Mapping Cell Phenomics with Multiparametric Flow Cytometry Assays

Phenomics explores the complex interactions among genes, epigenetics, symbiotic microorganisms, diet, and environmental exposure based on the physical, chemical, and biological characteristics of individuals and groups. Increasingly efficient and comprehensive phenotyping techniques have been integrated into modern phenomics-related research. Multicolor flow cytometry technology provides more measurement parameters than conventional flow cytometry. Based on detailed descriptions of cell phenotypes, rare cell populations and cell subsets can be distinguished, new cell phenotypes can be discovered, and cell apoptosis characteristics can be detected, which will expand the potential of cell phenomics research. Based on the enhancements in multicolor flow cytometry hardware, software, reagents, and method design, the present review summarizes the recent advances and applications of multicolor flow cytometry in cell phenomics, illuminating the potential of applying phenomics in future studies.

Phytochemical Profile and Anticancer Potential of Endophytic Microorganisms from Liverwort Species, Marchantia polymorpha L.

Liverwort endophytes could be a source of new biologically active substances, especially when these spore-forming plants are known to produce compounds that are not found in other living organisms. Despite the significant development of plant endophytes research, there are only a few studies describing liverwort endophytic microorganisms and their metabolites. In the presented study, the analysis of the volatile compounds obtained from thallose liverwort species, Marchantia polymorpha L., and its endophytes was carried out. For this purpose, non-polar extracts of plant material and symbiotic microorganisms were obtained. The extracts were analyzed using gas chromatography coupled to mass spectrometry. Compounds with the structure of diketopiperazine in the endophyte extract were identified. Liverwort volatile extract was a rich source of cuparane-, chamigrane-, acorane-, and thujopsane-type sesquiterpenoids. The cytotoxicity of ethyl acetate extracts from endophytic microorganisms was evaluated on a panel of cancer (FaDu, HeLa, and SCC-25) cell lines and normal (VERO), and revealed significant anticancer potential towards hypopharyngeal squamous cell carcinoma and cervical adenocarcinoma.

Multi-Omics Revealing the Response Patterns of Symbiotic Microorganisms and Host Metabolism in Scleractinian Coral Pavona minuta to Temperature Stresses

Global climate change has resulted in large-scale coral reef decline worldwide, for which the ocean warming has paid more attention. Coral is a typical mutually beneficial symbiotic organism with diverse symbiotic microorganisms, which maintain the stability of physiological functions. This study compared the responses of symbiotic microorganisms and host metabolism in a common coral species, Pavona minuta, under indoor simulated thermal and cold temperatures. The results showed that abnormal temperature stresses had unfavorable impact on the phenotypes of corals, resulting in bleaching and color change. The compositions of symbiotic bacteria and dinoflagellate communities only presented tiny changes under temperature stresses. However, some rare symbiotic members have been showed to be significantly influenced by water temperatures. Finally, by using ultra-performance liquid chromatography tandem mass spectrometry (UPLC–MS) method, we found that different temperature stresses had very different impacts on the metabolism of coral holobiont. The thermal and cold stresses induced the decrease of anti-oxidation metabolites, several monogalactosyldiacylglycerols (MGDGs), and the increase of lipotoxic metabolite, 10-oxo-nonadecanoic acid, in the coral holobiont, respectively. Our study indicated the response patterns of symbiotic microorganisms and host metabolism in coral to the thermal and cold stresses, providing theoretical data for the adaptation and evolution of coral to a different climate in the future.

Firmicutes and Bacteroidetes explain mass gain variation in an obligate hibernator

