbiota in clinical management of other diseases].

La Revue du praticien, 69(7):800-803.

Role and integration of the intestinal microbiota in clinical management of other diseases. Owing to its numerous functionalities, the microbiota is probably a key player in human health. It is altogether a source of signatures of alteration of host-microbes symbiosis and a potential modulator for prevention and therapy in a number of clinical conditions with high impact in terms of public health. Long term diseases use up to two third of health insurance expenses. In the following pages we bring a synthetic overview of diseases impacted by the microbiota, beyond inflammatory bowel diseases, and highlight the importance of prevention which only benefits from 1.5% of health expenses today.

RevDate: 2020-04-01

Silvestri A, Turina M, Fiorilli V, et al (2020)

Different Genetic Sources Contribute to the Small RNA Population in the Arbuscular Mycorrhizal Fungus Gigaspora margarita.

Frontiers in microbiology, 11:395.

RNA interference (RNAi) is a key regulatory pathway of gene expression in almost all eukaryotes. This mechanism relies on short non-coding RNA molecules (sRNAs) to recognize in a sequence-specific manner DNA or RNA targets leading to transcriptional or post-transcriptional gene silencing. To date, the fundamental role of sRNAs in the regulation of development, stress responses, defense against viruses and mobile elements, and cross-kingdom interactions has been extensively studied in a number of biological systems. However, the knowledge of the "RNAi world" in arbuscular mycorrhizal fungi (AMF) is still limited. AMF are obligate mutualistic endosymbionts of plants, able to provide several benefits to their partners, from improved mineral nutrition to stress tolerance. Here we described the RNAi-related genes of the AMF Gigaspora margarita and characterized, through sRNA sequencing, its complex small RNAome, considering the possible genetic sources and targets of the sRNAs. G. margarita indeed is a mosaic of different genomes since it hosts endobacteria, RNA viruses, and non-integrated DNA fragments corresponding to mitovirus sequences. Our findings show that G. margarita is equipped with a complete set of RNAi-related genes characterized by the expansion of the Argonaute-like (AGO-like) gene family that seems a common trait of AMF. With regards to sRNAs, we detected populations of sRNA reads mapping to nuclear, mitochondrial, and viral genomes that share similar features (25-nt long and 5'-end uracil read enrichments), and that clearly differ from sRNAs of endobacterial origin. Furthermore, the annotation of nuclear loci producing sRNAs suggests the occurrence of different sRNA-generating processes. In silico analyses indicate that the most abundant G. margarita sRNAs, including those of viral origin, could target transcripts in the host plant, through a hypothetical cross-kingdom RNAi.

RevDate: 2020-04-01

Katoh T, Ojima MN, Sakanaka M, et al (2020)

Enzymatic Adaptation of Bifidobacterium bifidum to Host Glycans, Viewed from Glycoside Hydrolyases and Carbohydrate-Binding Modules.

Microorganisms, 8(4): pii:microorganisms8040481.

Certain species of the genus Bifidobacterium represent human symbionts. Many studies have shown that the establishment of symbiosis with such bifidobacterial species confers various beneficial effects on human health. Among the more than ten (sub)species of human gut-associated Bifidobacterium that have significantly varied genetic characteristics at the species level, Bifidobacterium bifidum is unique in that it is found in the intestines of a wide age group, ranging from infants to adults. This species is likely to have adapted to efficiently degrade host-derived carbohydrate chains, such as human milk oligosaccharides (HMOs) and mucin O-glycans, which enabled the longitudinal colonization of intestines. The ability of this species to assimilate various host glycans can be attributed to the possession of an adequate set of extracellular glycoside hydrolases (GHs). Importantly, the polypeptides of those glycosidases frequently contain carbohydrate-binding modules (CBMs) with deduced affinities to the target glycans, which is also a distinct characteristic of this species among members of human gut-associated bifidobacteria. This review firstly describes the prevalence and distribution of B. bifidum in the human gut and then explains the enzymatic machinery that B. bifidum has developed for host glycan degradation by referring to the functions of GHs and CBMs. Finally, we show the data of co-culture experiments using host-derived glycans as carbon sources, which underpin the interesting altruistic behavior of this species as a cross-feeder.

RevDate: 2020-04-01

Anker A (2020)

Unesconia coibensis, gen. et sp. nov., a miniature sponge-associated shrimp from a biodiversity hotspot in the tropical eastern Pacific (Decapoda: Palaemonidae).

Zootaxa, 4731(1):zootaxa.4731.1.8 pii:zootaxa.4731.1.8.

A new palaemonid shrimp genus, Unesconia gen. nov., is established to accommodate a peculiar, small, presumably sponge-associated species, Unesconia coibensis gen. et sp. nov. The description of the new genus and species is based on several specimens found in the shallow marine waters of the Coiba Archipelago, Pacific coast of Panama. Unesconia gen. nov. does not seem to have close affinities to other eastern Pacific or western Atlantic palaemonid genera, including those harbouring sponge symbionts. On the other hand, it shares many characters with three Indo-West Pacific genera, which contain sponge-associated species, viz. Paraclimenaeus Bruce, 1988, Apopontonia Bruce, 1976 and Climeniperaeus Bruce, 1996. The most important diagnostic features of Unesconia gen. nov. are the strongly carinate, dorsally dentate rostrum, with its lateral carinae greatly expanded basally and armed with strong supraorbital teeth; the non-filtering mouthparts, with mandible lacking palp; the first pereiopod chela with excavated fingers and strongly tridentate fingertips; the asymmetrical second pereiopods (chelipeds), with the major chela bearing a double-fossa mechanism on the finger cutting edges; the ambulatory pereiopod dactylus armed with one large tooth and at least two small spinules on the ventral margin of the corpus, in addition to the terminal unguis; the lateral section of the uropodal diaeresis armed with five spiniform setae, the latter not extending to the lateral margin of the exopod; and the telson with two pairs of stout long cuspidate setae on dorsal surface and three pairs of strong, elongate spiniform setae on the posterior margin.

RevDate: 2020-04-01

Anker A (2020)

A remarkable burrow-dwelling alpheid shrimp, new genus and new species, from the tropical eastern Pacific (Malacostraca: Decapoda: Caridea).

Zootaxa, 4731(1):zootaxa.4731.1.5 pii:zootaxa.4731.1.5.

A new alpheid shrimp genus, Pachelpheus gen. nov., is established to accommodate Pachelpheus pachyacanthus sp. nov., described based on two specimens from the Las Perlas Archipelago, Pacific coast of Panama. Pachelpheus pachyacanthus sp. nov. appears to be an obligate symbiont dwelling in burrows of yet unknown infaunal hosts, on shallow near-shore subtidal sand flats. The main morphological characters of Pachelpheus gen. nov. are: (1) frontal margin of carapace with broadly rounded rostral projection, without orbital teeth; (2) sixth pleonite with articulated plate; (3) telson with two pairs of cuspidate setae dorsally, without anal tubercles; (4) eyes concealed in dorsal view, partly visible in lateral view; (5) chelipeds equal in size, symmetrical in shape, moderately enlarged, stout, carried extended; (6) cheliped carpus without rows of setae mesially; (7) cheliped fingers without snapping mechanism, each finger armed with one stout tooth; (8) second pereiopod carpus with five sub-articles; (9) third, fourth and fifth pereiopods with ischia armed with single robust cuspidate seta, meri armed with one to several unusually robust cuspidate setae; (10) second pleopod with appendix masculina in males only; (11) uropodal exopod and endopod with rows of slender spiniform setae on their distal margins; (12) uropodal diaeresis unusually thickened laterally, with two very stout spiniform setae; and (13) lateral lobe of the uropodal protopod rounded. The new genus appears to be morphologically most similar to Jengalpheops Anker Dworschak, 2007 and Leslibetaeus Anker, Poddoubtchenko Wehrtmann, 2006.

RevDate: 2020-04-01

Rolshausen G, Hallman U, Grande FD, et al (2020)

Expanding the mutualistic niche: parallel symbiont turnover along climatic gradients.

Proceedings. Biological sciences, 287(1924):20192311.

Keystone mutualisms, such as corals, lichens or mycorrhizae, sustain fundamental ecosystem functions. Range dynamics of these symbioses are, however, inherently difficult to predict because host species may switch between different symbiont partners in different environments, thereby altering the range of the mutualism as a functional unit. Biogeographic models of mutualisms thus have to consider both the ecological amplitudes of various symbiont partners and the abiotic conditions that trigger symbiont replacement. To address this challenge, we here investigate 'symbiont turnover zones'--defined as demarcated regions where symbiont replacement is most likely to occur, as indicated by overlapping abundances of symbiont ecotypes. Mapping the distribution of algal symbionts from two species of lichen-forming fungi along four independent altitudinal gradients, we detected an abrupt and consistent β-diversity turnover suggesting parallel niche partitioning. Modelling contrasting environmental response functions obtained from latitudinal distributions of algal ecotypes consistently predicted a confined altitudinal turnover zone. In all gradients this symbiont turnover zone is characterized by approximately 12°C average annual temperature and approximately 5°C mean temperature of the coldest quarter, marking the transition from Mediterranean to cool temperate bioregions. Integrating the conditions of symbiont turnover into biogeographic models of mutualisms is an important step towards a comprehensive understanding of biodiversity dynamics under ongoing environmental change.

RevDate: 2020-04-01
CmpDate: 2020-04-01

Nick P (2019)

Symbiotic secrets.

Protoplasma, 256(4):881-882.

RevDate: 2020-03-31

Vangelisti A, Turrini A, Sbrana C, et al (2020)

Gene expression in Rhizoglomus irregulare at two different time points of mycorrhiza establishment in Helianthus annuus roots, as revealed by RNA-seq analysis.

Mycorrhiza pii:10.1007/s00572-020-00950-2 [Epub ahead of print].

Arbuscular mycorrhizal fungi (AMF) play a fundamental role in plant growth and nutrition in natural and agricultural ecosystems. Despite the importance of such symbionts, the different developmental changes occurring during the AMF life cycle have not been fully elucidated at the molecular level. Here, the RNA-seq approach was used to investigate Rhizoglomus irregulare specific and common transcripts at two different time points of mycorrhizal establishment in Helianthus annuus in vivo. Four days after inoculation, transcripts related to cellular remodeling (actin and tubulin), cellular signaling (calmodulin, serine/threonine protein kinase, 14-3-3 protein, and calcium transporting ATPase), lipid metabolism (fatty acid desaturation, steroid hormone, and glycerophospholipid biosynthesis), and biosynthetic processes were detected. In addition to such transcripts, 16 days after inoculation, expressed genes linked to binding and catalytic activities; ion (K+, Ca2+, Fe2+, Zn2+, Mn2+, Pi, ammonia), sugar, and lipid transport; and those involved in vacuolar polyphosphate accumulation were found. Knowledge of transcriptomic changes required for symbiosis establishment and performance is of great importance to understand the functional role of AMF symbionts in food crop nutrition and health, and in plant diversity in natural ecosystems.

