scholarly journals Why Plants Harbor Complex Endophytic Fungal Communities: Insights From Perennial Bunchgrass Stipagrostis sabulicola in the Namib Sand Sea

2021 ◽  
Vol 12 ◽  
Author(s):  
Anthony J. Wenndt ◽  
Sarah E. Evans ◽  
Anne D. van Diepeningen ◽  
J. Robert Logan ◽  
Peter J. Jacobson ◽  
...  
Keyword(s):  
Focal Point ◽  
Nutrient Recycling ◽  
Fungal Endophyte ◽  
Fungal Communities ◽  
Island Effect ◽  
Endophyte Community ◽  
Standing Litter ◽  
Generation Sequencing ◽  
Laboratory Assay

All perennial plants harbor diverse endophytic fungal communities, but why they tolerate these complex asymptomatic symbioses is unknown. Using a multi-pronged approach, we conclusively found that a dryland grass supports endophyte communities comprised predominantly of latent saprophytes that can enhance localized nutrient recycling after senescence. A perennial bunchgrass, Stipagrostis sabulicola, which persists along a gradient of extreme abiotic stress in the hyper-arid Namib Sand Sea, was the focal point of our study. Living tillers yielded 20 fungal endophyte taxa, 80% of which decomposed host litter during a 28-day laboratory decomposition assay. During a 6-month field experiment, tillers with endophytes decomposed twice as fast as sterilized tillers, consistent with the laboratory assay. Furthermore, profiling the community active during decomposition using next-generation sequencing revealed that 59–70% of the S. sabulicola endophyte community is comprised of latent saprophytes, and these dual-niche fungi still constitute a large proportion (58–62%) of the litter community more than a year after senescence. This study provides multiple lines of evidence that the fungal communities that initiate decomposition of standing litter develop in living plants, thus providing a plausible explanation for why plants harbor complex endophyte communities. Using frequent overnight non-rainfall moisture events (fog, dew, high humidity), these latent saprophytes can initiate decomposition of standing litter immediately after tiller senescence, thus maximizing the likelihood that plant-bound nutrients are recycled in situ and contribute to the nutrient island effect that is prevalent in drylands.

scholarly journals Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland

2021 ◽  
Vol 11 (2) ◽  
pp. 620
Author(s):  
Magdalena Dyda ◽  
Agnieszka Laudy ◽  
Przemyslaw Decewicz ◽  
Krzysztof Romaniuk ◽  
Martyna Ciezkowska ◽  
...  
Keyword(s):  
Seasonal Changes ◽  
Microbial Community Composition ◽  
Fungal Communities ◽  
Bacterial Strains ◽  
Microbial Biodiversity ◽  
Acidophilic Bacteria ◽  
Almost All ◽  
Generation Sequencing ◽  
King John

The aim of the presented investigation was to describe seasonal changes of microbial community composition in situ in different biocenoses on historical sandstone of the Northern Pergola in the Museum of King John III’s Palace at Wilanow (Poland). The microbial biodiversity was analyzed by the application of Illumina-based next-generation sequencing methods. The metabarcoding analysis allowed for detecting lichenized fungi taxa with the clear domination of two genera: Lecania and Rhinocladiella. It was also observed that, during winter, the richness of fungal communities increased in the biocenoses dominated by lichens and mosses. The metabarcoding analysis showed 34 bacterial genera, with a clear domination of Sphingomonas spp. across almost all biocenoses. Acidophilic bacteria from Acidobacteriaceae and Acetobacteraceae families were also identified, and the results showed that a significant number of bacterial strains isolated during the summer displayed the ability to acidification in contrast to strains isolated in winter, when a large number of isolates displayed alkalizing activity. Other bacteria capable of nitrogen fixation and hydrocarbon utilization (including aromatic hydrocarbons) as well as halophilic microorganisms were also found. The diversity of organisms in the biofilm ensures its stability throughout the year despite the differences recorded between winter and summer.

