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 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 Influence of intramuscular depot-medroxyprogesterone acetate initiation on vaginal microbiota in the postpartum period

2020 ◽  
Author(s):  
Bridget M Whitney ◽  
Sujatha Srinivasan ◽  
Kenneth Tapia ◽  
Eric Munene Muriuki ◽  
Bhavna H Chohan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Medroxyprogesterone Acetate ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Bacterial Load ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Nugent Score ◽  
Depot Medroxyprogesterone Acetate ◽  
Significant Difference

Abstract Background The vaginal microbiome plays a key role in women’s reproductive health. Use of exogenous hormones, such as intramuscular depot-medroxyprogesterone acetate (DMPA-IM), may alter the composition of vaginal bacterial community. Methods Vaginal swabs were collected from postpartum Kenyan women initiating DMPA-IM or non-hormonal contraception (non-HC). Bacterial vaginosis was assessed by Nugent score (Nugent-BV) and bacterial community composition was evaluated using broad-range 16S rRNA gene PCR with high-throughput sequencing. Changes in Nugent score, alpha diversity (Shannon diversity index), and total bacterial load between contraceptive groups from enrollment to three-months post-initiation were estimated using multivariable linear mixed effects regression. Results Among 54 HIV-negative women, 33 choosing DMPA-IM and 21 choosing non-HC, Nugent-BV was more common among DMPA-IM users at enrollment. At follow-up, Nugent score had decreased significantly among DMPA-IM users (Δ=-1.89 (95%CI:-3.53, -0.25; p=0.02) while alpha diversity remained stable (Δ=0.03, 95%CI:-0.24, 0.30; p=0.83). Conversely, Nugent score remained relatively stable among non-HC users (Δ=-0.73, 95%CI:-2.18, 0.73; p=0.33) while alpha diversity decreased (Δ=-0.34, 95%CI:-0.67, -0.001; p=0.05). Total bacterial load decreased slightly in DMPA-IM users and increased slightly among non-HC users, resulting in a significant difference in change between the contraceptive groups (difference=-0.64 log10 gene copies/swab, 95%CI:-1.19, -0.08; p=0.02). While significant changes in Nugent score and alpha diversity were observed within contraceptive groups, changes between groups were not significantly different. Conclusions Postpartum vaginal bacterial diversity did not change in DMPA-IM users despite a reduction in Nugent-BV, but decreased significantly among women using non-HC. Choice of contraception may influence Lactobacillus recovery in postpartum women.

scholarly journals Niche specificity and functional diversity of the bacterial communities associated with Ginkgo biloba and Panax quinquefolius

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hanan R. Shehata ◽  
Subramanyam Ragupathy ◽  
Thomas A. Henry ◽  
Steven G. Newmaster
Keyword(s):  
Functional Diversity ◽  
Ginkgo Biloba ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Panax Quinquefolius ◽  
Tissue Type ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Kegg Pathways

AbstractPlant-associated bacteria can establish mutualistic relationships with plants to support plant health. Plant tissues represent heterogeneous niches with distinct characteristics and may thus host distinct microbial populations. The objectives of this study are to investigate the bacterial communities associated with two medicinally and commercially important plant species; Ginkgo biloba and Panax quinquefolius using high Throughput Sequencing (HTS) of 16S rRNA gene, and to evaluate the extent of heterogeneity in bacterial communities associated with different plant niches. Alpha diversity showed that number of operational taxonomic units (OTUs) varied significantly by tissue type. Beta diversity revealed that the composition of bacterial communities varied between tissue types. In Ginkgo biloba and Panax quinquefolius, 13% and 49% of OTUs, respectively, were ubiquitous in leaf, stem and root. Proteobacteria, Bacteroidetes, Actinobacteria and Acidobacteria were the most abundant phyla in Ginkgo biloba while Proteobacteria, Bacteroidetes, Actinobacteria, Plantomycetes and Acidobacteria were the most abundant phyla in Panax quinquefolius. Functional prediction of these bacterial communities using MicrobiomeAnalyst revealed 5843 and 6251 KEGG orthologs in Ginkgo biloba and Panax quinquefolius, respectively. A number of these KEGG pathways were predicted at significantly different levels between tissues. These findings demonstrate the heterogeneity, niche specificity and functional diversity of plant-associated bacteria.

