Fungal Communities in the Native New Zealand Medicinal Plant Pseudowintera colorata (Horopito) Are Determined by Plant Organ Type and Host Maturity with Key Members Promoting Plant Growth

The plant Pseudowintera colorata is well known for its antimicrobial and medicinal properties and is endemic to New Zealand. Using PCR-Denaturing gradient gel electrophoresis (DGGE), we investigated the factors influencing the composition of endophytic fungal communities in P. colorata from ten distinct sites across New Zealand. Our results showed that plant organs of P. colorata influenced the diversity and richness of endophytic fungi (PERMANOVA, p < 0.05). In addition, plant maturity and its interactions revealed that endophytic fungal communities formed discrete clusters in leaves, stems, and roots of mature and immature P. colorata plants (PERMANOVA; p = 0.002, p = 0.001 and p = 0.039, respectively). For identifying isolates with biocontrol potential, dual culture tests were set up against four different phytopathogenic fungi. Isolates with high activity (zone of inhibition >10 mm) were sequenced and identified as Trichoderma harzianum, Pezicula neosporulosa, Fusarium tricinctum, Metarhizium sp., and Chaetomium sp. Applying selected endophytic fungi (n = 7) as soil drenchers significantly increased the growth of P. colorata seedlings and produced more internodes. Seedling shoots treated with Trichoderma sp. PRY2BA21 were 2.2 × longer (8.36 cm) than the untreated controls (3.72 cm). Our results elucidate the main plant factors influencing fungal community composition and demonstrate a role for endophytic fungi in P. colorata growth and further demonstrate that medicinal plants are a rich source of endophytes with potential as biocontrol agents.

Bacterial variation in the oral microbiota in multiple sclerosis patients

Background Microorganisms in oral cavity are called oral microbiota, while microbiome consists of total genome content of microorganisms in a host. Interaction between host and microorganisms is important in nervous system development and nervous diseases such as Autism, Alzheimer, Parkinson and Multiple Sclerosis (MS). Bacterial infections, as an environmental factor in MS pathogenesis play role in T helper 17(Th17) increase and it enhancing the production of pro-inflammatory cytokines such as Interlukin-21(IL-21), IL-17 and IL -22. Oral microbiota consists diverse populations of cultivable and uncultivable bacterial species. Denaturing gradient gel electrophoresis (DGGE) is an acceptable method for identification of uncultivable bacteria. In this study, we compared the bacterial population diversity in the oral cavity between MS and healthy people. Methods From October to March 2019, samples were taken at Kermanshah University of Medical Sciences’ MS patients center. A total of 30 samples were taken from MS patients and another 30 samples were taken from healthy people. Phenotypic tests were used to identify bacteria after pure cultures were obtained. DNA was extracted from 1 mL of saliva, and PCR products produced with primers were electrophoresed on polyacrylamide gels. Results The genera Staphylococcus, Actinomyces, Fusobacterium, Bacteroides, Porphyromonas, Prevotella, Veillonella, Propionibacterium and uncultivable bacteria with accession number MW880919-25, JQ477416.1, KF074888.1 and several other un-culturable strains were significantly more abundant in the MS group while Lactobacillus and Peptostreptococcus were more prevalent in the normal healthy group according to logistic regression method. Conclusion Oral micro-organisms may alleviate or exacerbate inflammatory condition which impact MS disease pathogenesis. It may be assumed that controlling oral infections may result in reduction of MS disease progression.

The Root Mycobiota of Betula aetnensis Raf., an Endemic Tree Species Colonizing the Lavas of Mt. Etna (Italy)