scholarly journals Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap

2020 ◽  
Vol 9 (1) ◽  
pp. 64
Author(s):  
Maija Nuppunen-Puputti ◽  
Riikka Kietäväinen ◽  
Lotta Purkamo ◽  
Pauliina Rajala ◽  
Merja Itävaara ◽  
...  
Keyword(s):  
Significant Proportion ◽  
Debaryomyces Hansenii ◽  
Fungal Communities ◽  
Fungal Colonization ◽  
Rock Surface ◽  
Mica Schist ◽  
Deep Subsurface ◽  
Bacterial Phyla ◽  
In Situ Conditions

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii.

scholarly journals Challenging Diagnosis in NUT Carcinoma

2021 ◽  
pp. 106689692110195
Author(s):  
Grosse Claudia ◽  
Grosse Alexandra
Keyword(s):  
Nuclear Protein ◽  
Hematological Malignancy ◽  
Undifferentiated Carcinoma ◽  
Squamous Differentiation ◽  
Poorly Differentiated Carcinoma ◽  
Poorly Differentiated ◽  
Nut Carcinoma ◽  
Disseminated Disease ◽  
Generation Sequencing

Nuclear protein in testis (NUT) carcinoma represents a highly aggressive, poorly differentiated carcinoma that is genetically defined by rearrangement of NUT gene. The histomorphological appearance ranges from entirely undifferentiated carcinoma to carcinoma with prominent squamous differentiation. NUT carcinoma can display neuroendocrine features. Although it is typically distributed along the midline axis, it may manifest in nonmidline locations. The majority of patients develop rapidly disseminated disease. We illustrate 2 cases of NUT carcinoma, one located in the lung, which closely resembled a neuroendocrine carcinoma, and the other one with assumed lung origin demonstrating metastatic dissemination with diffuse bone involvement, which was clinically first suspected to be a hematological malignancy. Due to its undifferentiated nature, NUT carcinoma may be confused with many entities. NUT immunohistochemistry is considered to be sufficient for the diagnosis. Fluorescence in-situ hybridization analysis and next-generation sequencing are currently used to confirm the diagnosis.

scholarly journals Cannabis microbiome sequencing reveals several mycotoxic fungi native to dispensary grade Cannabis flowers

F1000Research ◽  
2016 ◽  
Vol 4 ◽  
pp. 1422 ◽  
Author(s):  
Kevin McKernan ◽  
Jessica Spangler ◽  
Lei Zhang ◽  
Vasisht Tadigotla ◽  
Yvonne Helbert ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Food Safety ◽  
Agricultural Products ◽  
Third Party ◽  
Fungal Communities ◽  
Regulatory Requirement ◽  
Safety Testing ◽  
Food Borne ◽  
Generation Sequencing ◽  
The U.S

The Center for Disease Control estimates 128,000 people in the U.S. are hospitalized annually due to food borne illnesses. This has created a demand for food safety testing targeting the detection of pathogenic mold and bacteria on agricultural products. This risk extends to medicalCannabisand is of particular concern with inhaled, vaporized and even concentratedCannabisproducts.As a result, third party microbial testing has become a regulatory requirement in the medical and recreationalCannabismarkets, yet knowledge of theCannabismicrobiome is limited. Here we describe the first next generation sequencing survey of the fungal communities found in dispensary basedCannabisflowers by ITS2 sequencing, and demonstrate the sensitive detection of several toxigenicPenicilliumandAspergillusspecies, includingP. citrinum and P. paxilli,that were not detected by one or more culture-based methods currently in use for safety testing.

scholarly journals Variations in the Community Structure of Fungal Microbiota Associated with Apple Fruit Shaped by Fruit Bagging-Based Practice

2021 ◽  
Vol 7 (9) ◽  
pp. 764
Author(s):  
Punda Khwantongyim ◽  
Somying Wansee ◽  
Xi Lu ◽  
Wei Zhang ◽  
Guangyu Sun
Keyword(s):  
Management Practice ◽  
Agricultural Practices ◽  
Apple Fruit ◽  
Fungal Communities ◽  
Compositional Variation ◽  
Fungal Microbiota ◽  
Abundance And Diversity ◽  
Generation Sequencing ◽  
Fruit Part ◽  
Fruit Bagging

