scholarly journals The effect of flue-curing procedure on the dynamic change of microbial diversity of tobaccos

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Binbin Hu ◽  
Kaiyuan Gu ◽  
Jiangshiqi Gong ◽  
Ke Zhang ◽  
Dan Chen ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Theoretical Basis ◽  
High Throughput Sequencing ◽  
Dynamic Change ◽  
Community Diversity ◽  
Curing Process ◽  
Tobacco Leaves ◽  
Culture Independent ◽  
Curing Procedure

AbstractThe purpose of the study is to explore the effect of flue-curing procedure on the diversity of microbial communities in tobaccos and the dynamic change of compositions of microbial communities in the flue-curing process. It expects to provide a theoretical basis for the application of microbes in tobacco leaves and a theoretical basis and idea for optimization of the flue-curing technologies. By investigating tobacco variety K326, the tests were carried out for comparing the conventional flue-curing procedure and dry-ball temperature set and wet-ball temperature degradation flue-curing procedure. Based on the culture-independent approach and high-throughput sequencing procedure, the relationship between the flue-curing procedure for tobaccos and microbial communities in tobaccos was revealed by measuring the dynamic change of microbial communities. The results indicated that:(1) Relative to surface wiping method, washing method was more suitable for the sampling of microbes on the surface of tobacco leaves; (2) Dry-ball temperature set and wet-ball temperature degradation flue-curing procedure was more favorable for maintaining the microbial diversity of tobaccos; (3) Relative to bacteria of the tobaccos, the succession rule of the fungal communities in tobaccos was relatively steady; (4)Compared with bacterial community diversity, the fungal community diversity presented an obvious negative correlation with temperature and humidity during the flue-curing process. (5) The function of bacterial communities in tobaccos matched with the material transformation law of tobaccos, having a direct correlation on the flue-curing process. In short, Dry-ball temperature set and wet-ball temperature degradation flue-curing procedure can more favorably maintain the microbial diversity of tobaccos; moreover, the function of the tobacco system involved in microbes in tobaccos was closely related to the material transformation law of tobaccos in the flue-curing process. It validated that the bacteria in tobaccos play an important role in the flue-curing process of tobaccos.

scholarly journals Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

2012 ◽  
Vol 78 (21) ◽  
pp. 7527-7537 ◽  
Author(s):  
David R. Andrew ◽  
Robert R. Fitak ◽  
Adrian Munguia-Vega ◽  
Adriana Racolta ◽  
Vincent G. Martinson ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Sonoran Desert ◽  
Abiotic Factors ◽  
Extreme Environments ◽  
Community Diversity ◽  
Rrna Gene ◽  
Content Type ◽  
Bacterial Phyla ◽  
Culture Independent

ABSTRACTHigh-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundantCrenarchaeotaclassThermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phylaProteobacteria,Actinobacteria,Planctomycetes,Firmicutes,Bacteroidetes,Chloroflexi, andAcidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.

scholarly journals Fine scale diversification of endolithic microbial communities in the hyper-arid Atacama Desert

2017 ◽  
Author(s):  
Victoria Meslier ◽  
Maria Cristina Casero ◽  
Micah Dailey ◽  
Jacek Wierzchos ◽  
Carmen Ascaso ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Water Retention ◽  
High Throughput Sequencing ◽  
Arid Zone ◽  
Global Climate ◽  
Atacama Desert ◽  
Sampling Strategy ◽  
Physical Structure ◽  
Community Diversity ◽  
Fine Scale

ABSTRACTThe expansion of desertification across our planet is accelerating as the result of human activity and global climate change. In hyper-arid deserts, endolithic microbial communities colonize the rocks’ interior as a survival strategy. Yet, the composition of these communities and the drivers promoting their assembly are still poorly understood. Using a sampling strategy that minimized climate regime and biogeography effects, we analyzed the diversity and community composition of endoliths from four different lithic substrates – calcite, gypsum, ignimbrite and granite – collected in the hyper-arid zone of the Atacama Desert, Chile. By combining microscopy, mineralogy, and high throughput sequencing, we found these communities to be highly specific to their lithic substrate, although they were all dominated by the same four main phyla, Cyanobacteria, Actinobacteria, Chloroflexi and Proteobacteria. This finding indicates a fine scale diversification of the microbial reservoir driven by substrate properties. Our data suggest that the overall rock chemistry is not an essential driver of community structure and we propose that the architecture of the rock, i.e. the space available for colonization and its physical structure, linked to water retention capabilities, is ultimately the driver of community diversity and composition at the dry limit of life.Originality-Significance StatementIn this study, we demonstrated that endolithic microbial communities are highly specific to their substrates, suggesting a fine scale diversification of the available microbial reservoir. By using an array of rock substrates from the same climatic region, we established, for the first time, that the architecture of the rock is linked to water retention and is ultimately the driver of community diversity and composition at the dry limit for life.

