scholarly journals Bacterial Diversity in Soil Surround Subterranean Termites-Damaged Wooden Buildings in Seonamsa Temple and Effect of the Termites on Bacterial Diversity in Humus Soil

2021 ◽  
Vol 37 (4) ◽  
pp. 357-361
Author(s):  
Young Hee Kim ◽  
Boa Lim ◽  
Jeung Min Lee ◽  
Jin Young Hong ◽  
Soo Ji Kim ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Soil Microorganisms ◽  
Operational Taxonomic Unit ◽  
Illumina Miseq ◽  
Subterranean Termites ◽  
Bacterial Composition ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Humus Soil

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple’s soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple’s soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

scholarly journals Profiling the Bacterial Diversity in a Typical Karst Tiankeng of China

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 187 ◽  
Author(s):  
Gaozhong Pu ◽  
Yanna Lv ◽  
Lina Dong ◽  
Longwu Zhou ◽  
Kechao Huang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Microorganisms ◽  
Operational Taxonomic Unit ◽  
Soil Characteristics ◽  
Soil Samples ◽  
Controlling Factors ◽  
Bacterial Composition ◽  
Microbial Distribution ◽  
Significant Difference

While karst tiankengs have a higher capacity to act as safe havens for biodiversity in changing climates, little is known about their soil microorganisms. To fill this gap, we investigate the distribution and driving factors of the bacterial community in karst tiankeng systems. There is a significant difference in the soil characteristics between the inside and the outside of a karst tiankeng. At the karst tiankeng considered in this study, the bacterial composition, in terms of the operational taxonomic unit (OTU), was found to be significantly different in different soil samples, taken from diverse sampling sites within the collapsed doline or the external area, and showed a high habitat heterogeneity. The dominant phylum abundances vary with the sampling sites and have their own indicator taxa from phylum to genus. Unlike the primary controlling factors of plant diversity, the microclimate (soil moisture and temperature), soil pH, and slope dominated the distribution of the bacterial community in karst tiankeng systems. Our results firstly showed the distribution characteristics of bacterial communities and then revealed the importance of microhabitats in predicting the microbial distribution in karst tiankeng systems.

scholarly journals Comparison of bacterial communities in roots of selected trees with and without summer truffle (Tuber aestivum) ectomycorrhiza

2021 ◽  
Vol 63 (2) ◽  
pp. 97-111
Author(s):  
Marta Siebyła ◽  
Iwona Szyp-Borowska
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Tuber Aestivum ◽  
Bacterial Composition ◽  
Next Generation Sequencing Ngs ◽  
And Control ◽  
Sanger Method ◽  
Generation Sequencing ◽  
Control Samples

Abstract In this study, we examined the effect of the presence of mycorrhiza and ascomata of summer truffle (Tuber aestivum) on the bacterial composition of roots from small trees growing in selected sites of the Nida Basin. Qualitative DNA sequencing methods such as Sanger and next-generation sequencing (NGS) were used. The Sanger method revealed different bacterial species compositions between the samples where summer truffle ascomata was recorded and control samples. Five genera of bacteria could be distinguished: Bacillus, Erwinia, Pseudomonas, Rahnella and Serratia, among which the most numerous were Pseudomonas (Gammmaproteobacteria class) at 32.9%. The results obtained by the NGS method also showed differences in species composition of the bacteria depending on the study sample. Seven genera of bacteria were distinguished: Rhizorhabdus, Methylotenera, Sphingomonas, Nitrosospira, Streptomyces, Methyloceanibacter and Niastella, which dominated in roots from the truffle sites. Telmatobacter, Roseiarcus, Granulicella, Paludibaculum, Acidipila, Acidisphaera and Aliidongia dominated in roots from the control sites. With the NGS method, it is possible to identify the microbiome of a whole root, while only a root fragment can be analysed by the Sanger method. These results extend the scope of knowledge on the preferences of certain groups of bacteria associated with truffles and their influence on the formation of ascomata in summer truffles. Our results may also be useful in selecting and monitoring sites that promote ascomata of Tuber aestivum.