The various fungal communities that adhere to apple fruit are influenced by agricultural practices. However, the effects of fruit bagging-based management practice on the fungal microbiota are still unknown, and little is known about the fungal communities of bagged apple fruit. We conducted a study using apple fruit grown in a conventionally managed orchard where pesticide use is an indispensable practice. Fungal communities were collected from the calyx-end and peel tissues of bagged and unbagged fruit and characterized using barcode-type next-generation sequencing. Fruit bagging had a stronger effect on fungal richness, abundance, and diversity of the fungal microbiota in comparison to non-bagging. In addition, bagging also impacted the compositional variation of the fungal communities inhabiting each fruit part. We observed that fruit bagging had a tendency to maintain ecological equilibrium since Ascomycota and Basidiomycota were more distributed in bagged fruit than in unbagged fruit. These fungal communities consist of beneficial fungi rather than potentially harmful fungi. Approximately 50 dominant taxa were detected in bagged fruit, for example, beneficial genera such as Articulospora, Bullera, Cryptococcus, Dioszegia, Erythrobasidium, and Sporobolomyces, as well as pathogenic genera such as Aureobasidium and Taphrina. These results suggested that fruit bagging could significantly increase fungal richness and promote healthy fungal communities, especially the harmless fungal communities, which might be helpful for protecting fruit from the effects of pathogens. This study provides a foundation for understanding the impacts of bagging-based practice on the associated fungal microbiota.

scholarly journals Transplantation of the Mediterranean seagrass Posidonia oceanica through naturalistic engineering techniques: value, weakness and further improvements

2015 ◽  
Author(s):  
Stefano Acunto ◽  
Luigi Piazzi ◽  
Francesco L. Cinelli ◽  
Anna Maria De Biasi ◽  
Lorenzo Pacciardi ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Large Scale ◽  
Focal Point ◽  
Posidonia Oceanica ◽  
Hydrodynamic Conditions ◽  
Coastal System ◽  
Pros And Cons ◽  
The Mediterranean ◽  
Selection Of

Transplantation of seagrasses is considered a useful method to favour the recovery of degraded meadows. Hence, many projects have been carried out worldwide and a manifold of techniques have been applied. However, the choice of transplantation procedures remains a main problem to be assessed. In order to optimize efforts and to minimize risks of plants loss, the applied methodologies should take into account typology of hosting substratum, hydrodynamic conditions, depth and seagrass species. Due to their fundamental ecological role in the Mediterranean coastal system, many restoration projects aiming to preserve Posidonia oceanica meadows took place in the last decades. Several transplantation techniques have produced different results. In fact the same transplanting methodology may originate diverse results under different environmental conditions. Recently, naturalistic engineering techniques developed on land, have been used for transplantations of P. oceanica. Pilot projects concerning small surfaces were carried out between 2006 and 2010. More recently, a large-scale program (0.1 km2) was realized in 2012 at Civitavecchia (Roma, Thyrrenian Sea). The applied technique consists basically of mattresses filled with sand coupled with a net covering able to hold steady in situ the plant rhizomes. These structures have been variously modified in time to be adapted to the different type of substratum and various hydrodynamic conditions of the transplanting sites. Following the results of these transplantation experiences, we analyzed pros and cons of the techniques in order to improve the methodology. Firstly, these techniques may be considered suitable to large-scale projects allowing to minimize transplantation times. Secondly, the rhizomes may be successfully fixed to the structures; the majority of the transplanted shoots was not damaged showing a very good vegetative vitality with the production of new rhizomes, leaves and roots few months after transplanting. Finally, this procedure is flexible, as the basic technique can be modified and tailored to the various environmental conditions of the different receiving site. However, the results obtained in different areas are highly heterogeneous suggesting that a careful selection of the hosting site is a focal point. To this aim, a pilot study before the beginning of large-scale project seems mandatory, providing a fundamental support to guarantee successful results.

scholarly journals Foliar fungal endophyte community structure is independent of phylogenetic relatedness in an Asteraceae common garden

2020 ◽  
Vol 10 (24) ◽  
pp. 13895-13912
Author(s):  
Briana K. Whitaker ◽  
Natalie Christian ◽  
Qing Chai ◽  
Keith Clay
Keyword(s):  
Community Structure ◽  
Common Garden ◽  
Fungal Endophyte ◽  
Phylogenetic Relatedness ◽  
Endophyte Community

scholarly journals Herpetological phylogeographic analyses support a Miocene focal point of Himalayan uplift and biological diversification