RevDate: 2020-03-31

Arcila F, J Meunier (2020)

Friend or foe? The apparent benefits of gregarine (Apicomplexa: Sporozoa) infection in the European earwig.

International journal for parasitology pii:S0020-7519(20)30057-6 [Epub ahead of print].

Studying the costs and benefits of host-parasite interactions is of central importance to shed light on the evolutionary drivers of host life history traits. Although gregarines (Apicomplexa: Sporozoa) are one of the most frequent parasites in the gut of invertebrates, the diversity of its potential impacts on a host remains poorly explored. In this study, we addressed this gap in knowledge by investigating the prevalence of natural infections by the gregarine Gregarina ovata and testing how these infections shape a large set of morphological, behavioural and physiological traits in the European earwig Forficula auricularia. Our results first show that G. ovata was present in 76.8% of 573 field-sampled earwigs, and that its prevalence was both higher in males compared with females and increased between July and September. The load of G. ovata in the infected individuals was higher in males than females, but this sex difference vanished during the season. Our experiments then surprisingly revealed apparent benefits of G. ovata infections. Food-deprived hosts survived longer when they exhibited high compared with low gregarine loads. Moreover, the presence of gregarines was associated with a reduced phenoloxidase activity, indicating a lower immune resistance or a higher immune tolerance of the infected hosts. By contrast, we found no effect of G. ovata presence and number on earwigs' development (eye distance, forceps length), activity, food consumption or resistance against a fungal pathogen. Overall, our findings suggest that G. ovata could be involved in a mutualistic relationship with the European earwig. Given the ubiquitous presence of gregarines among invertebrates, our data also suggest that this common member of insect gut flora could have a broad and positive role in the life history of many host species.

RevDate: 2020-03-31
CmpDate: 2020-03-31

Chuang JS, Frentz Z, S Leibler (2019)

Homeorhesis and ecological succession quantified in synthetic microbial ecosystems.

Proceedings of the National Academy of Sciences of the United States of America, 116(30):14852-14861.

The dynamics of ecological change following a major perturbation, known as succession, are influenced by random processes. Direct quantitation of the degree of contingency in succession requires chronological study of replicate ecosystems. We previously found that population dynamics in carefully controlled, replicated synthetic microbial ecosystems were strongly deterministic over several months. Here, we present simplified, two-species microbial ecosystems consisting of algae and ciliates, imaged in toto at single-cell resolution with fluorescence microscopy over a period of 1 to 2 weeks. To directly study succession in these ecosystems, we deliberately varied the initial cell abundances over replicates and quantified the ensuing dynamics. The distribution of abundance trajectories rapidly converged to a nearly deterministic path, with small fluctuations, despite variations in initial conditions, environmental perturbations, and intrinsic noise, indicative of homeorhesis. Homeorhesis was also observed for certain phenotypic variables, such as partitioning of the ciliates into distinct size classes and clumping of the algae. Although the mechanism of homeorhesis observed in these synthetic ecosystems remains to be elucidated, it is clear that it must emerge from the ways each species controls its own internal states, with respect to a diverse set of environmental conditions and ecological interactions.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Bermúdez-Barrientos JR, Ramírez-Sánchez O, Chow FW, et al (2020)

Disentangling sRNA-Seq data to study RNA communication between species.

Nucleic acids research, 48(4):e21.

Many organisms exchange small RNAs (sRNAs) during their interactions, that can target or bolster defense strategies in host-pathogen systems. Current sRNA-Seq technology can determine the sRNAs present in any symbiotic system, but there are very few bioinformatic tools available to interpret the results. We show that one of the biggest challenges comes from sequences that map equally well to the genomes of both interacting organisms. This arises due to the small size of the sRNAs compared to large genomes, and because a large portion of sequenced sRNAs come from genomic regions that encode highly conserved miRNAs, rRNAs or tRNAs. Here, we present strategies to disentangle sRNA-Seq data from samples of communicating organisms, developed using diverse plant and animal species that are known to receive or exchange RNA with their symbionts. We show that sequence assembly, both de novo and genome-guided, can be used for these sRNA-Seq data, greatly reducing the ambiguity of mapping reads. Even confidently mapped sequences can be misleading, so we further demonstrate the use of differential expression strategies to determine true parasite-derived sRNAs within host cells. We validate our methods on new experiments designed to probe the nature of the extracellular vesicle sRNAs from the parasitic nematode Heligmosomoides bakeri that get into mouse intestinal epithelial cells.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Hein AM, BT Martin (2020)

Information limitation and the dynamics of coupled ecological systems.

Nature ecology & evolution, 4(1):82-90.

The dynamics of large ecological systems result from vast numbers of interactions between individual organisms. Here, we develop mathematical theory to show that the rate of such interactions is inherently limited by the ability of organisms to gain information about one another. This phenomenon, which we call 'information limitation', is likely to be widespread in real ecological systems and can dictate both the rates of ecological interactions and long-run dynamics of interacting populations. We show how information limitation leads to sigmoid interaction rate functions that can stabilize antagonistic interactions and destabilize mutualistic ones; as a species or type becomes rare, information on its whereabouts also becomes rare, weakening coupling with consumers, pathogens and mutualists. This can facilitate persistence of consumer-resource systems, alter the course of pathogen infections within a host and enhance the rates of oceanic productivity and carbon export. Our findings may shed light on phenomena in many living systems where information drives interactions.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Manzano-Marı N A, Coeur d'acier A, Clamens AL, et al (2020)

Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems.

The ISME journal, 14(1):259-273.

Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera's. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera's. Additionally, we found that the Erwinia vitamin-biosynthetic genes not only compensate for Buchnera's deficiencies, but also provide a new nutritional function; whose genes have been horizontally acquired from a Sodalis-related bacterium. A subset of these genes have been subsequently transferred to a new Hamiltonella co-obligate symbiont in one specific Cinara lineage. These results show that the establishment and dynamics of multi-partner endosymbioses can be mediated by lateral gene transfers between co-ocurring symbionts.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Lynch JB, EY Hsiao (2019)

Microbiomes as sources of emergent host phenotypes.

Science (New York, N.Y.), 365(6460):1405-1409.

Microbial communities associated with animals exert powerful influences on host physiology, regulating metabolism and immune function, as well as complex host behaviors. The importance of host-microbiome interactions for maintaining homeostasis and promoting health raises evolutionarily complicated questions about how animals and their microbiomes have coevolved, and how these relationships affect the ways that animals interact with their environment. Here, we review the literature on the contributions of host factors to microbial community structure and corresponding influences of microbiomes on emergent host phenotypes. We focus in particular on animal behaviors as a basis for understanding potential roles for the microbiome in shaping host neurobiology.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Frazão N, Sousa A, Lässig M, et al (2019)

Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut.

Proceedings of the National Academy of Sciences of the United States of America, 116(36):17906-17915.

Bacteria evolve by mutation accumulation in laboratory experiments, but tempo and mode of evolution in natural environments are largely unknown. Here, we study the ubiquitous natural process of host colonization by commensal bacteria. We show, by experimental evolution of Escherichia coli in the mouse intestine, that the ecology of the gut controls the pace and mode of evolution of a new invading bacterial strain. If a resident E. coli strain is present in the gut, the invading strain evolves by rapid horizontal gene transfer (HGT), which precedes and outweighs evolution by accumulation of mutations. HGT is driven by 2 bacteriophages carried by the resident strain, which cause an epidemic phage infection of the invader. These dynamics are followed by subsequent evolution by clonal interference of genetically diverse lineages of phage-carrying (lysogenic) bacteria. We show that the genes uptaken by HGT enhance the metabolism of specific gut carbon sources and provide a fitness advantage to lysogenic invader lineages. A minimal dynamical model explains the temporal pattern of phage epidemics and the complex evolutionary outcome of phage-mediated selection. We conclude that phage-driven HGT is a key eco-evolutionary driving force of gut colonization-it accelerates evolution and promotes genetic diversity of commensal bacteria.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Hehenberger E, Gast RJ, PJ Keeling (2019)

A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis.

Proceedings of the National Academy of Sciences of the United States of America, 116(36):17934-17942.

Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Romero Picazo D, Dagan T, Ansorge R, et al (2019)

Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated.

The ISME journal, 13(12):2954-2968.

Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated subpopulations. The reconstruction of core genome-wide strains from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel life span and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Suzaki T, H Nishida (2019)

Autoregulation of Legume Nodulation by Sophisticated Transcriptional Regulatory Networks.

Molecular plant, 12(9):1179-1181.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Durante MK, Baums IB, Williams DE, et al (2019)

What drives phenotypic divergence among coral clonemates of Acropora palmata?.

Molecular ecology, 28(13):3208-3224.

Evolutionary rescue of populations depends on their ability to produce phenotypic variation that is heritable and adaptive. DNA mutations are the best understood mechanisms to create phenotypic variation, but other, less well-studied mechanisms exist. Marine benthic foundation species provide opportunities to study these mechanisms because many are dominated by isogenic stands produced through asexual reproduction. For example, Caribbean acroporid corals are long lived and reproduce asexually via breakage of branches. Fragmentation is often the dominant mode of local population maintenance. Thus, large genets with many ramets (colonies) are common. Here, we observed phenotypic variation in stress responses within genets following the coral bleaching events in 2014 and 2015 caused by high water temperatures. This was not due to genetic variation in their symbiotic dinoflagellates (Symbiodinium "fitti") because each genet of this coral species typically harbours a single strain of S. "fitti". Characterization of the microbiome via 16S tag sequencing correlated the abundance of only two microbiome members (Tepidiphilus, Endozoicomonas) with a bleaching response. Epigenetic changes were significantly correlated with the host's genetic background, the location of the sampled polyps within the colonies (e.g., branch vs. base of colony), and differences in the colonies' condition during the bleaching event. We conclude that long-term microenvironmental differences led to changes in the way the ramets methylated their genomes, contributing to the differential bleaching response. However, most of the variation in differential bleaching response among clonemates of Acropora palmata remains unexplained. This research provides novel data and hypotheses to help understand intragenet variability in stress phenotypes of sessile marine species.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Wang L, Sun Z, Su C, et al (2019)

A GmNINa-miR172c-NNC1 Regulatory Network Coordinates the Nodulation and Autoregulation of Nodulation Pathways in Soybean.