scholarly journals Factors Influencing the Fungal Diversity on Audio–Visual Materials

2021 ◽  
Vol 9 (12) ◽  
pp. 2497
Author(s):  
Tereza Branysova ◽  
Martina Kracmarova ◽  
Michal Durovic ◽  
Katerina Demnerova ◽  
Hana Stiborova
Keyword(s):  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Abundant Species ◽  
Future Generations ◽  
Fungal Communities ◽  
Air Contamination ◽  
Factors Influencing ◽  
Significant Difference ◽  
Visual Materials ◽  
Cultural Heritage Objects

The biodeterioration of audio–visual materials is a huge problem, as it can cause incalculable losses. To preserve these cultural heritage objects for future generations, it is necessary to determine the main agents of biodeterioration. This study focuses on identifying fungi, both from the air and smears from photographs and cinematographic films that differ in the type of carrier and binder, using high-throughput sequencing approaches. The alpha diversity measures of communities present on all types of carriers were compared, and a significant difference between cellulose acetate and baryta paper was observed. Next, the locality, type of carrier, and audio–visual material seem to affect the structure of fungal communities. Additionally, a link between the occurrence of the most abundant classes and species on audio–visual materials and air contamination in the archives was proven. In both cases, the most abundant classes were Agariomycetes, Dothideomycetes, and Eurotiomycetes, and approximately half of the 50 most abundant species detected on the audio–visual materials and in the air were identical.

scholarly journals The gut microbiota of wild wintering great bustard (Otis tarda dybowskii): survey data from two consecutive years

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12562
Author(s):  
Zhiyuan Lu ◽  
Sisi Li ◽  
Hongxia Li ◽  
Zhucheng Wang ◽  
Derong Meng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Health It ◽  
Great Bustard ◽  
Microbial Composition ◽  
Protective Measures ◽  
Essential Information ◽  
Evaluation Indicator

Background The composition of the intestinal microbiota plays a significant role in modulating host health. It serves as a sensitive evaluation indicator and has substantial implications in protecting endangered species. Great Bustards are typical farmland-dependent wintering birds that are highly susceptible to the interference of human activities. However, information regarding their gut microbiota remains scarce. Methods To ensure a comprehensive analysis of this crucial data, we collected fecal samples from wild Great Bustards at their wintering habitat for two consecutive years. High-throughput sequencing of the 16S rRNA gene was subsequently applied to characterize their core gut microbiota and determine whether the gut microbial composition was similar or varied interannually. Results The gut microbiota of the Great Bustard was primarily comprised of four phyla: Firmicutes (82.87%), Bacteroidetes (7.98%), Proteobacteria (4.49%), and Actinobacteria (3.67%), accounting for 99.01% of the microbial community in all samples. Further analysis revealed 22 genera of core microbes and several pathogens. Notably, there were no significant differences in the alpha-diversity and beta-diversity between the two sample groups from different years. Conclusions This study provides essential information for assessing the health and developing targeted protective measures of this threatened species.

scholarly journals Genetic Diversity, Community Assembly, and Shaping Factors of Benthic Microbial Eukaryotes in Dongshan Bay, Southeast China

2020 ◽  
Vol 11 ◽  
Author(s):  
Rong Gu ◽  
Ping Sun ◽  
Ying Wang ◽  
Fengling Yu ◽  
Nianzhi Jiao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput Sequencing ◽  
Sediment Cores ◽  
Geographic Distance ◽  
Alpha Diversity ◽  
Small Subunit ◽  
Rrna Gene ◽  
Anthropogenic Pressure ◽  
Southeast China ◽  
Microbial Eukaryotes