scholarly journals Skin microbiota differs drastically between co-occurring frogs and newts

2017 ◽  
Vol 4 (4) ◽  
pp. 170107 ◽  
Author(s):  
Molly C. Bletz ◽  
R. G. Bina Perl ◽  
Miguel Vences
Keyword(s):  
Bacterial Communities ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Amphibian Skin ◽  
Skin Microbiota ◽  
Triturus Cristatus ◽  
Bacterial Composition ◽  
Host Ecology ◽  
Rana Dalmatina ◽  
Ichthyosaura Alpestris

Diverse microbial assemblages inhabit amphibian skin and are known to differ among species; however, few studies have analysed these differences in systems that minimize confounding factors, such as season, location or host ecology. We used high-throughput amplicon sequencing to compare cutaneous microbiotas among two ranid frogs ( Rana dalmatina, R. temporaria ) and four salamandrid newts ( Ichthyosaura alpestris, Lissotriton helveticus, L. vulgaris, Triturus cristatus ) breeding simultaneously in two ponds near Braunschweig, Germany. We found that bacterial communities differed strongly and consistently between these two distinct amphibian clades. While frogs and newts had similar cutaneous bacterial richness, their bacterial composition strongly differed. Average Jaccard distances between frogs and newts were over 0.5, while between species within these groups distances were only 0.387 and 0.407 for frogs and newts, respectively. At the operational taxonomic unit (OTU) level, 31 taxa exhibited significantly different relative abundances between frogs and newts. This finding suggests that chemical or physical characteristics of these amphibians' mucosal environments provide highly selective conditions for bacterial colonizers. Multi-omics analyses of hosts and their microbiota as well as directed efforts to understand chemical differences in the mucosal environments (e.g. pH), and the specificities of host-produced compounds against potential colonizers will help to better understand this intriguing pattern.

scholarly journals Rootstocks Shape the Rhizobiome: Rhizosphere and Endosphere Bacterial Communities in the Grafted Tomato System

2018 ◽  
Vol 85 (2) ◽  
Author(s):  
Ravin Poudel ◽  
Ari Jumpponen ◽  
Megan M. Kennelly ◽  
Cary L. Rivard ◽  
Lorena Gomez-Montano ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Crop Production ◽  
Operational Taxonomic Unit ◽  
The Self ◽  
Plant Genotype ◽  
Tomato Cultivar ◽  
Abundant Otus ◽  
And Performance

ABSTRACTRoot-associated microbes are critical to plant health and performance, although understanding of the factors that structure these microbial communities and the theory to predict microbial assemblages are still limited. Here, we use a grafted tomato system to study the effects of rootstock genotypes and grafting in endosphere and rhizosphere microbiomes that were evaluated by sequencing 16S rRNA. We compared the microbiomes of nongrafted tomato cultivar BHN589, self-grafted BHN589, and BHN589 grafted to Maxifort or RST-04-106 hybrid rootstocks. Operational taxonomic unit (OTU)-based bacterial diversity was greater in Maxifort compared to the nongrafted control, whereas bacterial diversity in the controls (self-grafted and nongrafted) and the other rootstock (RST-04-106) was similar. Grafting itself did not affect bacterial diversity; diversity in the self-graft was similar to that of the nongraft. Bacterial diversity was higher in the rhizosphere than in the endosphere for all treatments. However, despite the lower overall diversity, there was a greater number of differentially abundant OTUs (DAOTUs) in the endosphere, with the greatest number of DAOTUs associated with Maxifort. In a permutational multivariate analysis of variance (PERMANOVA), there was evidence for an effect of rootstock genotype on bacterial communities. The endosphere-rhizosphere compartment and study site explained a high percentage of the differences among bacterial communities. Further analyses identified OTUs responsive to rootstock genotypes in both the endosphere and rhizosphere. Our findings highlight the effects of rootstocks on bacterial diversity and composition. The influence of rootstock and plant compartment on microbial communities indicates opportunities for the development of designer communities and microbiome-based breeding to improve future crop production.IMPORTANCEUnderstanding factors that control microbial communities is essential for designing and supporting microbiome-based agriculture. In this study, we used a grafted tomato system to study the effect of rootstock genotypes and grafting on bacterial communities colonizing the endosphere and rhizosphere. To compare the bacterial communities in control treatments (nongrafted and self-grafted plants) with the hybrid rootstocks used by farmers, we evaluated the effect of rootstocks on overall bacterial diversity and composition. These findings indicate the potential for using plant genotype to indirectly select bacterial taxa. In addition, we identify taxa responsive to each rootstock treatment, which may represent candidate taxa useful for biocontrol and in biofertilizers.