Molecular plant, 12(9):1211-1226.

Symbiotic root nodules are root lateral organs of plants in which nitrogen-fixing bacteria (rhizobia) convert atmospheric nitrogen to ammonia. The formation and number of nodules in legumes are precisely controlled by a rhizobia-induced signal cascade and host-controlled autoregulation of nodulation (AON). However, how these pathways are integrated and their underlying mechanisms are unclear. Here, we report that microRNA172c (miR172c) activates soybean (Glycine max) Rhizobia-Induced CLE1 (GmRIC1) and GmRIC2 by removing the transcriptional repression of these genes by Nodule Number Control 1 (NNC1), leading to the activation of the AON pathway. NNC1 interacts with GmNINa, the soybean ortholog of Lotus NODULE INCEPTION (NIN), and hampers its transcriptional activation of GmRIC1 and GmRIC2. Importantly, GmNINa acts as a transcriptional activator of miR172c. Intriguingly, NNC1 can transcriptionally repress miR172c expression, adding a negative feedback loop into the NNC1 regulatory network. Moreover, GmNINa interacts with NNC1 and can relieve the NNC1-mediated repression of miR172c transcription. Thus, the GmNINa-miR172c-NNC1 network is a master switch that coordinately regulates and optimizes NF and AON signaling, supporting the balance between nodulation and AON in soybean.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Li F, He X, Tang M, et al (2020)

Adaptation of plants to high-calcium content kart regions: possible involvement of symbiotic microorganisms and underlying mechanisms.

Brazilian journal of biology = Revista brasleira de biologia, 80(1):209-214.

Rhizosphere microorganisms and endophytes can help their hosts absorb nutrients and regulate the levels of plant hormones. Moreover, they can modulate the expressions of host genes, assist hosts in eliminating reactive oxygen species (ROS) and secreting volatile organic compounds. Therefore, rhizosphere microorganisms and endophytes are considered as determinant factors driving processes involved in the growth of host plants. However, the physiological and ecological functions, as well as the molecular mechanism underlying the behavior of rhizosphere microorganisms and endophytes in their role in the adaptive capacity of host plants in the karstic high-calcium environment have not been systematically studied. This review summarizes the physiological and molecular mechanisms of rhizosphere microorganisms and endophytes which help host plants to adapt to various kinds of adverse environments. The adaptive capacities of plants growing in adverse environments, partly, or totally, depends on microorganisms co-existing with the host plants.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Morikawa MK, SR Palumbi (2019)

Using naturally occurring climate resilient corals to construct bleaching-resistant nurseries.

Proceedings of the National Academy of Sciences of the United States of America, 116(21):10586-10591.

Ecological restoration of forests, meadows, reefs, or other foundational ecosystems during climate change depends on the discovery and use of individuals able to withstand future conditions. For coral reefs, climate-tolerant corals might not remain tolerant in different environments because of widespread environmental adjustment of coral physiology and symbionts. Here, we test if parent corals retain their heat tolerance in nursery settings, if simple proxies predict successful colonies, and if heat-tolerant corals suffer lower growth or survival in normal settings. Before the 2015 natural bleaching event in American Samoa, we set out 800 coral fragments from 80 colonies of four species selected by prior tests to have a range of intraspecific natural heat tolerance. After the event, nursery stock from heat-tolerant parents showed two to three times less bleaching across species than nursery stock from less tolerant parents. They also retained higher individual genetic diversity through the bleaching event than did less heat-tolerant corals. The three best proxies for thermal tolerance were response to experimental heat stress, location on the reef, and thermal microclimate. Molecular biomarkers were also predictive but were highly species specific. Colony genotype and symbiont genus played a similarly strong role in predicting bleaching. Combined, our results show that selecting for host and symbiont resilience produced a multispecies coral nursery that withstood multiple bleaching events, that proxies for thermal tolerance in restoration can work across species and be inexpensive, and that different coral clones within species reacted very differently to bleaching.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Lagunas B, Achom M, Bonyadi-Pour R, et al (2019)

Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula.

Molecular plant, 12(6):833-846.

Understanding how plants respond to nitrogen in their environment is crucial for determining how they use it and how the nitrogen use affects other processes related to plant growth and development. Under nitrogen limitation the activity and affinity of uptake systems is increased in roots, and lateral root formation is regulated in order to adapt to low nitrogen levels and scavenge from the soil. Plants in the legume family can form associations with rhizobial nitrogen-fixing bacteria, and this association is tightly regulated by nitrogen levels. The effect of nitrogen on nodulation has been extensively investigated, but the effects of nodulation on plant nitrogen responses remain largely unclear. In this study, we integrated molecular and phenotypic data in the legume Medicago truncatula and determined that genes controlling nitrogen influx are differently expressed depending on whether plants are mock or rhizobia inoculated. We found that a functional autoregulation of nodulation pathway is required for roots to perceive, take up, and mobilize nitrogen as well as for normal root development. Our results together revealed that autoregulation of nodulation, root development, and the location of nitrogen are processes balanced by the whole plant system as part of a resource-partitioning mechanism.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Hager FA, K Krausa (2019)

Acacia Ants Respond to Plant-Borne Vibrations Caused by Mammalian Browsers.

Current biology : CB, 29(5):717-725.e3.

Living in the African savanna is dangerous, especially for plants. Many plants therefore engage in mutualism with ants, in which plants provide food and shelter in exchange for protection against herbivores. Ants become alarmed when the plant takes on some sort of damage. They immediately emerge from their plant shelter and aggressively defend the plant. Mammalian herbivores can have devastating effects on trees by browsing, breaking tree branches, stripping bark, and pushing over entire trees. However, mutualistic ants substantially reduce the amount of damage. To efficiently protect the tree, ants need to rapidly react together when the tree is under attack. Here, we show that the acacia ant Crematogaster mimosae defends its host tree by exploiting plant-borne vibrations caused by browsers feeding on the tree. Experiments with controlled vibrations show that ants discriminate browser-induced vibrations from those induced by wind, become alarmed, and patrol on the branches. Browser-induced vibrations serve as a long-distance alarm cue. The vibrations propagate through the whole acacia tree and trigger ants' defensive behavior, even on the other side of the tree. Furthermore, the ants make use of tropotactic directional vibration sensing to orient to the attacked part of the tree and fight back the attacker.

RevDate: 2020-03-29

Zhang C, Qi M, Zhang X, et al (2020)

Rhizobial infection triggers systemic transport of endogenous RNAs between shoots and roots in soybean.

Science China. Life sciences pii:10.1007/s11427-019-1608-7 [Epub ahead of print].

Legumes have evolved a symbiotic relationship with rhizobial bacteria and their roots form unique nitrogen-fixing organs called nodules. Studies have shown that abiotic and biotic stresses alter the profile of gene expression and transcript mobility in plants. However, little is known about the systemic transport of RNA between roots and shoots in response to rhizobial infection on a genome-wide scale during the formation of legume-rhizobia symbiosis. In our study, we found that two soybean (Glycine max) cultivars, Peking and Williams, show a high frequency of single nucleotide polymorphisms; this allowed us to characterize the origin and mobility of transcripts in hetero-grafts of these two cultivars. We identified 4,552 genes that produce mobile RNAs in soybean, and found that rhizobial infection triggers mass transport of mRNAs between shoots and roots at the early stage of nodulation. The majority of these mRNAs are of relatively low abundance and their transport occurs in a selective manner in soybean plants. Notably, the mRNAs that moved from shoots to roots at the early stage of nodulation were enriched in many nodule-related responsive processes. Moreover, the transcripts of many known symbiosis-related genes that are induced by rhizobial infection can move between shoots and roots. Our findings provide a deeper understanding of endogenous RNA transport in legume-rhizobia symbiotic processes.

RevDate: 2020-03-28

Roy P, Achom M, Wilkinson H, et al (2020)

Symbiotic Outcome Modified by the Diversification from 7 to over 700 Nodule-Specific Cysteine-Rich Peptides.

Genes, 11(4): pii:genes11040348.

Legume-rhizobium symbiosis represents one of the most successfully co-evolved mutualisms. Within nodules, the bacterial cells undergo distinct metabolic and morphological changes and differentiate into nitrogen-fixing bacteroids. Legumes in the inverted repeat lacking clade (IRLC) employ an array of defensin-like small secreted peptides (SSPs), known as nodule-specific cysteine-rich (NCR) peptides, to regulate bacteroid differentiation and activity. While most NCRs exhibit bactericidal effects in vitro, studies confirm that inside nodules they target the bacterial cell cycle and other cellular pathways to control and extend rhizobial differentiation into an irreversible (or terminal) state where the host gains control over bacteroids. While NCRs are well established as positive regulators of effective symbiosis, more recent findings also suggest that NCRs affect partner compatibility. The extent of bacterial differentiation has been linked to species-specific size and complexity of the NCR gene family that varies even among closely related species, suggesting a more recent origin of NCRs followed by rapid expansion in certain species. NCRs have diversified functionally, as well as in their expression patterns and responsiveness, likely driving further functional specialisation. In this review, we evaluate the functions of NCR peptides and their role as a driving force underlying the outcome of rhizobial symbiosis, where the plant is able to determine the outcome of rhizobial interaction in a temporal and spatial manner.

RevDate: 2020-03-28

Gusmão LC, Van Deusen V, Daly M, et al (2020)

Origin and evolution of the symbiosis between sea anemones (Cnidaria, Anthozoa, Actiniaria) and hermit crabs, with additional notes on anemone-gastropod associations.

Molecular phylogenetics and evolution pii:S1055-7903(20)30077-4 [Epub ahead of print].

