scholarly journals Managed and Unmanaged Pinus sylvestris Forest Stands Harbour Similar Diversity and Composition of the Phyllosphere and Soil Fungi

2020 ◽  
Vol 8 (2) ◽  
pp. 259 ◽  
Author(s):  
Jūratė Lynikienė ◽  
Diana Marčiulynienė ◽  
Adas Marčiulynas ◽  
Artūras Gedminas ◽  
Miglė Vaičiukynė ◽  
...  
Keyword(s):  
Pinus Sylvestris ◽  
National Parks ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Forest Stands ◽  
Forest Zone ◽  
The North ◽  
Study Sites

The aim was to assess fungal communities associated with living needles and soil of Pinus sylvestris in managed and unmanaged forest stands to get a better understanding of whether and how different intensities of forest management affects fungal diversity and community composition under the north temperate forest zone conditions. The study was carried out in three national parks in Lithuania. Each included five study sites in managed stands and five in unmanaged stands. At each site, three random soil cores and five random last-year needle samples were collected. Following DNA isolation, a DNA fragment of the ITS2 rRNA gene region of each sample was individually amplified and subjected to high-throughput sequencing. Analysis of 195,808 high-quality reads showed the presence of 1909 fungal taxa. Richness and composition of fungal taxa were similar in each substrate (needles and soil) in managed vs. unmanaged sites. The most common fungi in needles were Coleosporium campanulae (12.4% of all fungal sequences), Unidentified sp. 3980_1 (12.4%), Unidentified sp. 3980_4 (4.1%) and Sydowia polyspora (3.1%). In soil: Unidentified sp. 3980_21 (8.6%), Umbelopsis nana (8.2%), Archaeorhizomyces sp. 3980_5 (8.1%) and Penicillium spinulosum (6.3%). The results demonstrated that managed and unmanaged P. sylvestris stands support similar diversity and composition of fungal communities associated with living needles and soil.

scholarly journals Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota

2013 ◽  
Vol 80 (2) ◽  
pp. 478-485 ◽  
Author(s):  
Yue Tang ◽  
Anthony Underwood ◽  
Adriana Gielbert ◽  
Martin J. Woodward ◽  
Liljana Petrovska
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Abundant Species ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Content Type ◽  
Chicken Gut Microbiota

ABSTRACTThe animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identifiedClostridiales,Bacteroidaceae, andLactobacillaceaespecies as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged toLactobacillusspp., 155 belonged toClostridiumspp., and 66 belonged toStreptococcusspp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.

Early ecological succession patterns of bacterial, fungal and plant communities along a chronosequence in a recently deglaciated area of the Italian Alps

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
A Franzetti ◽  
F Pittino ◽  
I Gandolfi ◽  
R S Azzoni ◽  
G Diolaiuti ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Inorganic Compounds ◽  
Alpha Diversity ◽  
Ecological Succession ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Italian Alps ◽  
Weathering Processes ◽  
Pioneer Plants ◽  
Heterotrophic Metabolism

ABSTRACT In this study, the early ecological succession patterns of Forni Glacier (Ortles-Cevedale group, Italian Alps) forefield along an 18-year long chronosequence (with a temporal resolution of 1 year) has been reported. Bacterial and fungal community structures were inferred by high-throughput sequencing of 16S rRNA gene and ITS, respectively. In addition, the occurrence of both herbaceous and arboreous plants was also recorded at each plot. A significant decrease of alpha-diversity in more recently deglaciated areas was observed for both bacteria and plants. Time since deglaciation and pH affected the structure of both fungal and bacterial communities. Pioneer plants could be a major source of colonization for both bacterial and fungal communities. Consistently, some of the most abundant bacterial taxa and some of those significantly varying with pH along the chronosequence (Polaromonas, Granulicella, Thiobacillus, Acidiferrobacter) are known to be actively involved in rock-weathering processes due to their chemolithotrophic metabolism, thus suggesting that the early phase of the chronosequence could be mainly shaped by the biologically controlled bioavailability of metals and inorganic compounds. Fungal communities were dominated by ascomycetous filamentous fungi and basidiomycetous yeasts. Their role as cold-adapted organic matter decomposers, due to their heterotrophic metabolism, was suggested.