scholarly journals The study of hybridization processes within genus Sparganium L. Subgenus Xanthosparganium holmb. Based on data of next generation sequencing (NGS)

2019 ◽  
Vol 17 (4) ◽  
pp. 27-35
Author(s):  
Evgeniy A. Belyakov ◽  
Eduard M. Machs ◽  
Yulia V. Mikhailova ◽  
Aleksandr V. Rodionov
Keyword(s):  
Next Generation Sequencing ◽  
North American ◽  
Illumina Miseq ◽  
Rrna Genes ◽  
Next Generation ◽  
Close Relationship ◽  
Species Characteristics ◽  
High Level ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The study represents the results of research of intragenic polymorphism in transcribed spacer ITS1 of the 35S rRNA genes in representatives of subgenus Xanthosparganium genus Sparganium which were obtained by means of locus-specific next generation sequencing on the platform Illumina MiSeq. It was shown that ribotype variations in studied samples generally correspond to the division of this genus into three sections Erecta (subgenus Sparganium), Natantia and Minima (subgenus Xanthosparganium). High level of intragenic polymorphism was revealed in S. hyperboreum, with ribotypes distributed among several groups. Genome of this species includes ribotypes which are typical for other species in subgenus Xanthosparganium. For two investigated S. glomeratum samples, there were no ribotypes similar to such ribotypes in other species of Natantia section. S. glomeratum has got ribotypes identical with S. hyperboreum of Minima section. This feature may be the evidence of ancient intersectional hybridization of these two species. Characteristics of rDNA in S. glomeratum are in favor of putting this species into Minima section. It was suggested that speciation processes within the genus could be based not only on hybridization but also went on in allopatric way. The fist statement is supported by the presence of similar and identical ribotypes in S. emersum, S. longifolium, S. gramineum and S. hyperboreum, the second as it was mentioned by other researchers, is due to close relationship between North American and Eurasian taxa.

scholarly journals Metagenomic Profiling and Identification of Antimicrobial Resistance Genes from Airborne Microbial Communities

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Tamar Dickerson ◽  
Jonathan L. Jacobs ◽  
Nicole Waybright ◽  
Danielle Swales ◽  
Peggy Lowary ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Animal Health ◽  
Functional Metagenomics ◽  
Antimicrobial Resistance Genes ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Antimicrobial resistance (AMR) is recognized as a severe threat to human and animal health worldwide, yet relatively little is known regarding the bioavailability of AMR genes in airborne microbial communities. Hence, the objective of our study is to use next generation sequencing (NGS) to assess the temporal dynamics of airborne bacterial communities as well as functional metagenomics to investigate the dispersion of AMR genes present within them.

scholarly journals Metagenomic Analysis of the Gut Bacteriome of Usherhopper, Poekilocerus bufonius (Klug) from Hadda, Saudi Arabia

2021 ◽  
Author(s):  
Nabih A. Baeshen ◽  
Mazen A. Majeed ◽  
Mohammed Abdullah T Alotaibi ◽  
Mohamed Hamed Alnefai ◽  
Aala A. Abulfaraj ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Next Generation Sequencing ◽  
Pest Management ◽  
Bacterial Communities ◽  
The Other ◽  
Economic Losses ◽  
Plant Fibers ◽  
Next Generation Sequencing Ngs ◽  
Effective Conservation ◽  
Generation Sequencing