The anemone-crab mutualism is ubiquitous in temperate and tropical marine environments. In this symbiosis, one or more anemones live on a shell inhabited by a hermit crab and reciprocal phoretic, trophic, and defensive benefits are exchanged between the partners. Sea anemone-hermit crab symbionts belong to three families: Hormathiidae (Calliactis and Paracalliactis), Sagartiidae (Carcinactis and Verrillactis), and Actiniidae (Stylobates). Hermit crabs establish most partnerships by detaching anemones and placing them on their shell; sea anemones can also mount shells unaided, triggered by a mollusc-derived substance in the periostracum of the shell. At least partial cooperation by the anemones is necessary for successful establishment of the symbiosis. Here, we expand the evolutionary framework provided by Gusmão and Daly (2010) for hormathiid symbionts by generating a phylogeny with at least one member of each actiniarian symbiotic genus with hermit crabs using five molecular markers (16S, 12S, 18S, 28S, CO3). We not only corroborated the results from Gusmão and Daly (2010) by finding two origins of hermit crab symbiosis within Hormathiidae, but also find additional origins for hermit crab symbiosis within Actiniaria. We provide for the first time evidence of a close relationship between symbionts Carcinactis dolosa and V. paguri. The ability to secrete chitin by the ectoderm of the column is inferred to be broadly convergent within Actiniaria whereas the secretion of a chitinous carcinoecium by the pedal disc is a distinct but convergent morphological adaptation of several lineages within Actiniaria. Our finding of multiple origins for both the hermit crab and gastropod symbioses suggests that the shell-mounting behavior might only have been the precursor of the hermit crab association among Calliactis spp.

RevDate: 2020-03-27

Rapport DJ (2007)

Sustainability science: an ecohealth perspective.

Sustainability science, 2(1):77-84.

Sustainability science is emerging as a transdisciplinary effort to come to grips with the much-needed symbiosis between human activity and the environment. While there is recognition that conventional economic growth must yield to policies that foster sustainable development, this has not yet occurred on any broad scale. Rather, there is clear evidence that the Earth's ecosystems and landscapes continue to degrade as a consequence of the cumulative impact of human activities. Taking an ecohealth approach to sustainability science provides a unique perspective on both the goals and the means to achieve sustainability. The goals should be the restoration of full functionality to the Earth's ecosystems and landscapes, as measured by the key indicators of health: resilience, organization, vitality (productivity), and the absence of ecosystem distress syndrome. The means should be the coordinated (spatially and temporally) efforts to modify human behaviors to reduce cumulative stress impacts. Achieving ecosystem health should become the cornerstone of sustainability policy-for healthy ecosystems are the essential precondition for achieving sustainable livelihoods, human health, and many other societal objectives, as reflected in the Millennium Development Goals.

RevDate: 2020-03-27

Velichko NS, Grinev VS, YP Fedonenko (2020)

Characterization of biopolymers produced by planktonic and biofilm cells of Herbaspirillum lusitanum P6-12.

Journal of applied microbiology [Epub ahead of print].

AIMS: The goal of this study was to characterize the Herbaspirillum lusitanum P6-12 biopolymers under various environmental conditions.

METHODS AND RESULTS: Differences in biopolymers composition from planktonic and biofilm cells of H. lusitanum strain P6-12 were analyzed using Fourier transform infrared spectroscopy (FTIR), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and colorimetric and gas-liquid chromatography (GLC). A high degree of polymer separation and purification was achieved by ultracentrifugation, and column chromatography allowed us to identify the chemical differences between biopolymers from biofilm and planktonic Herbaspirillum lusitanum. The planktonic cells of H. lusitanum P6-12 had capsules containing two high-molecular-weight glycoconjugates (CPS-I and CPS-II) of a lipopolysaccharide (LPS) nature and one EPS as a lipid-polysaccharide complex. The EPS, CPS-I, CPS-II had different monosaccharide and lipid compositions. The extracellular polymeric matrix (EPM) produced by the biofilm cells was mostly proteinaceous, with a small amount of carbohydrates (up to 3%). From the biofilm culture medium, a free extracellular polymeric substance (fEPS) was obtained that contained proteins and carbohydrates (up to 7%). The cells outside the biofilm produced capsules (CPSFBC) that consisted of carbohydrates (up to 10%), proteins (up to 16%), and lipids.

CONCLUSIONS: During biofilm formation, the bacteria secreted surface biopolymers that differed from those of the planktonic cells. The heterogeneity of the polysaccharidic polymers of the H. lusitanum P6-12 surface is probably conditioned by their different functions in plant colonization and formation of an efficient symbiosis, as well as in cell adaptation to existence in plant tissues.

The results of the study permit a better understanding of the physiological properties of the biopolymers, e.g., in plant-microbe interactions.

RevDate: 2020-03-26

Dunkley K, Ward AJW, Perkins SE, et al (2020)

To clean or not to clean: Cleaning mutualism breakdown in a tidal environment.

Ecology and evolution, 10(6):3043-3054 pii:ECE36120.

The dynamics and prevalence of mutualistic interactions, which are responsible for the maintenance and structuring of all ecological communities, are vulnerable to changes in abiotic and biotic environmental conditions. Mutualistic outcomes can quickly shift from cooperation to conflict, but it unclear how resilient and stable mutualistic outcomes are to more variable conditions. Tidally controlled coral atoll lagoons that experience extreme diurnal environmental shifts thus provide a model from which to test plasticity in mutualistic behavior of dedicated (formerly obligate) cleaner fish, which acquire all their food resources through client interactions. Here, we investigated cleaning patterns of a model cleaner fish species, the bluestreak wrasse (Labroides dimidiatus), in an isolated tidal lagoon on the Great Barrier Reef. Under tidally restricted conditions, uniquely both adults and juveniles were part-time facultative cleaners, pecking on Isopora palifera coral. The mutualism was not completely abandoned, with adults also wandering across the reef in search of clients, rather than waiting at fixed site cleaning stations, a behavior not yet observed at any other reef. Contrary to well-established patterns for this cleaner, juveniles appeared to exploit the system, by biting ("cheating") their clients more frequently than adults. We show for the first time, that within this variable tidal environment, where mutualistic cleaning might not represent a stable food source, the prevalence and dynamics of this mutualism may be breaking down (through increased cheating and partial abandonment). Environmental variability could thus reduce the pervasiveness of mutualisms within our ecosystems, ultimately reducing the stability of the system.

RevDate: 2020-03-26

Casarrubia S, Martino E, Daghino S, et al (2020)

Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus.

Frontiers in microbiology, 11:341.

The success of Ericaceae in stressful habitats enriched in heavy metals has been ascribed to the distinctive abilities of their mycorrhizal fungal partners to withstand heavy metal stress and to enhance metal tolerance in the host plant. Whereas heavy metal tolerance has been extensively investigated in some ericoid mycorrhizal (ERM) fungi, the molecular and cellular mechanisms that extend tolerance to the host plant are currently unknown. Here, we show a reduced Cd content in Cd-exposed mycorrhizal roots of Vaccinium myrtillus colonized by a metal tolerant isolate of the fungus Oidiodendron maius as compared to non-mycorrhizal roots. To better understand this phenotype, we applied Next Generation Sequencing technologies to analyze gene expression in V. myrtillus and O. maius Zn grown under normal and Cd-stressed conditions, in the free living and in the mycorrhizal status. The results clearly showed that Cd had a stronger impact on plant gene expression than symbiosis, whereas fungal gene expression was mainly regulated by symbiosis. The higher abundance of transcripts coding for stress related proteins in non-mycorrhizal roots may be related to the higher Cd content. Regulated plant metal transporters have been identified that may play a role in reducing Cd content in mycorrhizal roots exposed to this metal.

RevDate: 2020-03-26

Rahman MA, Parvin M, Das U, et al (2020)

Arbuscular Mycorrhizal Symbiosis Mitigates Iron (Fe)-Deficiency Retardation in Alfalfa (Medicago sativa L.) Through the Enhancement of Fe Accumulation and Sulfur-Assisted Antioxidant Defense.

International journal of molecular sciences, 21(6): pii:ijms21062219.

Iron (Fe)-deficiency is one of the major constraints affecting growth, yield and nutritional quality in plants. This study was performed to elucidate how arbuscular mycorrhizal fungi (AMF) alleviate Fe-deficiency retardation in alfalfa (Medicago sativa L.). AMF supplementation improved plant biomass, chlorophyll score, Fv/Fm (quantum efficiency of photosystem II), and Pi_ABS (photosynthesis performance index), and reduced cell death, electrolyte leakage, and hydrogen peroxide accumulation in alfalfa. Moreover, AMF enhanced ferric chelate reductase activity as well as Fe, Zn, S and P in alfalfa under Fe-deficiency. Although Fe-transporters (MsIRT1 and MsNramp1) did not induce in root but MsFRO1 significantly induced by AMF under Fe deficiency in roots, suggesting that AMF-mediated Fe enhancement is related to the bioavailability of Fe at rhizosphere/root apoplast rather than the upregulation of Fe transporters under Fe deficiency in alfalfa. Several S-transporters (MsSULTR1;1, MsSULTR1;2, MsSULTR1;3, and MsSULTR3;1) markedly increased following AMF supplementation with or without Fe-deficiency alfalfa. Our study further suggests that Fe uptake system is independently influenced by AMF regardless of the S status in alfalfa. However, the increase of S in alfalfa is correlated with the elevation of GR and S-metabolites (glutathione and cysteine) associated with antioxidant defense under Fe deficiency.

RevDate: 2020-03-26

Doin de Moura GG, Remigi P, Masson-Boivin C, et al (2020)

Experimental Evolution of Legume Symbionts: What Have We Learnt?.

Genes, 11(3): pii:genes11030339.

Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. They likely emerged and diversified through independent horizontal transfers of key symbiotic genes. To replay the evolution of a new rhizobium genus under laboratory conditions, the symbiotic plasmid of Cupriavidus taiwanensis was introduced in the plant pathogen Ralstonia solanacearum, and the generated proto-rhizobium was submitted to repeated inoculations to the C. taiwanensis host, Mimosa pudica L.. This experiment validated a two-step evolutionary scenario of key symbiotic gene acquisition followed by genome remodeling under plant selection. Nodulation and nodule cell infection were obtained and optimized mainly via the rewiring of regulatory circuits of the recipient bacterium. Symbiotic adaptation was shown to be accelerated by the activity of a mutagenesis cassette conserved in most rhizobia. Investigating mutated genes led us to identify new components of R. solanacearum virulence and C. taiwanensis symbiosis. Nitrogen fixation was not acquired in our short experiment. However, we showed that post-infection sanctions allowed the increase in frequency of nitrogen-fixing variants among a non-fixing population in the M. pudica-C. taiwanensis system and likely allowed the spread of this trait in natura. Experimental evolution thus provided new insights into rhizobium biology and evolution.

RevDate: 2020-03-26

Storey MA, Andreassend SK, Bracegirdle J, et al (2020)

Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts.

mBio, 11(2): pii:mBio.02997-19.