scholarly journals Endophytic Fungal Community of Tobacco Leaves and Their Potential Role in the Formation of “Cherry-Red” Tobacco

2021 ◽  
Vol 12 ◽  
Author(s):  
Yonglei Jiang ◽  
Xing Chen ◽  
Gaokun Zhao ◽  
Jiahong Liu ◽  
Yan Xie ◽  
...  
Keyword(s):  
Fungal Community ◽  
High Throughput Sequencing ◽  
Potential Role ◽  
Local Community ◽  
Community Diversity ◽  
Tobacco Leaves ◽  
Mature Leaves ◽  
Community Turnover ◽  
Robust Network ◽  
Network Complex

“Cherry-red” tobacco is the superior variant of tobacco, appearing with the apperance of red dapples on cured leaves due to the demethylation of nicotine to nornicotine during maturation and curing. Fungi are known to have the capacity to convert nicotine to nornicotine. However, an endophytic fungal community of “cherry-red” tobacco has never been reported to our best knowledge. Here, we sampled mature leaves from both “cherry-red” and ordinary tobacco at lower, center, and upper plant sections, and we analyzed the ITS diversity using high-throughput sequencing. Results revealed a significantly different fungal community of foliar endophyte in “cherry-red” and ordinary tobacco. In comparison to the ordinary control, higher diversity and a co-occurrence network complex were found in “cherry-red” samples, especially in the center and upper leaves, where the red dapples mainly emerged. More taxa were enriched in the “cherry-red” than ordinary tobacco leaves at all plant sections. In particular, Aspergillus, some strains of which are reported capable of converting nicotine to nornicotine, was specifically enriched in upper “cherry-red” tobacco leaves, which showed most red dapples after curing. A less robust network structure was detected in the “cherry-red” tobacco compared to ordinary tobacco. The nearest taxon index (NTI) and β NTI indicated that the local community structuration of tobacco endophytic fungi mainly driven by deterministic process, while the community turnover among plant sections was stochastic. In conclusion, our study provides the earliest information of endophytic fungal community in “cherry-red” tobacco leaf, and the community diversity, composition, and network features are synchronously varied with the appearance of red dapples, which is suggestive of their relationship to the formation of “cherry-red” tobacco.

scholarly journals Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiota analysis

2019 ◽  
Author(s):  
Emilie Lejal ◽  
Agustín Estrada-Peña ◽  
Maud Marsot ◽  
Jean-François Cosson ◽  
Olivier Rué ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Extraction ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Community Diversity ◽  
Analytical Process ◽  
Sequencing Technologies ◽  
And Gender ◽  
The Impact

AbstractBackgroundThe development of high throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g. individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: crushing, DNA extraction, and DNA amplification.ResultsControls yielded a significant number of sequences (1,126 to 13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e. the percentage of sequences belonging to OTUs identified as contaminants) varied with tick stage and gender: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in crushing and DNA extraction controls, highlighting the importance of carefully controlling these steps.ConclusionHere, we showed that contaminant OTUs from extraction and amplification steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples.

scholarly journals Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System

mBio ◽  
2016 ◽  
Vol 7 (6) ◽  
Author(s):  
Sean M. Gibbons ◽  
Monika Scholz ◽  
Alan L. Hutchison ◽  
Aaron R. Dinner ◽  
Jack A. Gilbert ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Empirical Support ◽  
Community Diversity ◽  
Ecological Communities ◽  
Disturbance Regimes ◽  
Environmental Perturbations ◽  
Compositional Stability ◽  
Wide Range ◽  
Life History Tradeoffs

ABSTRACTDiversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems.IMPORTANCEThe diversity of microbial communities is linked to the functioning and stability of ecosystems. As humanity continues to impact ecosystems worldwide, and as diet and disease perturb our own commensal microbial communities, the ability to predict how microbial diversity will respond to disturbance is of critical importance. Using microbial microcosm experiments, we find that community diversity responds to different disturbance regimes in a reproducible and predictable way. Maximum diversity occurs when two communities, each suited to different environmental conditions, are mixed due to disturbance. This maximum diversity is transient except under specific regimes. Using a simple mathematical model, we show that transient unimodality is likely a common feature of microbial diversity-disturbance relationships in fluctuating environments.

Microbiology of AD

2020 ◽  
Author(s):  
Jacob Joseph Lamb
Keyword(s):  
Anaerobic Digestion ◽  
High Resolution ◽  
16S Rrna ◽  
Microbial Diversity ◽  
High Performance ◽  
Molecular Methods ◽  
Community Diversity ◽  
Culture Independent ◽  
Anaerobic Environment ◽  
Microorganism Community

Anaerobic digestion is performed by a wide variety of microorganisms in an anaerobic environment. In order to understand the microbial diversity, high-performance sequencing of 16S rRNA can offer high-resolution diversity data. Moreover, to understand the dynamics of the microorganisms, further analysis of the culture-independent systems through meta-omic techniques can be achieved to understand the function and structure of the microorganism community. This chapter will provide the main molecular methods for determining community diversity and dynamics.

scholarly journals Cutting wedge: bacterial community diversity and structure associated with the cheese rind and curd of seven natural rind cheeses

Fine Focus ◽  
2017 ◽  
Vol 3 (1) ◽  
pp. 09-31
Author(s):  
Lei Wei ◽  
Rebecca J. Rubenstein ◽  
Kathleen M. Hanlon ◽  
Heidi Wade ◽  
Celeste N. Peterson ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Taxonomic Diversity ◽  
Structure And Function ◽  
Community Diversity ◽  
Limited Information ◽  
Carbon Source Utilization ◽  
Community Profiling ◽  
Culture Independent ◽  
And Function

The microorganisms that inhabit cheese contribute greatly to the flavor and development of the final product. While the rind and curd microbiota have been characterized separately, there is limited information on how the structure and function of microbial communities in rinds and curds vary within and amongst cheeses. To better understand the differences in community structure and function between communities of cheese rinds and curds, we combined culture-based methods with culture-independent community profiling of curds and rinds. Rinds contained greater taxonomic diversity than curds. Lactobacillales dominated curd communities while members from the order Actinomycetales were found in high abundance in rind communities. Communities varied more between rinds and curds than among cheeses produced from different milk types. To better understand microbial community functions, we cultured and assayed isolates for antibiotic susceptibility and carbon source utilization. Among European and U.S. cheeses, 70% of all susceptible isolates were cultured from U.S. cheeses. Overall, our study explored the differences within and between rind and curd microbial communities of natural rind cheeses, provided insights into the environmental factors that shape microbial communities, and demonstrated that at the community and isolate level the cheese microbiome was diverse and metabolically complex.

scholarly journals Fungal Composition and Diversity of the Tobacco Leaf Phyllosphere during Curing of Leaves

2020 ◽  
Author(s):  
Qian-Li Chen ◽  
Lin Cai ◽  
Hancheng Wang ◽  
Liu-Ti Cai ◽  
Paul Goodwin ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Rhizopus Oryzae ◽  
Curing Process ◽  
Leaf Lamina ◽  
Saprotrophic Fungi ◽  
Tobacco Leaves ◽  
Fungal Sequence ◽  
Abundant Genus