Betula aetnensis is an endemic tree of high conservation value, which thrives on the nutrient-poor volcanic soils of Mount Etna. Since plant–microbe interactions could play a crucial role in plant growth, resource uptake, and resistance to abiotic stresses, we aimed to characterize the root and rhizosphere microbial communities. Individuals from natural habitat (NAT) and forest nursery (NURS) were surveyed through microscopy observations and molecular tools: bacterial and fungal automated ribosomal intergenic spacer analysis (ARISA), fungal denaturing gradient gel electrophoresis (DGGE). B. aetnensis was found to be simultaneously colonized by arbuscular (AM), ectomycorrhizal (ECM), ericoid (ERM) fungi, and dark septate endophytes (DSE). A high diversity of the bacterial community was observed whilst the root fungal assemblage of NAT plants was richer than that of NURS. Root and rhizosphere fungal communities from NAT plants were characterized by Illumina MiSeq sequencing. Most of the identified sequences were affiliated to Helotiales, Pezizales, and Malasseziales. Ascomycota and Basidiomycota dominated roots and rhizosphere but differed in community structure and composition. ECM in the roots mainly belonged to Tylospora and Leccinum, while Rhizopogon was abundant in the rhizosphere. The Helotiales, including ERM (mostly Oidiodendron) and DSE (mostly Phialocephala), appeared the dominant component of the fungal community. B. aetnensis harbors an extraordinarily wide array of root-associated soil microorganisms, which are likely to be involved in the adaptation and resistance mechanisms to the extreme environmental conditions in volcano Etna. We argue that nursery-produced seedlings could lack the necessary microbiota for growth and development in natural conditions.

An Early Diagnosis of Thalassemia: A Boon to a Healthy Society

The β-thalassemia is a hereditary blood disorders, characterized by reduced or absent synthesis of the hemoglobin beta chain that cause microcytic hypochromic anemia. An early diagnosis, economical test, awareness programs and prenatal screening will be a milestone for the eradication of this genetic disorder and to reduce burden of the health sector of a country subsequently the economics. Initially, the diagnosis of β-thalassemia depends on the hematological tests with red cell indices that disclosed the microcytic hypochromic anemia.Hemoglobin analysis shows the abnormal peripheral blood smear with nucleated red blood cells, and reduced amounts of hemoglobin A (HbA). In severe anemia, the hemoglobin analysis by HPLC reveals decreased quantities of HbA and increased the level of hemoglobin F (HbF).The decrease level of MCV and MCH are also associated with β-thalassemia. There are various different molecular techniques such as ARMS PCR, allele-specific PCR, Gap PCR, denaturing gradient gel electrophoresis, reverse dot blotting, DGGE, SSCP, HRM, MLPA, sequencing technology and microarray available to identify the globin chain gene mutations. These molecular techniques can be clustered for detection by mutation types and alteration in gene sequences.

Identification of Mycoplasma species and related organisms from ruminants in England and Wales during 2005–2019

Background Mycoplasma species have been associated with economically important diseases affecting ruminants worldwide and include contagious bovine pleuropneumonia (CBPP), contagious caprine pleuropneumonia (CCPP) and contagious agalactia, listed by the World Organisation for Animal Health (OIE). The Mycoplasma Team at the Animal and Plant Health Agency provides an identification service for Mycoplasma and Ureaplasma species of veterinary importance to the United Kingdom (UK), supporting the detection of new and emerging pathogens, as well as contributing to the surveillance of endemic, and the OIE listed diseases exotic to the UK. Mycoplasma and other Mollicutes species were identified from diagnostic samples from farmed ruminants in England and Wales using a combination of culture and 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis, submitted between 2005 and 2019. Results A total of 5578 mollicutes identifications, which include mycoplasmas and the related acholeoplasmas and ureaplasmas, were made from farmed ruminant animals during the study period. Throughout the study period, the pathogen Mycoplasma bovis was consistently the most frequently identified species, accounting for 1411 (32%) of 4447 molecular identifications in cattle, primarily detected in the lungs of pneumonic calves, followed by joints and milk of cattle showing signs of arthritis and mastitis, respectively. M. bovirhinis, M. alkalescens, M. dispar, M. arginini and Ureaplasma diversum, were also common. Mixed species, principally M. bovis with M. alkalescens, M. arginini or M. bovirhinis were also prevalent, particularly from respiratory samples. The non-cultivable blood-borne haemoplasmas Candidatus ‘Mycoplasma haemobos’ and Mycoplasma wenyonii were identified from cattle, with the latter species most often associated with milk-drop. M. ovipneumoniae was the predominant species identified from sheep and goats experiencing respiratory disease, while M. conjunctivae preponderated in ocular samples. The UK remains free of the ruminant mycoplasmas listed by OIE. Conclusions The continued high prevalence of M. bovis identifications confirms its ongoing dominance and importance as a significant pathogen of cattle in England and Wales, particularly in association with respiratory disease. M. ovipneumoniae has seen a general increase in prevalence in recent years, notably in coughing lambs and should therefore be considered as a primary differential diagnosis of respiratory disease in small ruminants.