Marine sponges have been a prolific source of unique bioactive compounds that are presumed to act as a deterrent to predation. Many of these compounds have potential therapeutic applications; however, the lack of efficient and sustainable synthetic routes frequently limits clinical development. Here, we describe a metagenomic investigation of Mycale hentscheli, a chemically gifted marine sponge that possesses multiple distinct chemotypes. We applied shotgun metagenomic sequencing, hybrid assembly of short- and long-read data, and metagenomic binning to obtain a comprehensive picture of the microbiome of five specimens, spanning three chemotypes. Our data revealed multiple producing species, each having relatively modest secondary metabolomes, that contribute collectively to the chemical arsenal of the holobiont. We assembled complete genomes for multiple new genera, including two species that produce the cytotoxic polyketides pateamine and mycalamide, as well as a third high-abundance symbiont harboring a proteusin-type biosynthetic pathway that appears to encode a new polytheonamide-like compound. We also identified an additional 188 biosynthetic gene clusters, including a pathway for biosynthesis of peloruside. These results suggest that multiple species cooperatively contribute to defensive symbiosis in M. hentscheli and reveal that the taxonomic diversity of secondary-metabolite-producing sponge symbionts is larger and richer than previously recognized.IMPORTANCEMycale hentscheli is a marine sponge that is rich in bioactive small molecules. Here, we use direct metagenomic sequencing to elucidate highly complete and contiguous genomes for the major symbiotic bacteria of this sponge. We identify complete biosynthetic pathways for the three potent cytotoxic polyketides which have previously been isolated from M. hentscheli Remarkably, and in contrast to previous studies of marine sponges, we attribute each of these metabolites to a different producing microbe. We also find that the microbiome of M. hentscheli is stably maintained among individuals, even over long periods of time. Collectively, our data suggest a cooperative mode of defensive symbiosis in which multiple symbiotic bacterial species cooperatively contribute to the defensive chemical arsenal of the holobiont.

RevDate: 2020-03-26

Clarke DJ (2020)

Photorhabdus: a tale of contrasting interactions.

Microbiology (Reading, England) [Epub ahead of print].

Different model systems have, over the years, contributed to our current understanding of the molecular mechanisms underpinning the various types of interaction between bacteria and their animal hosts. The genus Photorhabdus comprises Gram-negative insect pathogenic bacteria that are normally found as symbionts that colonize the gut of the infective juvenile stage of soil-dwelling nematodes from the family Heterorhabditis. The nematodes infect susceptible insects and release the bacteria into the insect haemolymph where the bacteria grow, resulting in the death of the insect. At this stage the nematodes feed on the bacterial biomass and, following several rounds of reproduction, the nematodes develop into infective juveniles that leave the insect cadaver in search of new hosts. Therefore Photorhabdus has three distinct and obligate roles to play during this life-cycle: (1) Photorhabdus must kill the insect host; (2) Photorhabdus must be capable of supporting nematode growth and development; and (3) Photorhabdus must be able to colonize the gut of the next generation of infective juveniles before they leave the insect cadaver. In this review I will discuss how genetic analysis has identified key genes involved in mediating, and regulating, the interaction between Photorhabdus and each of its invertebrate hosts. These studies have resulted in the characterization of several new families of toxins and a novel inter-kingdom signalling molecule and have also uncovered an important role for phase variation in the regulation of these different roles.

RevDate: 2020-03-26
CmpDate: 2020-03-26

Blacher E, Bashiardes S, Shapiro H, et al (2019)

Potential roles of gut microbiome and metabolites in modulating ALS in mice.

Nature, 572(7770):474-480.

Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disorder, in which the clinical manifestations may be influenced by genetic and unknown environmental factors. Here we show that ALS-prone Sod1 transgenic (Sod1-Tg) mice have a pre-symptomatic, vivarium-dependent dysbiosis and altered metabolite configuration, coupled with an exacerbated disease under germ-free conditions or after treatment with broad-spectrum antibiotics. We correlate eleven distinct commensal bacteria at our vivarium with the severity of ALS in mice, and by their individual supplementation into antibiotic-treated Sod1-Tg mice we demonstrate that Akkermansia muciniphila (AM) ameliorates whereas Ruminococcus torques and Parabacteroides distasonis exacerbate the symptoms of ALS. Furthermore, Sod1-Tg mice that are administered AM are found to accumulate AM-associated nicotinamide in the central nervous system, and systemic supplementation of nicotinamide improves motor symptoms and gene expression patterns in the spinal cord of Sod1-Tg mice. In humans, we identify distinct microbiome and metabolite configurations-including reduced levels of nicotinamide systemically and in the cerebrospinal fluid-in a small preliminary study that compares patients with ALS with household controls. We suggest that environmentally driven microbiome-brain interactions may modulate ALS in mice, and we call for similar investigations in the human form of the disease.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Kusakabe S, Higasitani N, Kaneko T, et al (2020)

Lotus Accessions Possess Multiple Checkpoints Triggered by Different Type III Secretion System Effectors of the Wide-Host-Range Symbiont Bradyrhizobium elkanii USDA61.

Microbes and environments, 35(1):.

Bradyrhizobium elkanii, a rhizobium with a relatively wide host range, possesses a functional type III secretion system (T3SS) that is involved in symbiotic incompatibility against Rj4-genotype soybean (Glycine max) and some accessions of mung bean (Vigna radiata). To expand our knowledge on the T3SS-mediated partner selection mechanism in the symbiotic legume-rhizobia association, we inoculated three Lotus experimental accessions with wild-type and T3SS-mutant strains of B. elkanii USDA61. Different responses were induced by T3SS in a host genotype-dependent manner. Lotus japonicus Gifu inhibited infection; L. burttii allowed infection, but inhibited nodule maturation at the post-infection stage; and L. burttii and L. japonicus MG-20 both displayed a nodule early senescence-like response. By conducting inoculation tests with mutants of previously reported and newly identified effector protein genes of B. elkanii USDA61, we identified NopF as the effector protein triggering the inhibition of infection, and NopM as the effector protein triggering the nodule early senescence-like response. Consistent with these results, the B. elkanii USDA61 gene for NopF introduced into the Lotus symbiont Mesorhizobium japonicum induced infection inhibition in L. japonicus Gifu, but did not induce any response in L. burttii or L. japonicus MG-20. These results suggest that Lotus accessions possess at least three checkpoints to eliminate unfavorable symbionts, including the post-infection stage, by recognizing different T3SS effector proteins at each checkpoint.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Rejili M, Ruiz-Argueso T, M Mars (2020)

Novel putative Mesorhizobium and Ensifer genomospecies together with a novel symbiovar psoraleae nodulate legumes of agronomic interest grown in Tunisia.

Systematic and applied microbiology, 43(2):126067.

Forty rhizobial strains were isolated from Lotus creticus, L. pusillus and Bituminaria bituminosa endemic to Tunisia, and they belonged to the Mesorhizobium and Ensifer genera based on 16S rDNA sequence phylogeny. According to the concatenated recA and glnII sequence-based phylogeny, four Bituminaria isolates Pb5, Pb12, Pb8 and Pb17 formed a monophyletic group with Mesorhizobium chacoense ICMP14587T, whereas four other strains Pb1, Pb6, Pb13 and Pb15 formed two separate lineages within the Ensifer genus. Among the L. pusillus strains, Lpus9 and Lpus10 showed a 96% identical nucleotide with Ensifer meliloti CCBAU83493T; whereas six other strains could belong to previously undescribed Mesorhizobium and Ensifer species. For L. creticus strains, Lcus37, Lcus39 and Lcus44 showed 98% sequence identity with Ensifer aridi JNVU TP6, and Lcus42 shared a 96% identical nucleotide with Ensifer meliloti CCBAU83493T; whereas another four strains were divergent from all the described Ensifer and Mesorhizobium species. The analysis of the nodC gene-based phylogeny identified four symbiovar groups; Mesorhizobium sp. sv. anthyllidis (Lpus3 and Lpus11 from L. pusillus, Lcus43 from L. creticus), Ensifer medicae sv. meliloti (four strains from L. creticus and two strains from L. pusillus), E. meliloti sv. meliloti (four from L. creticus, four from L. pusillus and four from B. bituminosa). In addition, four B. bituminosa strains (Pb5, Pb8, Pb12, and Pb17) displayed a distinctive nodC sequence distant from those of other symbiovars described to date. According to their symbiotic gene sequences and host range, the B. bituminosa symbionts (Pb5, Pb8, Pb12 and Pb17) would represent a new symbiovar of M. chacoense for which sv. psoraleae is proposed.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Yuan K, Reckling M, Ramirez MDA, et al (2020)

Characterization of Rhizobia for the Improvement of Soybean Cultivation at Cold Conditions in Central Europe.

Microbes and environments, 35(1):.

In central Europe, soybean cultivation is gaining increasing importance to reduce protein imports from overseas and make cropping systems more sustainable. In the field, despite the inoculation of soybean with commercial rhizobia, its nodulation is low. In many parts of Europe, limited information is currently available on the genetic diversity of rhizobia and, thus, biological resources for selecting high nitrogen-fixing rhizobia are inadequate. These resources are urgently needed to improve soybean production in central Europe. The objective of the present study was to identify strains that have the potential to increase nitrogen fixation by and the yield of soybean in German soils. We isolated and characterized 77 soybean rhizobia from 18 different sampling sites. Based on a multilocus sequence analysis (MLSA), 71% of isolates were identified as Bradyrhizobium and 29% as Rhizobium. A comparative analysis of the nodD and nifH genes showed no significant differences, which indicated that the soybean rhizobia symbiotic genes in the present study belong to only one type. One isolate, GMF14 which was tolerant of a low temperature (4°C), exhibited higher nitrogen fixation in root nodules and a greater plant biomass than USDA 110 under cold conditions. These results strongly suggest that some indigenous rhizobia enhance biological nitrogen fixation and soybean yield due to their adaption to local conditions.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Ferraz Helene LC, O'Hara G, M Hungria (2020)

Characterization of Bradyrhizobium strains indigenous to Western Australia and South Africa indicates remarkable genetic diversity and reveals putative new species.

Systematic and applied microbiology, 43(2):126053.