Microbial eukaryotes are pivotal components of marine ecosystems. However, compared with the pelagic environments, the diversity distribution and the driving mechanisms of microbial eukaryotes in the marine sediments have rarely been explored. In this study, sediment cores were collected along a transect from inner to outer Dongshan Bay, Southeast China. By combining high throughput sequencing of small-subunit (SSU) rRNA gene with measurements on multiple environmental variables, the genetic diversity, community structure and assembly processes, and environmental shaping factors were investigated. Alveolata (mainly Ciliophora and Dinophyceae), Rhizaria (mainly Cercozoa), and Stramenopiles (mainly Bacillariophyta) were the most dominant groups in terms of both relative sequence abundance and operational taxonomic unit (OTU) richness. Grain size composition of the sediment was the primary factor determining the alpha diversity of microbial eukaryotes followed by sediment depth and heavy metal, including chromium (Cr), zinc (Zn), and plumbum (Pb). Geographic distance and water depth surpassed other environmental factors to be the primary factors shaping the microbial eukaryotic communities. Dispersal limitation was the primary driver of the microbial eukaryotic communities, followed by drift and homogeneous selection. Overall, our study shed new light on the spatial distribution patterns and controlling factors of benthic microbial eukaryotes in a subtropical bay which is subjected to increasing anthropogenic pressure.

scholarly journals Root-Associated Mycobiome Differentiate between Habitats Supporting Production of Different Truffle Species in Serbian Riparian Forests

2020 ◽  
Vol 8 (9) ◽  
pp. 1331
Author(s):  
Žaklina Marjanović ◽  
Ali Nawaz ◽  
Katarina Stevanović ◽  
Elmira Saljnikov ◽  
Irena Maček ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Forest Type ◽  
Alpha Diversity ◽  
Riparian Forests ◽  
Fungal Communities ◽  
Soil Conditions ◽  
Black Truffle ◽  
Taxonomic Profiling ◽  
The Core ◽  
White Truffle

Balkan lowlands bordering with the Pannonia region are inhabited by diverse riparian forests that support production of different truffle species, predominantly the most prized white truffle of Piedmont (Tuber magnatum Pico), but also other commercial species (T.macrosporum Vitt., T. aestivum Vitt.). Surprisingly, little is known about the native root-associated mycobiome (RAM) of these lowland truffle-producing forests. Therefore, in this study we aim at exploring and comparing the RAMs of three different truffle-producing forests from Kolubara river plane in Serbia. Molecular methods based on next generation sequencing (NGS) were used to evaluate the diversity of root-associated fungal communities and to elucidate the influence of environmental factors on their differentiation. To our knowledge, this is the first study from such habitats with a particular focus on comparative analysis of the RAM in different truffle-producing habitats using a high-throughput sequencing approach. Our results indicated that the alpha diversity of investigated fungal communities was not significantly different between different truffle-producing forests and within a specific forest type, while the seasonal differences in the alpha diversity were only observed in the white truffle-producing forests. Taxonomic profiling at phylum level indicated the dominance of fungal OTUs belonging to phylum Ascomycota and Basidiomycota, with very minor presence of other phyla. Distinct community structures of root-associated mycobiomes were observed for white, mixed, and black truffle-producing forests. The core mycobiome analysis indicated a fair share of fungal genera present exclusively in white and black truffle-producing forest, while the core genera of mixed truffle-producing forests were shared with both white and black truffle-producing forests. The majority of detected fungal OTUs in all three forest types were symbiotrophs, with ectomycorrhizal fungi being a dominant functional guild. Apart from assumed vegetation factor, differentiation of fungal communities was driven by factors connected to the distance from the river and exposure to fluvial activities, soil age, structure, and pH. Overall, Pannonian riparian forests appear to host diverse root-associated fungal communities that are strongly shaped by variation in soil conditions.

scholarly journals Diet Induces the Difference of Gut Fungal Communities between Anser erythropus Wintering at Shengjin and Caizi Lakes, China

2021 ◽  
Author(s):  
Gang Liu ◽  
Zhizhong Gong ◽  
Jiahui Feng ◽  
Na Xu
Keyword(s):  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Fungal Communities ◽  
Pathogenic Species ◽  
Potential Pathogen ◽  
Host Nutrition ◽  
The Difference ◽  
Serious Disease ◽  
Anser Erythropus