Bacterioplankton Community as a Biological Element for Reservoirs Water Quality Assessment

The Water Framework Directive (WFD) is used to evaluate the water quality of aquatic ecosystems. Phytoplankton is the only biological element considered in the reservoirs water quality assessment. In this study, we aimed to assess the use of the bacterioplankton community as an indicator of water quality, using a culture-independent assay (denaturing gradient gel electrophoresis, DGGE). Four Portuguese reservoirs (Miranda, Pocinho, Aguieira and Alqueva) were analysed in four periods (autumn 2018, spring and autumn 2019, and spring 2020). Bacterial total abundance had similar values for Miranda, Pocinho and Aguieira, and generally lower values for Alqueva. Diversity and richness values did not show a clear trend. Negative correlations were observed between some nutrients and the bacterial community. Overall, members of Actinobacteria, Bacteroidetes, Cyanobacteria, Nitrospirae and Proteobacteria were identified in all sampling sites. In Alqueva, no spatial, temporal or water body quality relationships with bacterial community were observed, which may be due to its higher size, low water velocity rate and higher residence times. However, in Miranda, Pocinho and Aguieira, a strong spatial and temporal bacterial community dynamic was observed. Furthermore, the presence of some species (e.g., Acinetobacter sp.) may reflect the poor water quality that was not detected by the WFD approach.

Impact of Hinoki Cypress Wood on Diversity of Microflora: A Case Study from Owase City Hall

Hinoki cypress (Chamaecyparis obtusa) shows durability against termites and wood decay-causing fungi and is used as a construction material in Japan. However, the effects of the material are still not fully understood. The aim of this study was to evaluate whether Hinoki cypress has antimicrobial effects against airborne microorganisms. We examined the influence of Hinoki cypress on the growth of airborne bacteria and fungi using culture-based methods. The growth of bacterial colonies was observed after day 3 in the control group without Hinoki material. In contrast, the growth of bacterial colonies was observed after day 13 in the experimental group containing Hinoki material. In the experimental group, the number of fungal colonies was smaller than that in the control group, suggesting the antifungal effect of Hinoki cypress to some extent. In addition, we characterized the community structure of airborne bacteria in two rooms with and without cypress wood by the culture-independent method of PCR-denaturing gradient gel electrophoresis. This also suggested differences in the community structure of airborne bacteria depending on the presence or absence of Hinoki cypress wood. These results indicate that Hinoki cypress might be a useful functional material in building environments.

Analysis of microflora in dentinal tubule by denaturing gradient gel electrophoresis

This study was performed to apply denaturing gradient gel electrophoresis to microbiological examination of endodontic infections. The method was used to assess the bacterial communities in dentinal tubules. Samples were collected using #15, #35, and #60 K-type files from five infected root canals during treatment. Deoxyribonucleic acid(DNA) was extracted from the samples, and 16S ribosomal DNA was amplified by PCR using universal primers. The polymerase chain reaction(PCR) products were separated in the denaturing gel and band patterns were compared between the deep (#60 file) and superficial layers (#15 file) of the dentin. The major bands were then excised and DNA fragments in the gel were cloned and sequenced. The sequence data were subjected to BLAST search in the GenBank database for determination of bacterial species or closest relatives. In three root canals, similar band patterns were observed in both superficial and deep layers of the dentin, while several specific bands remained in the deep layer in two roots. The bacteria isolated from the deep layers were Porphyromonas gingivalis, Olsenella profuse, Atopobium rimae, and Prevotella, Flexistipes, Firmicutes, Peptostreptococcus, Dialister, and Eubacterium spp. Unlike previous studies, gram-negative anaerobic rods were isolated from the deep layers. Clone library analysis was simultaneously performed and similar results were obtained. The method utilized here will be useful for microbiological examination of endodontic infections. In addition, although it is still unknown whether they were viable, this study demonstrated the presence of gram-negative rods in dentinal tubules.