Body condition is an important life history challenge that directly impacts individual fitness and is particularly important for hibernating animals, whose maintenance of adequate body fat and mass is essential for survival. It is well documented that symbiotic microorganisms play a vital role in animal physiology and behaviour. Recent work demonstrates that gut microbes are associated with fat accumulation and obesity; Firmicutes is consistently associated with obesity while Bacteroidetes is associated with leanness both in humans and other animals.The focus of most microbiome studies has been on human health or involved lab reared animals used as a model system. However, these microbes likely are important for individual fitness in wild populations and provide potential mechanistic insights into the adaptability and survival of wildlife. Here we test whether symbiotic microorganisms within the phyla of Firmicutes and Bacteroidetes are associated with summer mass gain in an exceptionally well-studied wild population of yellow-bellied marmots (Marmota flaviventer) by quantifying microbial abundance over five years of fecal samples (2015 - 2019) collected during their summer active season. Results show that marmots with higher mass gain rates have a greater abundance of Firmicutes. In contrast, higher abundance of Bacteroidetes was associated with lower mass gain rates, but only for marmots living in harsher environments. Similar patterns were found at the family level where Ruminococcaceae, a member of Firmicutes, was associated with higher mass gain rates, and Muribaculaceae, a member of Bacteroidetes, was associated with lower mass gain rates, and similarly in harsher environments. Although correlative, these results highlight the importance of symbiotic gut microbiota to mass gain in the wild, a trait associated with survival and fitness in many taxonomic groups.

Interaction of Viruses with the Insect Intestine

In nature, insects face a constant threat of infection by numerous exogeneous viruses, and their intestinal tracts are the predominant ports of entry. Insects can acquire these viruses orally during either blood feeding by hematophagous insects or sap sucking and foliage feeding by insect herbivores. However, the insect intestinal tract forms several physical and immunological barriers to defend against viral invasion, including cell intrinsic antiviral immunity, the peritrophic matrix and the mucin layer, and local symbiotic microorganisms. Whether an infection can be successfully established in the intestinal tract depends on the complex interactions between viruses and those barriers. In this review, we summarize recent progress on virus-intestinal tract interplay in insects, in which various underlying mechanisms derived from nutritional status, dynamics of symbiotic microorganisms, and virus-encoded components play intricate roles in the regulation of virus invasion in the intestinal tract, either directly or indirectly. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Plant evolution driven by interactions with symbiotic and pathogenic microbes

During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today’s continuum of associations, ranging from parasitism to mutualism. Through phylogenetics, cell biology, and reverse genetics extending beyond flowering plants into bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms used in nonflowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen-resilient crops.

Bioactivity of carotenoid produced by soft coral symbiotic microorganisms from Panjang and Karimunjawa Island, Centra Java, Indonesia

Kusmita L, Nuryadi H, Widyananto PA, Muchlissin S, Sabdono A, Trianto A, Radjasa OK. 2021. Bioactivity of carotenoid produced by soft coral symbiotic microorganisms from Panjang and Karimunjawa Island, Centra Java, Indonesia. Biodiversitas 22: 732-740. The diversity of soft corals is more varied in waters. One of the characteristics of soft corals is the production of secondary metabolites, i. i.e. carotenoids. Carotenoids are phytonutrients found in the cells of a wide variety of plants, algae, and bacteria as secondary metabolic compounds with antioxidant functions. Carotenoid biosynthesis is strongly influenced by the environment in which the producing organism grows. This study was aimed to uncover the antioxidant and anti-ultraviolet activities of carotenoids produced by soft coral symbiotic microorganisms in the waters surrounding the Panjang and Karimunjawa Islands in the North Java Sea, Indonesia. The parameters observed included water quality, antioxidant activity, and anti-ultraviolet activity. The results indicated that the water quality at Panjang Island did not meet quality standards (including salinity, visibility, dissolved oxygen, ammonia, and nitrate) while that at Karimunjawa did. The diversity of soft corals was more varied at Karimunjawa Island than at Panjang Island. In contrast to the bioactivity, the carotenoid extracts from the Panjang Island soft coral symbiotic microorganisms showed higher activity than those from Karimunjawa Island microorganisms. The highest antioxidant activity was found in the bacterial isolate 19.PP.Sc1.6 from Panjang Island and was identified based on the 16S rRNA gene as Virgibacillus salarius, with 99% similarity.

Simbiotisko asociāciju ietekme uz pupu Vicia faba L. produktivitāti = Influence of symbiotic associations on yield formation of beans (Vicia faba L.)