2020 ◽  
Author(s):  
Wei Xu ◽  
Wen-Jie Dong ◽  
Ting-Ting Fu ◽  
Wei Gao ◽  
Chen-Qi Lu ◽  
...  
Keyword(s):  
Middle Miocene ◽  
Focal Point ◽  
Himalayan Region ◽  
The World ◽  
Early Paleocene ◽  
The Rich ◽  
Source Of Information ◽  
The Himalaya ◽  
Exact Timing

Abstract The Himalaya are among the youngest and highest mountains in the world, but the exact timing of their uplift and origins of their biodiversity are still in debate. The Himalayan region is a relatively small area but with exceptional diversity and endemism. One common hypothesis to explain the rich montane diversity is uplift-driven diversification–that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We test this hypothesis in the Himalayan region using amphibians and reptiles, two environmental sensitive vertebrate groups. In addition, analysis of diversification of the herpetofauna provides an independent source of information to test competing geological hypotheses of Himalayan orogenesis. We conclude that the origins of the Himalayan herpetofauna date to the early Paleocene, but that diversification of most groups was concentrated in the Miocene. There was an increase in both rates and modes of diversification during the early to middle Miocene, together with regional interchange (dispersal) between the Himalaya and adjacent regions. Our analyses support a recently proposed stepwise geological model of Himalayan uplift beginning in the Paleocene, with a subsequent rapid increase of uplifting during the Miocene, finally give rise to the intensification of the modern South Asia Monsoon.

scholarly journals Stem Endophytic Mycobiota in Wild and Domesticated Wheat: Structural Differences and Hidden Resources for Wheat Improvement

2020 ◽  
Vol 6 (3) ◽  
pp. 180
Author(s):  
Xiang Sun ◽  
Evsey Kosman ◽  
Amir Sharon
Keyword(s):  
Plant Species ◽  
Crop Improvement ◽  
Abundant Species ◽  
Fungal Endophyte ◽  
Wild Plants ◽  
Wheat Improvement ◽  
Structural Differences ◽  
Alternaria Infectoria ◽  
Candida Sake ◽  
Generation Sequencing

Towards the identification of entophytic fungal taxa with potential for crop improvement, we characterized and compared fungal endophyte communities (FECs) from domesticated bread wheat and two wheat ancestors, Aegilopssharonensis and Triticumdicoccoides. Data generated by next generation sequencing identified a total of 1666 taxa. The FECs in the three plant species contained high proportions of random taxa with low abundance. At plant species level, the majority of abundant taxa were common to all host plants, and the collective FECs of each of the three plant species had similar diversity. However, FECs from the wild plants in specific sites were more diverse and had greater richness than wheat FECs from corresponding specific fields. The wild plants also had higher numbers of differentially abundant fungal taxa than wheat, with Alternaria infectoria being the most abundant species in wild plants and Candida sake the most abundant in wheat. Network analysis on co-occurrence association revealed a small number of taxa with a relatively high number of co-occurrence associations, which might be important in community assembly. Our results show that the actual endophytic cargo in cultivated wheat plants is limited relative to wild plants, and highlight putative functional and hub fungal taxa with potential for wheat improvement.

Role of Ancillary Techniques in Biliary Cytopathology Specimens

2019 ◽  
Vol 64 (1-2) ◽  
pp. 175-181 ◽  
Author(s):  
Lester Layfield
Keyword(s):  
Mutational Analysis ◽  
Diagnostic Sensitivity ◽  
Individual Gene ◽  
Duct Systems ◽  
Brushing Cytology ◽  
Standard Of Practice ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Biliary brushing cytology has become the standard of practice for the investigation of strictures of the biliary and pancreatic duct systems. The methodology however has a limitation in that it has low diagnostic sensitivity when only cytologic evaluation is used. A number of testing methodologies have been applied to brushing specimens in an attempt to improve overall sensitivity without loss of specificity. These have included DNA ploidy analysis, immunocytochemistry, individual gene mutational analysis, fluorescence in-situ hybridization (FISH), and next generation sequencing (NGS). Currently, FISH coupled with routine cytology appears to be the method of choice for improving diagnostic sensitivity. NGS shows significant promise for improvement of diagnostic sensitivity.

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