Bradyrhizobium are N2-fixing microsymbionts of legumes with relevant applications in agricultural sustainability, and we investigated the phylogenetic relationships of conserved and symbiotic genes of 21 bradyrhizobial strains. The study included strains from Western Australia (WA), isolated from nodules of Glycine spp. the country is one genetic center for the genus and from nodules of other indigenous legumes grown in WA, and strains isolated from forage Glycine sp. grown in South Africa. The 16S rRNA phylogeny divided the strains in two superclades, of B. japonicum and B. elkanii, but with low discrimination among the species. The multilocus sequence analysis (MLSA) with four protein-coding housekeeping genes (dnaK, glnII, gyrB and recA) pointed out seven groups as putative new species, two within the B. japonicum, and five within the B. elkanii superclades. The remaining eleven strains showed higher similarity with six species, B. lupini, B. liaoningense, B. yuanmingense, B. subterraneum, B. brasilense and B. retamae. Phylogenetic analysis of the nodC symbiotic gene clustered 13 strains in three different symbiovars (sv. vignae, sv. genistearum and sv. retamae), while seven others might compose new symbiovars. The genetic profiles of the strains evaluated by BOX-PCR revealed high intra- and interspecific diversity. The results point out the high level of diversity still to be explored within the Bradyrhizobium genus, and further studies might confirm new species and symbiovars.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Wackett LP (2019)

Rhizobial strains.

Environmental microbiology reports, 11(4):616-617.

RevDate: 2020-03-24

Wang C, Cheng T, Li X, et al (2020)

Metronidazole-Treated Porphyromonas gingivalis Persisters Invade Human Gingival Epithelial Cells and Perturb Innate Responses.

Antimicrobial agents and chemotherapy pii:AAC.02529-19 [Epub ahead of print].

Periodontitis as a biofilm-associated inflammatory disease is highly prevalent worldwide. It severely affects oral health and yet closely links to systemic diseases like diabetes and cardiovascular disease. Porphyromonas gingivalis as a 'keystone' periodontopathogen drives the shift of microbe-host symbiosis to dysbiosis, and critically contributes to the pathogenesis of periodontitis. Persisters are a tiny subset of biofilm-associated microbes highly tolerant to lethal treatment of antimicrobials, and notably metronidazole-tolerant P. gingivalis persisters have recently been identified by our group. This study further explored the interactive profiles of metronidazole-treated P. gingivalis persisters (M-PgPs) with human gingival epithelial cells (HGECs). P. gingivalis cells (ATCC 33277) at stationary phase were treated with lethal dosage of metronidazole (100 μg/ml, 6 hours) for generating M-PgPs. The interaction of M-PgPs with HGECs was assessed by microscopy, flow cytometry, cytokine profiling and qPCR. We demonstrated that the overall morphology and ultra-cellular structure of M-PgPs remained unchanged. Importantly, M-PgPs maintained the capabilities to adhere to and invade into HGECs. Moreover, M-PgPs significantly suppressed pro-inflammatory cytokine expression in HGECs at a comparable level with the untreated P. gingivalis cells, through the thermo-sensitive components. The present study reveals that P. gingivalis persisters induced by lethal treatment of antibiotics could maintain their capabilities to adhere to and invade into human gingival epithelial cells, and perturb the innate host responses. Novel strategies and approaches need to be developed for tackling P. gingivalis and favourably modulating the dysregulated immuno-inflammatory responses for oral/periodontal health and general wellbeing.

RevDate: 2020-03-24

Shitole AA, Raut P, Giram P, et al (2020)

Poly (vinylpyrrolidone)‑iodine engineered poly (ε-caprolactone) nanofibers as potential wound dressing materials.

Materials science & engineering. C, Materials for biological applications, 110:110731.

Facilitating the process of wound healing and effective treatment of wounds remains a serious challenge in healthcare. Wound dressing materials play a major role in the protection of wounds and in accelerating the natural healing process. In the present study, novel core/shell (c/s) nanofibrous mats of poly(vinyl pyrrolidone)‑iodine (PVPI) and polycaprolactone (PCL) were fabricated using a co-axial electrospinning process followed by their surface modification with poly-l-lysine. The developed nanofibrous mats were extensively characterized for their physicochemical properties using various analytical techniques. The core/shell structure of the PVP-I/PCL nanofibers was confirmed using TEM analysis. The PVP-I release studies showed an initial burst phase followed by a sustained release pattern of PVP-I over a period of 30 days. The developed nanofibers exhibited higher BSA and fibrinogen adsorption as compared to pristine PCL. Cytotoxicity studies using MTT assay demonstrated that the PVP-I/PCL (c/s) nanofibers were cytocompatible at optimized PVP-I concentration (3 wt%). The PCL-poly-l-lysine and PVP-I/PCL-poly-l-lysine nanofibers exhibited higher cell viability (24.2% and 21.4% higher at day 7) when compared to uncoated PCL and PVP-I/PCL nanofibers. The PVP-I/PCL nanofibers showed excellent antimicrobial activity against both Gram-positive (S. aureus) and Gram-negative (E. coli) bacteria. The inflammatory response of Mouse RAW 264.7 macrophage cells towards the nanofibers was studied using RT-PCR. It revealed that the pro-inflammatory cytokines (TNF-α and IL-1β) were significantly upregulated on PCL nanofibers, while their expression was comparatively lower on poly-l-lysine coated PCL or PVP-I/PCL(c/s) nanofibers. Overall, the study highlights the ability of poly-l-lysine coated PVP-I/PCL (c/s) nanofibers as potential wound dressing materials effectively facilitating the early stage wound healing and repair process by virtue of their selective modulation of inflammation, cell adhesion and antimicrobial properties.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Živković D, John S, Verin M, et al (2019)

Neutral genomic signatures of host-parasite coevolution.

BMC evolutionary biology, 19(1):230.

BACKGROUND: Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build an eco-evolutionary model, where neutral genomic changes over time are driven by a single selected locus in hosts and parasites via a simple biallelic gene-for-gene or matching-allele interaction. This coevolutionary process may lead to cyclic changes in the sizes of the interacting populations.

RESULTS: We investigate if and when these changes can be observed in the site frequency spectrum of neutral polymorphisms from host and parasite full genome data. We show that changes of the host population size are too smooth to be observable in its polymorphism pattern over the course of time. Conversely, the parasite population may undergo a series of strong bottlenecks occurring on a slower relative time scale, which may lead to observable changes in a time series sample. We also extend our results to cases with 1) several parasites per host accelerating relative time, and 2) multiple parasite generations per host generation slowing down rescaled time.

CONCLUSIONS: Our results show that time series sampling of host and parasite populations with full genome data are crucial to understand if and how coevolution occurs. This model provides therefore a framework to interpret and draw inference from genome-wide polymorphism data of interacting species.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Fazzino L, Anisman J, Chacón JM, et al (2020)

Lytic bacteriophage have diverse indirect effects in a synthetic cross-feeding community.

The ISME journal, 14(1):123-134.

Bacteriophage shape the composition and function of microbial communities. Yet it remains difficult to predict the effect of phage on microbial interactions. Specifically, little is known about how phage influence mutualisms in networks of cross-feeding bacteria. We mathematically modeled the impacts of phage in a synthetic microbial community in which Escherichia coli and Salmonella enterica exchange essential metabolites. In this model, independent phage attack of either species was sufficient to temporarily inhibit both members of the mutualism; however, the evolution of phage resistance facilitated yields similar to those observed in the absence of phage. In laboratory experiments, attack of S. enterica with P22vir phage followed these modeling expectations of delayed community growth with little change in the final yield of bacteria. In contrast, when E. coli was attacked with T7 phage, S. enterica, the nonhost species, reached higher yields compared with no-phage controls. T7 infection increased nonhost yield by releasing consumable cell debris, and by driving evolution of partially resistant E. coli that secreted more carbon. Our results demonstrate that phage can have extensive indirect effects in microbial communities, that the nature of these indirect effects depends on metabolic and evolutionary mechanisms, and that knowing the degree of evolved resistance leads to qualitatively different predictions of bacterial community dynamics in response to phage attack.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Assié A, Leisch N, Meier DV, et al (2020)

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).

The ISME journal, 14(1):104-122.

Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Ogawa M, Takahashi M, Matsutani M, et al (2020)

Obligate intracellular bacteria diversity in unfed Leptotrombidium scutellare larvae highlights novel bacterial endosymbionts of mites.

Microbiology and immunology, 64(1):1-9.

It is well known that the mite Leptotrombidium scutellare carries the pathogen of scrub typhus, Orientia tsutsugamushi. However, our understanding of other bacterial endosymbionts of mites is limited. This study investigated the diversity of the obligate intracellular bacteria carried by L. scutellare using 16S rRNA gene amplicon analysis with next-generation sequencing. The results showed that the detected bacteria were classified into the genera Rickettsia, Wolbachia, and Rickettsiella and an unknown genus of the order Rickettsiales. For further classification of the detected bacteria, a representative read that was most closely related to the assigned taxonomic classification was subjected to homology search and phylogenic analysis. The results showed that some bacteria of the genus Rickettsia were identical or very close to the human pathogens Rickettsia akari, Rickettsia aeschlimannii, Rickettsia felis, and Rickettsia australis. The genetic distance between the genus Wolbachia bacteria in the present study and in previous reports is highly indicative that the bacteria in the present study can be classified as a new taxon of Wolbachia. This study detected obligate intracellular bacteria from unfed mites; thus, the mites did not acquire bacteria from infected animals or any other infectious sources. Finally, the present study demonstrated that various and novel bacterial endosymbionts of mites, in addition to O. tsutsugamushi, might uniquely evolve with the host mites throughout overlapping generations of the mite life cycle. The roles of the bacteria in mites and their pathogenicity should be further examined in studies based on bacterial isolation.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Imai A, Ohtani M, Nara A, et al (2020)

The Lotus japonicus nucleoporin GLE1 is involved in symbiotic association with rhizobia.

Physiologia plantarum, 168(3):590-600.

Nucleoporins are components of the nuclear pore complexes, channels that regulate the transport of macromolecules between the nucleus and cytoplasm. The nucleoporin GLE1 (GLFG lethal1) functions in the export of messenger RNAs containing poly(A) tails from the nucleus into the cytoplasm. Here we investigated a mutant of the model legume Lotus japonicus that was defective in GLE1, which we designated Ljgle1. The growth of Ljgle1 was retarded under symbiotic association with rhizobia, and the nitrogen-fixation activities of the nodules were around one-third of those in the wild-type plant. The growth of Ljgle1 was not substantialy recovered by supplemention of combined nitrogen. Nodules formed on the Ljgle1 were smaller than those on the wild-type and colored faint pink. The numbers of infected cells of nodules on the Ljgle1 were smaller than on the wild-type plant, and the former cells remained undeveloped. Rhizobia in the cells of the Ljgle1 exhibited disordered forms, and the symbiosome membrane was closely attached to the bacterial membrane. These results indicate that GLE1 plays a distinct role in the symbiotic association between legumes and rhizobia.