Dubova L., 2020. Influence of symbiotic associations on yield formation of beans (Vicia faba L.) Latvia University of Life Scienes and Technologies: Jelgava. Legumes are widely grown crops, which symbiotically fix nitrogen from the atmosphere. Following the decline in legume production at the turn of the century, sown areas in Latvia have expanded rapidly in recent years. EU directives, which set requirements for the diversification of arable crops, are an important contributor to the growing popularity of legumes. The intensification of legume cultivation is linked to changes in cultivation technologies and to the amount of varieties available to growers. The beneficial effects of legumes on various environmental processes are possible with the interaction with symbiotic microorganisms. With the growth of bean-cultivation areas in compliance with the requirements of European directives, as well as with the changing cultivation technologies and agro-climatic conditions, the need to intensify research on the interaction of beans and microorganisms is becoming more and more important. In Latvia, rhizobia have been studied for a long period of time. However, the research has been carried out with varying intensity. There is little research done on the role of mycorrhizal fungi in agroecosystems, but the interaction between rhizobia and mycorrhizal fungi has not been studied at all in Latvia yet. The aim of this study is to evaluate the effect of symbiotic associations on the bean (Vicia faba L). The following tasks have been set: to evaluate the suitability of Rhizobium leguminosarum strains of the Rhizobia collection of the LLU Institute of Soil and Plant Science for efficient symbiosis of faba beans; to clarify the influence of environmental factors on the formation and efficiency of symbiotic associations, to assess whether it is appropriate to double seed inoculation with symbiotic microorganisms in order to increase the quality of a bean crop. The research has been carried out between 2014 – 2019. The trials were set up under controlled conditions in the vegetation pots and in field conditions. Rhizobia from the LLU Institute of Soil and Plant Science collection were used, mycorrhizal fungi preparation was obtained from the Czech company Symbiom® and contains three mycorrhizal fungal species - Glomus claroideum, G. intraradices and G. mosseae. The research was done within the framework of the European Union 7th Framework Program project EUROLEGUME (Enhancing legumes growing in Europe through sustainable cropping for protein supply for food and feed). It was concluded that bacterial strains of the LLU Rhizobia Collection has different activity and ability to form symbiosis with beans. Evaluating dehydrogenase activity and nodule formation it has been found that to reduce the inhibitory effect of environmental factors, it is useful to use rhizobia associations for inoculation. The use of rhizobia together with mycorrhizal fungi stimulated mycorrhizal intensity. It was found that supplemental mineral nitrogen fertilizers did not promote colonisation of mycorrhizal fungi in bean roots, the mean mycorrhization rate was lower than with double inoculation. Mycorrhizal fungi were presented in all soil types analyzed. There was a difference in mycorrhizal rate (F %) and arbuscular incidence (A %) in small seed and coarse seed bean. Positive effects on crop yield and quality can be observed in the double-inoculation variants. However, the positive effect varied from year to year. In most cases, only a positive trend occurred. The Ph.D. Thesis consists of 105 pages (apart from references). Thesis contains 8 tables and 54 figures.

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil

Aluminium being one of the most abundant elements is very toxic for plants causing inhibition of nutrient uptake and productivity. The aim of this study was to evaluate the potential of microbial consortium consisting of arbuscular mycorrhizal fungus (AMF), rhizobia and PGPR for counteracting negative effects of Al toxicity on four pea genotypes differing in Al tolerance. Pea plants were grown in acid soil supplemented with AlCl3 (pHKCl = 4.5) or neutralized with CaCO3 (pHKCl = 6.2). Inoculation increased shoot and/or seed biomass of plants grown in Al-supplemented soil. Nodule number and biomass were about twice on roots of Al-treated genotypes after inoculation. Inoculation decreased concentrations of water-soluble Al in the rhizosphere of all genotypes grown in Al-supplemented soil by about 30%, improved N2 fixation and uptake of fertilizer 15N and nutrients from soil, and increased concentrations of water-soluble nutrients in the rhizosphere. The structure of rhizospheric microbial communities varied to a greater extent depending on the plant genotype, as compared to soil conditions and inoculation. Thus, this study highlights the important role of symbiotic microorganisms and the plant genotype in complex interactions between the components of the soil-microorganism-plant continuum subjected to Al toxicity.