Succession and Catabolic Properties of Fungal Community During Composting of Fruit Waste at Sub-Tropical Environment

A comprehensive profile of structural and functional dynamics of fungal community during fruit waste composting was investigated. For this purpose, fruit waste was composted in a windrow setup. Representative samples were collected at varied range of incubation temperatures during composting period and employed to physicochemical and microbiological culture dependent and independent analysis. Time-series data revealed that variation in fungal load is temperature dependent that influenced morphotypes’ shifts during different stages of composting. Shifts in abiotic factors, availability of accessible nutrients, water loss, pH and electrical conductivity participated in the transition of community and compost maturity. Culture-based analysis showed rich microbial compost community, dominant with Aspergillus, Mucor, Rhizopus and Penicillium. Denaturing gradient gel electrophoresis analyses demonstrated the prevalence of diverse community in compost with detectable bands corresponding to Penicillium at mesophilic temperature while undetectable bands corresponding for Aspergillus. Succession in microbial community was observed during composting as with temperature variations. Illumina Miseq revealed fungal diversity including Mortierella sp from phylum Zygomycota as the most dominant fungi and Coprinopsis sp as second dominant from Basidiomycota, mainly associated with lignocellulosic degradation. Moreover, Aspergillus fumigatus (ADIF1) was found as the most promising cellulase and pectinase producers at higher temperature showing its potential for efficient environmental management utilization. Current findings suggest that transformation of fruit waste into seed germination friendly compost that can be used as an efficient organic fertilizer and incorporation of sensitive molecular technique suggests the transition of microbial community and improvement in microbial diversity.

Responsiveness of Elite Cultivars vs. Ancestral Genotypes of Barley to Beneficial Rhizosphere Microbiome, Supporting Plant Defense Against Root-Lesion Nematodes

Harnessing plant-microbe interactions to advance crop resistance to pathogens could be a keystone in sustainable agriculture. The breeding of crops to maximize yield in intensive agriculture might have led to the loss of traits that are necessary for beneficial plant-soil feedback. In this study, we tested whether the soil microbiome can induce a stronger plant defense against root-lesion nematodes in ancestral genotypes of barley than in elite cultivars. Plants were grown in a sterile substrate with or without the inoculation of rhizosphere microbiomes, and Pratylenchus neglectus was inoculated to the roots. Unexpectedly, elite cultivars profited significantly more from the microbiome than ancestral genotypes, by the reduction of nematodes in roots and the increased shoot weight relative to control plants. The elite cultivars had higher microbial densities in the rhizosphere, which were correlated with root weight. The structure of the bacterial and fungal community of elite and ancestral genotypes differed, as compared by 16S rDNA or internal transcribed spacer amplicon profiles in denaturing gradient gel electrophoresis. The elite cultivars differed in responsiveness to the microbiome. For the most responsive cultivars Beysehir and Jolgeh, the strong microbe-induced suppression of nematodes coincided with the strongest microbe-dependent increase in transcripts of salicylic acid-regulated defense genes after nematode invasion, while the jasmonate-regulated genes LOX2 and AOS were downregulated in roots with the inoculated microbiome. The microbe-triggered modulation of defense gene expression differed significantly between elite and ancestral genotypes of barley. Soil microbiomes conditioned by maize roots suppressed the nematodes in elite cultivars, while the corresponding bulk soil microbiome did not. In conclusion, cultivars Beysehir and Jolgeh harbor the genetic background for a positive plant-microbiome feedback. Exploiting these traits in breeding for responsiveness to beneficial soil microbiomes, accompanied by soil biome management for compatible plant-microbe interactions, will support low-input agriculture and sustainability.