scholarly journals Molecular Survey and Genetic Identification of Anaplasma Species in Goats from Central and Southern China

2011 ◽  
Vol 78 (2) ◽  
pp. 464-470 ◽  
Author(s):  
Zhijie Liu ◽  
Miling Ma ◽  
Zhaowen Wang ◽  
Jing Wang ◽  
Yulv Peng ◽  
...  
Keyword(s):  
Southern China ◽  
Genetic Identification ◽  
Single Infection ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Anaplasma Ovis ◽  
Content Type ◽  
Obligate Intracellular ◽  
The North

ABSTRACTAnaplasmaspecies are obligate intracellular rickettsial pathogens that impact the health of humans and animals. Few studies have been carried out onAnaplasmainfections in central and southern China. This study was conducted to determine the coinfection rates ofAnaplasma ovis,A. bovis, andA. phagocytophilumfrom 262 field blood samples of goats in these regions. The average prevalences of single infection ofA. ovis,A. bovis, andA. phagocytophilumwere 15.3, 16.0, and 6.1%, respectively. Coinfection ofA. ovisandA. boviswas dominant, with an infection rate of 27.1%. Coinfection ofA. ovisandA. phagocytophilumwas 1.9% and that ofA. bovisandA. phagocytophilumwas 4.2%. Three-pathogen coinfection was found in three of four investigated provinces with a prevalence between 0 and 5.3%. The accuracy of the PCR results was corroborated by sequencing. Analysis of the 16S rRNA gene sequences ofA. bovisandA. phagocytophilumconfirmed the presence of these pathogens at the investigated sites and indicated the possible genetic diversity ofA. phagocytophilum. Field blood inoculation of experimental animals led to successful identification and observation of the morphological shapes ofA. bovisin the infected monocytes of sheep. Phylogenetic study withmsp4sequences ofA. ovisindicated that theA. ovisgenotypes from sheep in the north differed from the genotypes of goats in the investigated sites.

scholarly journals Fungal communities in the biofilms colonizing the basalt sculptures of the Leizhou Stone Dogs and assessment of a conservation measure

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yali Wang ◽  
Huan Zhang ◽  
Xiaobo Liu ◽  
Xiaoqing Liu ◽  
Wei Song
Keyword(s):  
High Throughput Sequencing ◽  
Antimicrobial Agents ◽  
Fungal Communities ◽  
Water Repellent ◽  
Sequencing Analysis ◽  
Fungal Community Structure ◽  
Conservation Measure ◽  
History Of ◽  
Effective Conservation ◽  
Microbial Attack

AbstractThe Leizhou Peninsula in China is very famous for its unique folk art creation, especially for the stonework, like the basalt sculptures of the Leizhou Stone Dogs, which have a history of more than two thousand years. Since these sculptures are usually exposed outdoors, many of them are suffering from severe damage by lichen and fungi. To protect them from microbial attack, we determined fungal communities in the biofilms colonizing the stone dogs and explored an effective conservation measure. Specifically, the micromorphology analysis of the biofilms on the stone dogs was performed through both on-site and laboratory-based microscopies in order to provide an overview of the fungal community structure. High-throughput sequencing analysis revealed that the predominant fungi in the biofilms belong to the following genera Caloplaca, Chaetomium, Clitopilus, Acanthostigma, Tolypocladium, Aspergillus, and Toxicocladosporium. The energy dispersive X-ray spectrometry (EDS) showed that the basalt is mainly composed of silica (53% by weight), followed by Al2O3 (14.4%), Fe2O3 (10.1%), CaO (8.4%), and MgO (7.4%) that are oxides susceptible to corrosion of biogenic acids. The EDS analysis of the hyphae provided the direct evidence on the leaching of the minerals of the sculptures. To control microbial attack, three kinds of antimicrobial agents were tested for 2 years. As a result, the mixture of biocide and water repellent showed the best effectiveness. Our findings provide an overview of fungi diversity in the biofilms on the stone dogs and help the investigation of fungi-induced biodeterioration and the exploration of specific conservation measure.