Abstract Background:Microbial communities that colonize insect guts contribute positively to the absorption of nutrients, immunity and the overall health of the host. Recent studies have been tapered towards only economically important arthropods, particularly honeybees. On the other hand, arthropods such as grasshoppers are considered as pests because they create havoc leading to economic losses. Grasshoppers are considered phytophagous pests that have a large appetite for plant fibers, whose digestion depend largely on the bacterial communities in their guts. This study characterises the gut microbiome in Usherhopper, Poekilocerus bufonius using the metagenomics methods through the next generation sequencing (NGS). Results:A total of 59,072,222 bacterial reads were recorded which were classified into phylum and genus levels. Proteobacteria were the most shared at the phylum-level whereas Wolbachia were the most dominant genera based on the total reads. Conclusions: The host-microbiome interactions and their perceived influence on the ecosystem are yet to be fully explained, therefore a detailed study is pivotal in order to enforce effective conservation and pest management.

scholarly journals Analysis of Bacterial Diversity in Relation to the Presence of the Top 7 Shiga Toxin–Producing Escherichia coli throughout Australian Beef Abattoirs

2020 ◽  
Vol 83 (10) ◽  
pp. 1812-1821
Author(s):  
SANGA KANG ◽  
JOSHUA T. RAVENSDALE ◽  
RANIL COOREY ◽  
GARY A. DYKES ◽  
ROBERT S. BARLOW
Keyword(s):  
Escherichia Coli ◽  
Bacterial Diversity ◽  
Shiga Toxin ◽  
Bacterial Communities ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Bacterial Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Surface Samples ◽  
Inspection Service

ABSTRACT There is increasing evidence that diversity changes in bacterial communities of beef cattle correlate to the presence of Shiga toxin–producing Escherichia coli (STEC). However, studies that found an association between STEC and bacterial diversity have been focused on preslaughter stages in the beef supply chain. This study was designed to test a hypothesis that there are no differences in bacterial diversity between samples with and those without the presence of the top 7 STEC (O26, O45, O103, O111, O121, O145, and O157) throughout processing in an integrated (abattoir A) and a fragmented (abattoir B) Australian beef abattoir. Slaughter and boning room surface samples from each abattoir were analyzed using 16S rRNA amplicon sequencing and tested for the top 7 STEC following the Food Safety and Inspection Service protocol. Potential positives through slaughter were similar between the abattoirs (64 to 81%). However, abattoir B had substantially reduced potential positives in the boning room compared with abattoir A (abattoir A: 23 and 48%; abattoir B: 2 and 7%). Alpha diversity between the sample groups was not significantly different (P > 0.05) regardless of different STEC markers. Nonmetric multidimensional scaling of slaughter samples showed that the bacterial composition in fecal and hide samples shared the least similarity with the communities in carcass and environmental samples. Surface samples from slaughter (carcass and environmental) and boning (carcass, beef trim, and environmental) all appeared randomly plotted on the scale. This indicated that the STEC presence also did not have a significant effect (P > 0.05) on beta diversity. Although presence of STEC appeared to correlate with changes in diversity of fecal and hide bacterial communities in previous studies, it did not appear to have the same effect on other samples throughout processing. HIGHLIGHTS

scholarly journals Eukaryotic and Prokaryotic Microbiota Interactions

2020 ◽  
Author(s):  
Aly Kodio ◽  
Estelle Menu ◽  
Stéphane Ranque
Keyword(s):  
Bacterial Communities ◽  
Current Knowledge ◽  
Experimental Models ◽  
Medical Practices ◽  
Host Genetics ◽  
Next Generation Sequencing Ngs ◽  
The Relationship ◽  
Generation Sequencing ◽  
Health Applications

The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites, and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g. antibiotic treatment), climate, season, and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths, and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.

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