Abstract Background: Rhizopus oryzae causes tobacco pole rot in China during tobacco flue-curing. Flue-curing is a post-harvest process done to prepare tobacco leaves and involves three different stages: the yellowing stage has the lowest temperatures and highest humidity, then the color-fixing stage has higher temperatures and medium humidity, and finally the stem-drying stage has the highest temperatures and lowest humidity.Results: In this study, fungal culturing and IonS5TMXL high-throughput sequencing techniques were used to reveal the fungal community of the petioles and lamina of tobacco leaves infected with pole rot during flue-curing. A total of 108 fungal isolates belonging to 5 genera and 10 species were isolated on media. The most common fungi isolated was R. oryzae, most often found equally on petioles and laminas in the color-fixing stage, followed by saprotrophs, mostly Aspergillus fumigatus and Aspergillus flavus. High-throughput sequencing revealed saprotrophs, Alternaria being the most abundant genus, followed by Phoma, Cercospora and Aspergillus, whereas Rhizopus was the tenth most abundant genus, which was mostly found on petioles at the yellowing stage. Both culturable fungal diversity and fungal sequence diversity was higher at stem-drying stage than the yellowing and color-fixing stages, and diversity was higher with leaf lamina than petioles revealing that the changes in fungal composition and diversity during the curing process were similar with both methods.Conclusions: A better understanding of the saprotrophic fungi during curing of leaves with pole rot could result in the identification of highly competitive saproptrophs that may act as potential biocontrol agents of tobacco pole rot.

scholarly journals Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques

2021 ◽  
Author(s):  
Alyssa M. Demko ◽  
Nastassia V. Patin ◽  
Paul R. Jensen
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Shallow Water ◽  
Marine Sediments ◽  
Ecosystem Dynamics ◽  
Rare Taxa ◽  
Culture Independent ◽  
Cultivation Techniques ◽  
Shallow Water Sediment ◽  
Culture Dependent

AbstractThe microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) approaches capture the broadest perspective on community composition, culture-dependent (CD) methods can capture low abundance taxa that are missed using CI approaches. The aim of this study was to assess microbial diversity in tropical marine sediments collected from five shallow water sites in Belize using both CD and CI approaches. CD methods captured approximately 3% of the >800 genera detected across the five sites. Additionally, 39 genera were only detected using CD approaches revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in the delineation of sediment communities. This study provides important baseline data describing shallow water sediment microbial communities and evidence that standard cultivation techniques may be more effective than previously recognized.Originality-Significance StatementMarine sediments host some of the most diverse microbial communities on the planet. While these communities are critical for global nutrient cycling, the oceanic food web, and the maintenance of ecosystem dynamics, they remain poorly studied. Studies that have assessed sediment communities typically use culture-independent approaches, which have known biases and can miss ecologically important taxa. Here we describe microbial diversity in marine sediments using both culture-dependent and culture-independent approaches. Our culturing approach, sequencing communities as opposed to individual colonies, revealed an additional 39 genera that were not detected with culture-independent methods. Additionally, we cultured numerous, as-yet undescribed species, suggesting that traditional culturing practices can be more efficient than commonly thought. Moreover, our results indicate rare taxa play an important role in distinguishing microbial communities at different sites, thus highlighting the importance of deep sequencing and incorporating culture-dependent approaches for diversity assessments.

scholarly journals Soil microbial diversity impacts plant microbiomes more than herbivory

2020 ◽  
Author(s):  
Antonino Malacrinò ◽  
Alison J. Karley ◽  
Leonardo Schena ◽  
Alison E. Bennett
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Plant Species ◽  
Plant Protection ◽  
Relative Strength ◽  
Community Diversity ◽  
Soil Microbiome ◽  
Soil Microbial Diversity ◽  
Microbiome Composition ◽  
Soil Microbial

AbstractInteractions between plants and microbiomes play a key role in ecosystem functioning, and are of broad interest due to their influence on nutrient cycling and plant protection. However, we do not yet have a complete understanding of how plant microbiomes are assembled. Here, for the first time, we show interactions between plant-associated microbial communities that drive their diversity and community composition. We manipulated soil microbial diversity, plant species, and herbivory, and found that soil microbial diversity influenced the herbivore-associated microbiome composition, but also plant species and herbivory influenced the soil microbiome composition. We used a novel approach, quantifying the relative strength of these effects, and demonstrated that the initial soil microbiome diversity explained the most variation in plant- and herbivore-associated microbial communities. Our findings strongly suggest that soil microbial community diversity is a driver of the composition of multiple associated microbiomes (plant and insect), and this has implications for the importance of management of soil microbiomes in multiple systems.

Sign in / Sign up

Export Citation Format

Share Document