RevDate: 2020-03-23

Kikuchi Y, Ohbayashi T, Jang S, et al (2020)

Burkholderia insecticola triggers midgut closure in the bean bug Riptortus pedestris to prevent secondary bacterial infections of midgut crypts.

The ISME journal pii:10.1038/s41396-020-0633-3 [Epub ahead of print].

In addition to abiotic triggers, biotic factors such as microbial symbionts can alter development of multicellular organisms. Symbiont-mediated morphogenesis is well-investigated in plants and marine invertebrates but rarely in insects despite the enormous diversity of insect-microbe symbioses. The bean bug Riptortus pedestris is associated with Burkholderia insecticola which are acquired from the environmental soil and housed in midgut crypts. To sort symbionts from soil microbiota, the bean bug develops a specific organ called the "constricted region" (CR), a narrow and symbiont-selective channel, located in the midgut immediately upstream of the crypt-bearing region. In this study, inoculation of fluorescent protein-labeled symbionts followed by spatiotemporal microscopic observations revealed that after the initial passage of symbionts through the CR, it closes within 12-18 h, blocking any potential subsequent infection events. The "midgut closure" developmental response was irreversible, even after symbiont removal from the crypts by antibiotics. It never occurred in aposymbiotic insects, nor in insects infected with nonsymbiotic bacteria or B. insecticola mutants unable to cross the CR. However, species of the genus Burkholderia and its outgroup Pandoraea that can pass the CR and partially colonize the midgut crypts induce the morphological alteration, suggesting that the molecular trigger signaling the midgut closure is conserved in this bacterial lineage. We propose that this drastic and quick alteration of the midgut morphology in response to symbiont infection is a mechanism for stabilizing the insect-microbe gut symbiosis and contributes to host-symbiont specificity in a symbiosis without vertical transmission.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Araújo JR, Tazi A, Burlen-Defranoux O, et al (2020)

Fermentation Products of Commensal Bacteria Alter Enterocyte Lipid Metabolism.

Cell host & microbe, 27(3):358-375.e7.

Despite the recognized capacity of the gut microbiota to regulate intestinal lipid metabolism, the role of specific commensal species remains undefined. Here, we aimed to understand the bacterial effectors and molecular mechanisms by which Lactobacillus paracasei and Escherichia coli regulate lipid metabolism in enterocytes. We show that L-lactate produced by L. paracasei inhibits chylomicron secretion from enterocytes and promotes lipid storage by a mechanism involving L-lactate absorption by enterocytes, its conversion to malonyl-CoA, and the subsequent inhibition of lipid beta-oxidation. In contrast, acetate produced by E. coli also inhibits chylomicron secretion by enterocytes but promotes lipid oxidation by a mechanism involving acetate absorption by enterocytes, its metabolism to acetyl-CoA and AMP, and the subsequent upregulation of the AMPK/PGC-1α/PPARα pathway. Our study opens perspectives for developing specific bacteria- and metabolite-based therapeutic interventions against obesity, atherosclerosis, and malnutrition by targeting lipid metabolism in enterocytes.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Zhu W, Winter MG, Spiga L, et al (2020)

Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis.

Cell host & microbe, 27(3):376-388.e8.

During short-lived perturbations, such as inflammation, the gut microbiota exhibits resilience and reverts to its original configuration. Although microbial access to the micronutrient iron is decreased during colitis, pathogens can scavenge iron by using siderophores. How commensal bacteria acquire iron during gut inflammation is incompletely understood. Curiously, the human commensal Bacteroides thetaiotaomicron does not produce siderophores but grows under iron-limiting conditions using enterobacterial siderophores. Using RNA-seq, we identify B. thetaiotaomicron genes that were upregulated during Salmonella-induced gut inflammation and were predicted to be involved in iron uptake. Mutants in the xusABC locus (BT2063-2065) were defective for xenosiderophore-mediated iron uptake in vitro. In the normal mouse gut, the XusABC system was dispensable, while a xusA mutant colonized poorly during colitis. This work identifies xenosiderophore utilization as a critical mechanism for B. thetaiotaomicron to sustain colonization during inflammation and suggests a mechanism of how interphylum iron metabolism contributes to gut microbiota resilience.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Parra-Tabla V, Angulo-Pérez D, Albor C, et al (2019)

The role of alien species on plant-floral visitor network structure in invaded communities.

PloS one, 14(11):e0218227.

The interactions between pairs of native and alien plants via shared use of pollinators have been widely studied. Community level studies however, are necessary in order to fully understand the factors and mechanisms that facilitate successful plant invasion, but these are still scarce. Specifically, few community level studies have considered how differences in invasion level (alien flower abundance), and degree of floral trait similarity between native and invasive species, mediate effects on native plant-pollinator communities. Here, we evaluated the role of alien species on overall plant-floral visitor network structure, and on species-level network parameters, across nine invaded coastal communities distributed along 205 km in Yucatán, México that vary in alien species richness and flower abundance. We further assessed the potential the role of alien plant species on plant-floral visitor network structure and robustness via computational simulation of native and invasive plant extinction scenarios. We did not find significant differences between native and alien species in their functional floral phenotypes or in their visitation rate and pollinator community composition in these invaded sites. Variation in the proportion of alien plant species and flower abundance across sites did not influence plant-pollinator network structure. Species-level network parameters (i.e., normalized degree and nestedness contribution) did not differ between native and alien species. Furthermore, our simulation analyses revealed that alien species are functionally equivalent to native species and contribute equally to network structure and robustness. Overall, our results suggest that high levels of floral trait similarity and pollinator use overlap may help facilitate the integration of alien species into native plant-pollinator networks. As a result, alien species may also play a similar role than that of natives in the structure and stability of native plant and pollinator communities in the studied coastal sand dune ecosystem.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Wei Y, X Xia (2019)

Unique Shine-Dalgarno Sequences in Cyanobacteria and Chloroplasts Reveal Evolutionary Differences in Their Translation Initiation.

Genome biology and evolution, 11(11):3194-3206.

Microorganisms require efficient translation to grow and replicate rapidly, and translation is often rate-limited by initiation. A prominent feature that facilitates translation initiation in bacteria is the Shine-Dalgarno (SD) sequence. However, there is much debate over its conservation in Cyanobacteria and in chloroplasts which presumably originated from endosymbiosis of ancient Cyanobacteria. Elucidating the utilization of SD sequences in Cyanobacteria and in chloroplasts is therefore important to understand whether 1) SD role in Cyanobacterial translation has been reduced prior to chloroplast endosymbiosis or 2) translation in Cyanobacteria and in plastid has been subjected to different evolutionary pressures. To test these alternatives, we employed genomic, proteomic, and transcriptomic data to trace differences in SD usage among Synechocystis species, Microcystis aeruginosa, cyanophages, Nicotiana tabacum chloroplast, and Arabidopsis thaliana chloroplast. We corrected their mis-annotated 16S rRNA 3' terminus using an RNA-Seq-based approach to determine their SD/anti-SD locational constraints using an improved measurement DtoStart. We found that cyanophages well-mimic Cyanobacteria in SD usage because both have been under the same selection pressure for SD-mediated initiation. Whereas chloroplasts lost this similarity because the need for SD-facilitated initiation has been reduced in plastids having much reduced genome size and different ribosomal proteins as a result of host-symbiont coevolution. Consequently, SD sequence significantly increases protein expression in Cyanobacteria but not in chloroplasts, and only Cyanobacterial genes compensate for a lack of SD sequence by having weaker secondary structures at the 5' UTR. Our results suggest different evolutionary pressures operate on translation initiation in Cyanobacteria and in chloroplast.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Zheng Y, Shen W, Bi J, et al (2019)

Small RNA analysis provides new insights into cytoplasmic incompatibility in Drosophila melanogaster induced by Wolbachia.

Journal of insect physiology, 118:103938.

Wolbachia is a genus of endosymbiotic bacteria that induce a wide range of effects on their insect hosts. Cytoplasmic incompatibility (CI) is the most common phenotype mediated by Wolbachia and results in embryonic lethality when Wolbachia-infected males mate with uninfected females. Studies have revealed that bacteria can regulate many cellular processes in their hosts using small non-coding RNAs, so we investigated the involvement of small RNAs (sRNAs) in CI. Comparison of sRNA libraries between Wolbachia-infected and uninfected Drosophila melanogaster testes revealed 18 novel microRNAs (miRNAs), of which 12 were expressed specifically in Wolbachia-infected flies and one specifically in Wolbachia-uninfected flies. Furthermore, ten miRNAs showed differential expression, with four upregulated and six downregulated in Wolbachia-infected flies. Of the upregulated miRNAs, nov-miR-12 exhibited the highest upregulation in the testes of D. melanogaster. We then identified pipsqueak (psq) as the target gene of nov-miR-12 with the greatest complementarity in its 3' untranslated region (UTR). Wolbachia infection was correlated with reduced psq expression in D. melanogaster, and luciferase assays demonstrated that nov-miR-12 could downregulate psq through binding to its 3'UTR region. Knockdown of psq in Wolbachia-free fly testes significantly reduced egg hatching rate and mimicked the cellular abnormalities of Wolbachia-induced CI in embryos, including asynchronous nuclear division, chromatin bridging, and chromatin fragmentation. These results suggest that Wolbachia may induce CI in insect hosts by miRNA-mediated changes in host gene expression. Moreover, these findings reveal a potential molecular strategy for elucidating the complex interactions between endosymbionts and their insect hosts, such as Wolbachia-driven CI.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Nakabachi A, M Fujikami (2019)

Concentration and distribution of diaphorin, and expression of diaphorin synthesis genes during Asian citrus psyllid development.

Journal of insect physiology, 118:103931.

The Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Sternorrhyncha: Psylloidea: Liviidae) is an important pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria); the causative agents of an incurable citrus disease known as huanglongbing or greening disease. D. citri possesses a vertically transmitted intracellular symbiont, Candidatus Profftella armatura (Betaproteobacteria), which produces diaphorin; a polyketide that is toxic to various eukaryotic organisms. Our previous study demonstrated that the total amount and average concentration of diaphorin in adult D. citri, when homogeneous distribution is assumed within the insect, are sufficient to exert inhibitory effects on fungi and insects, including the Asian lady beetle Harmonia axyridis (Coleoptera: Coccinellidae); one of the major predators of D. citri. However, diaphorin may be localized to a limited body area within D. citri, and its concentration may change during development. In the present study, to better understand the physiological and ecological function of diaphorin, we assessed the distribution of diaphorin within the D. citri body and analyzed concentrations of diaphorin in various developmental stages. Expression of genes involved in diaphorin synthesis was also analyzed. The results demonstrated that diaphorin is distributed widely in the D. citri body, which appears to be a prerequisite for effective deterrence of natural enemies. The concentration of diaphorin was shown to change significantly during the development of D. citri. It was highest in mature adults, followed by embryos and teneral adults, and lowest in nymphs. The lowest concentrations of diaphorin observed in nymphs are still presumed to be effective in deterring invasive natural enemies, including parasites, parasitoids, and entomopathogenic fungi. Quantitative RT-PCR indicated that amounts of transcripts for diaphorin synthesis genes dipP and dipT were at a minimum in embryos, increased during the nymphal period, and reached a maximum level just after adult eclosion. The alteration pattern of the amounts of transcripts for diaphorin synthesis genes appeared to partially disagree with that of the concentration of diaphorin. The present study provides new insights into the function of diaphorin, which is essential for further investigations that aim to improve the efficacy of D. citri biological control.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Thongpoo P, Tsai S, C Lin (2019)

Assessing the impacts of cryopreservation on the mitochondria of a thermotolerant Symbiodinium lineage: Implications for reef coral conservation.

Cryobiology, 89:96-99.

Earth's coral reefs are threatened by a barrage of anthropogenic insults, and cryopreservation-based conservation measures are warranted. Successfully cryopreserved corals could then thawed and out-planted on reefs when ocean temperatures stabilize. In such efforts, it will be necessary to also cryopreserve the photosynthetic dinoflagellates (genus Symbiodinium) that reside within the corals' gastrodermal cells. Given this need, Symbiodinium (clade D) cells were cryopreserved in 2 M propylene glycol by a two-step freezing protocol herein and then cultured for 42 days post-thaw. To gauge the effect of cryopreservation, mitochondrial DNA content and intracellular ATP concentration were assessed, and the former parameter was nearly 2-fold higher in freeze-thawed cells compared to controls after 14 days of post-thaw culture. In contrast, intracellular ATP concentration was relatively lower in freeze-thawed cells after seven days of post-thaw culture, though returned to control levels in samples cultured for 42 days post-thaw.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Jimenez-Jimenez S, Hashimoto K, Santana O, et al (2019)

Emerging roles of tetraspanins in plant inter-cellular and inter-kingdom communication.

Plant signaling & behavior, 14(4):e1581559.

Inter-cellular and inter-kingdom signaling systems of various levels of complexity regulate pathogenic and mutualistic interactions between bacteria, parasites, and fungi and animal and plant hosts. Inter-kingdom interactions between mutualistic bacteria such as rhizobia and legumes during nodulation and between fungi and plants during mycorrhizal associations, are characterized by the extensive exchange of molecular signals, which allow nitrogen and phosphate assimilation, respectively. A novel aspect of this signaling exchange is the existence of specific structures, the exosomes, that carry important molecules that shape the plant-pathogen interactions. Exosomes contain a wide array of molecules, such as lipids, proteins, messenger RNA, and microRNAs, that play important roles in cell-to-cell communication in animal and plant cells by affecting gene expression and other physiological activity in distant cells within the same organism (e.g., during cancer metastases and neuron injuries). In plant cells, it has been recently reported that exosomes go beyond organism boundaries and inhibit a pathogenic interaction in plants. Plant produce and send exosomes loaded with specific small miRNA which inhibit the pathogen infection, but the pathogen can also produce exosomes carrying pro-pathogenic proteins and microRNAs. Therefore, exosomes are the important bridge regulating the signal exchange. Exosomes are small membrane-bound vesicles derived from multivesicular bodies (MVBs), which carries selected cargos from the cytoplasm (protein, lipids, and microRNAs) and under certain circumstances, they fuse with the plasma membrane, releasing the small vesicles as cargo-carrying exosomes into the extracellular space during intercellular and inter-kingdom communication. Animal and plant proteomic studies have demonstrated that tetraspanin proteins are an integral part of exosome membranes, positioning tetraspanins as essential components for endosome organization, with key roles in membrane fusion, cell trafficking, and membrane recognition. We discuss the similarities and differences between animal tetraspanins and plant tetraspanins formed during plant-microbe interactions and their potential role in mutualistic communication.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Lugli GA, Duranti S, Albert K, et al (2019)

Unveiling Genomic Diversity among Members of the Species Bifidobacterium pseudolongum, a Widely Distributed Gut Commensal of the Animal Kingdom.

Applied and environmental microbiology, 85(8):.

Bifidobacteria are commensals of the animal gut and are commonly found in mammals, birds, and social insects. Specifically, strains of Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium longum, and Bifidobacterium pseudolongum are widely distributed in the mammalian gut. In this context, we investigated the genetic variability and metabolic abilities of the B. pseudolongum taxon, whose genomic characterization has so far not received much attention. Phylogenomic analysis of the genome sequences of 60 B. pseudolongum strains revealed that B. pseudolongum subsp. globosum and B. pseudolongum subsp. pseudolongum may actually represent two distinct bifidobacterial species. Furthermore, our analysis highlighted metabolic differences between members of these two subspecies. Moreover, comparative analyses of genetic strategies to prevent invasion of foreign DNA revealed that the B. pseudolongum subsp. globosum group exhibits greater genome plasticity. In fact, the obtained findings indicate that B. pseudolongum subsp. globosum is more adaptable to different ecological niches such as the mammalian and avian gut than is B. pseudolongum subsp. pseudolongumIMPORTANCE Currently, little information exists on the genetics of the B. pseudolongum taxon due to the limited number of sequenced genomes belonging to this species. In order to survey genome variability within this species and explore how members of this taxon evolved as commensals of the animal gut, we isolated and decoded the genomes of 51 newly isolated strains. Comparative genomics coupled with growth profiles on different carbohydrates has further provided insights concerning the genotype and phenotype of members of the B. pseudolongum taxon.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Eroglu C, Cimen H, Ulug D, et al (2019)

Acaricidal effect of cell-free supernatants from Xenorhabdus and Photorhabdus bacteria against Tetranychus urticae (Acari: Tetranychidae).

Journal of invertebrate pathology, 160:61-66.

The effects of secondary metabolites produced by the following symbiotic bacteria, Xenorhabdus szentirmaii, X. nematophila, X. bovienii, X. cabanillasii, Photorhabdus luminescens and P. temperata, associated with entomopathogenic nematodes, were investigated against various developmental stages of Tetranychus urticae (Acari: Tetranychidae) using cell-free bacterial supernatants in Petri dishes. In addition, the effects of the most active bacterial supernatant(s) found in Petri dish experiments were tested on T. urticae in pot experiments. All studies were conducted at 25 ± 1 °C temperature, 70 ± 5% relative humidity and a light cycle of 16 h in a climate room. The result of the Petri dish experiments showed that the supernatants had little or no effect on the egg stage, as less than 4% mortality was recorded. Depending on the bacterial supernatant, mortality in the other stages was 46-97% for larvae, 30-96% for protonymphs, 41-92% for deutonymphs, 92-100% for adult males and 46-93% for adult females. Control mortalities ranged from 1-7% for larvae, 2-9% for protonymphs, 4-10% for deutonymphs, 6-10% for adult males and 4-8% for adult females. Among supernatants tested, X. szentirmaii and X. nematophila were the most efficacious with mortality greater than 90% on the mobile stages of T. urticae. According to the results from pot experiments, the supernatants of X. szentirmaii and X. nematophila, singularly and in combination, significantly reduced the T. urticae population. However, the mixture of X. szentirmaii and X. nematophila supernatants did not increase efficiency to reduce T. urticae population compared to each supernatant alone. Further studies are warranted to find the active compound(s) in the supernatants of X. szentirmaii or and X. nematophila and assess whether the supernatant(s) has the potential of being a practical and economical control agent for T. urticae.

RevDate: 2020-03-23
CmpDate: 2020-03-23

De Jaegher K (2019)

Harsh environments: Multi-player cooperation with excludability and congestion.

Journal of theoretical biology, 460:18-36.

The common-enemy hypothesis of by-product mutualism proposes that organisms are more likely to cooperate when facing the common enemy of a harsher environment. Micro-foundations of this hypothesis have so far focused on the case where cooperation consists of the production of a pure public good. In this case, the effect of a harsher environment is ambiguous: not only a common-enemy effect is possible, but also an opposite, competing effect where the harsher environment reduces the probability of cooperation. This paper shows that unambiguous effects of a harsher environment are predicted when considering the realistic case where the collective good produced is excludable (in the sense that whether or not a player benefits from the collective good depends on whether or not he is contributing) and/or congestible (in the sense that the benefits the individual player obtains from the collective good are affected by the number of contributing players). In particular, the competing effect is systematically predicted for club goods, where defectors are excluded from the benefits of the collective good. A common-enemy effect is instead systematically predicted for charity goods, where cooperators are excluded from the benefits of the collective good. These effects are maintained for congestible club goods and for congestible charity goods. As the degree to which a collective good is excludable can be meaningfully compared across different instances of cooperation, these contrasting predictions for public good, charity goods and club goods yield testable hypotheses for the common-enemy hypothesis of by-product mutualism.

RevDate: 2020-03-22

Ferreira DA, da Silva TF, Pylro VS, et al (2020)

Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi.

Microbial ecology pii:10.1007/s00248-020-01502-z [Epub ahead of print].

Terrestrial plants establish symbiosis with arbuscular mycorrhizal fungi (AMF) to exchange water and nutrients. However, the extent to which soil biodiversity influences such association remains still unclear. Here, we manipulated the soil microbial diversity using a "dilution-to-extinction" approach in a controlled pot microcosm system and quantified the root length colonization of maize plants by the AMF Rhizophagus clarus. The experiment was performed by manipulating the soil microbiome within a native and foreign soil having distinct physicochemical properties. Overall, our data revealed significant positive correlations between the soil microbial diversity and AMF colonization. Most importantly, this finding opposes the diversity-invasibility hypothesis and highlights for a potential overall helper effect of the soil biodiversity on plant-AMF symbiosis.


ESP Quick Facts

ESP Origins

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

ESP Support

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

ESP Rationale

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

ESP Goal

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

ESP Usage

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

ESP Content

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

ESP Help

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

ESP Plans

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

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

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

Digital Books

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


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


Biographical information about many key scientists.

Selected Bibliographies

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

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