scholarly journals Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis

2018 ◽  
Vol 83 (5) ◽  
pp. 1333-1341 ◽  
Author(s):  
Maria Teresa P. Gonçalves ◽  
María José Benito ◽  
María de Guía Córdoba ◽  
Conceição Egas ◽  
Almudena V. Merchán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Rrna Gene Sequencing ◽  
Culture Dependent

scholarly journals Decaying Logs Enrich Soil Fungal Communities in the Forest Ecosystem

2021 ◽  
Author(s):  
Qin Wang ◽  
Josep Peñuelas ◽  
Bo Tan ◽  
Zhuang Wang ◽  
Han Li ◽  
...  
Keyword(s):  
Forest Ecosystem ◽  
Soil Fungi ◽  
High Throughput Sequencing ◽  
Coniferous Forest ◽  
Biochemical Properties ◽  
Fungal Communities ◽  
Tibet Plateau ◽  
Sequencing Analysis ◽  
Fungal Community Composition ◽  
Microbial Biomass Nitrogen

Abstract Aims: Soil fungi are crucial drivers of log decomposition in forest ecosystems. The objective of this study was thus to assess the conservation roles of decaying logs on soil fungi.Methods: Five classes of decaying Minjiang fir (Abies faxoniana) logs were incubated on the forest floor in a subalpine coniferous forest on the eastern Qinghai-Tibet Plateau, China, and the fungal communities compositions of the soil under decaying logs were assessed using high-throughput sequencing. Results: A total of 4321 operational taxonomic units (OTUs) were detected by Illumina MiSeq sequencing analysis. Basidiomycota and Ascomycota were dominant phyla regardless of log decay classes. With the log decomposition, the proportion of arbuscular mycorrhiza, wood saprotroph and saprotroph increased, but that of ectomycorrhiza decreased. Moreover, the diversity of soil fungal communities also increased along the decomposing process of logs. The decaying logs significantly altered soil fungal community composition by affecting biochemical properties (e.g. pH and concentrations of microbial biomass nitrogen and total phosphorus) and environmental factors (e.g. soil water content). Conclusion: Different decay classes of logs favor special fungal species, implying that the logs conservation with different decay classes in the forest ecosystem is of great significance for improving the diversity of soil fungi.

scholarly journals Bacterial and plankton communities in mariculture water sources: a case study in Nampu and Sembukan seawaters, Wonogiri, Indonesia

2021 ◽  
Vol 30 (2) ◽  
pp. 351-366
Author(s):  
Yuni Puji Hastuti ◽  
◽  
Yuli Siti Fatma ◽  
Hardi Pitoyo ◽  
Yusli Wardiatno ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Marine Ecosystem ◽  
Water Source ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Phyla ◽  
Central Java ◽  
Seawater Samples ◽  
Plankton Diversity ◽  
Plankton Communities

Seawaters in Indonesia, part of the tropical marine ecosystem, have great microbial and plankton diversity. Seawater is used as a water source for marine aquacultures, such as shrimp, milkfish, lobster, and mud crab. Sustainability of environmental resources for supporting aquaculture activities can be assessed by analyzing the actual conditions of the water source environment, including bacterial and plankton communities. However, the characteristics of bacteria and plankton communities in Indonesian seawaters have not been well documented. In this study, we investigated the bacterial and plankton communities in surface seawater from two coastal areas, i.e. Nampu and Sembukan, Wonogiri regency, Central Java, Indonesia. Bacterial diversity was analyzed using the Illumina-based high throughput sequencing with a primer set targeting the V3-V4 region of the bacterial 16S rRNA gene. Meanwhile, the plankton community (phytoplankton and zooplankton) was calculated and identified using a counting chamber method. Sequencing analysis revealed that the five dominant bacterial phyla in the two seawater samples were similar, consisting of Proteobacteria, Firmicutes, Actinobacteria, Bacteriodetes, and Cyanobacteria. Although the two sites are separated by several kilometres, the distribution of dominant bacterial phyla in both seawater samples is similar. Phytoplankton in Nampu and Sembukan were similarly dominated by Trichodesmium sp., Navicula sp., and Rhabdonema sp. Dominant zooplankton in the two sites were Euterpina, Nauplius, Oithona sp., Oncaea sp., Tigriopus sp., and Gastropoda larvae. The seawater in Nampu and Sembukan is suitable as a water source for aquaculture.

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

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