Abstract The gut microbiota play major roles in host nutrition and metabolism, and even potential to cause serious disease for animals and human, however, the knowledge of waterbirds’ gut fungal communities are quite limited at present. In this paper, the gut fungal communities and infer the potential pathogens isolated from the feces of Anser erythropus wintering at Shengjin Lake (SJ) and Caizi Lake (CZ) were investigated based on ITS gene region by using high-throughput sequencing. 1,302,562 valid tags corresponding to 2,102 OTUs were retained from 20 fecal samples, including 10 samples per lake. The OTUs from SJ geese represented seven phyla and 27 classes, seven phyla and 28 classes were identified from CZ samples. Ascomycota, Basidiomycota, Zygomycota and Rozellomycota were the dominant gut fungal phyla in this study, accounted for 61.60%, 35.60%, 1.84%, and 0.30% of the OTUs, respectively. The alpha diversity indices showed significantly different between the geese from SJ and CZ. The Anser erythropus mainly ate Poaceae spp. at SJ, while Carex spp. component was identified at CZ, suggesting that the variations in fungal community between the two lake geese might be induced by different diets. We also observed a fungal pattern with a higher number of significant correlations to bacterial genus, and Ceratobasidium, Tomentella, Paurocotylis, Tuber, Podospora and Mortierella were core fungal genus in the two lake geese. Nine potential pathogenic species were identified in the guts across all samples of Anser erythropus at SJ and CZ, it also showed the relative abundance of potential pathogen was significantly higher from SJ samples than that from CZ samples. These findings expanded our knowledge on the gut fungi for waterbirds, indicating the fungi are highly sensitive to diet at two lakes and should pay more attention to the potential pathogenic species of Anser erythropus.

scholarly journals Cetobacterium Is a Major Component of the Microbiome of Giant Amazonian Fish (Arapaima gigas) in Ecuador

Animals ◽  
2018 ◽  
Vol 8 (11) ◽  
pp. 189 ◽  
Author(s):  
Carolina Ramírez ◽  
Jaime Coronado ◽  
Arturo Silva ◽  
Jaime Romero
Keyword(s):  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Large Fish ◽  
Differential Distribution ◽  
Intestinal Bacterial Community ◽  
Arapaima Gigas ◽  
Fast Growth Rate

Arapaima gigas is a large air-breathing fish found in Amazonian rivers, a characteristic that gives this species an advantage in oxygen-deprived waters. It shows high potential for aquaculture in the Amazon region due to its fast growth rate that approaches 10–15 kg/year. The aim of this study was to explore the composition of the intestinal bacterial community of Arapaima gigas reared in Ecuador using 16S rRNA gene high-throughput sequencing. The analysis revealed significant differences in alpha diversity indices (p < 0.05) and differential distribution of minor components of the intestinal microbiome between small and large fish. However, components with greater relative abundance, such as Cetobacterium, are found in similar proportions.

scholarly journals Streptomyces Application Triggers Reassembly and Optimization of the Rhizosphere Microbiome of Cucumber

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 413
Author(s):  
Yanjiang Zhang ◽  
Tian Zhang ◽  
Zhijing Xue ◽  
Yifan Liu ◽  
Yongzhe Li ◽  
...  
Keyword(s):  
Plant Growth ◽  
Relative Abundance ◽  
Stress Resistance ◽  
Growth Promotion ◽  
Alpha Diversity ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Cucumis Sativus L ◽  
Genus Streptomyces ◽  
Rhizosphere Microbiome

Streptomyces partum Act12 and Streptomyces roche D74 are biocontrol strains that can promote plant growth and enhance stress resistance in different crops. However, their effects on the rhizosphere microbiome and the role of the reassembled microbiome in plant growth promotion and stress resistance enhancement remain unclear. This study investigated the variation in the rhizosphere microbiome induced by Streptomyces application through a cucumber (Cucumis sativus L. cv. “Youliang”) pot experiment. The bacterial and fungal communities of rhizosphere soils inoculated with and without Streptomyces were, respectively, compared based on 16S rRNA and internal transcribed spacer rRNA gene sequences. Following Streptomyces application, the bacterial alpha diversity increased significantly, while the fungal alpha diversity exhibited the opposite trend. The bacterial and fungal communities’ compositions clearly shifted in the inoculated soil. Compared with the uninoculated control, the relative abundance of the genus Streptomyces increased by 68.3%, and the bacterial co-occurrence network in the rhizosphere soil was enriched significantly. The relative abundance of bacteria associated with nitrogen fixation was increased by 7.5% following Streptomyces application. Based on the results of this study, we conclude that the application of Streptomyces Act12 and D74 can be used to reassemble and optimize the rhizosphere microbiome of cucumber, which is conducive to plant survival.

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