scholarly journals Identification of Bacterial and Fungal Communities in the Roots of Orchids and Surrounding Soil in Heavy Metal Contaminated Area of Mining Heaps

2020 ◽  
Vol 10 (20) ◽  
pp. 7367
Author(s):  
Miroslav Böhmer ◽  
Daniel Ozdín ◽  
Matúš Račko ◽  
Michal Lichvár ◽  
Jaroslav Budiš ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Mining Sites ◽  
Mining Areas ◽  
Sequencing Method ◽  
The Family ◽  
Generation Sequencing ◽  
Surrounding Soil

Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas.

scholarly journals The Mitochondrial Genome of Amara aulica (Coleoptera, Carabidae, Harpalinae) and Insights into the Phylogeny of Ground Beetles

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 181
Author(s):  
Zhenya Li ◽  
Xinxin Li ◽  
Nan Song ◽  
Huiji Tang ◽  
Xinming Yin
Keyword(s):  
Ribosomal Rna ◽  
Mitochondrial Protein ◽  
Carabid Beetles ◽  
Protein Coding ◽  
Sequencing Method ◽  
The Family ◽  
Outgroup Species ◽  
Complete Mitogenome ◽  
Rna Genes ◽  
Generation Sequencing

Carabidae are one of the most species-rich families of beetles, comprising more than 40,000 described species worldwide. Forty-three complete or partial mitochondrial genomes (mitogenomes) from this family have been published in GenBank to date. In this study, we sequenced a nearly complete mitogenome of Amara aulica (Carabidae), using a next-generation sequencing method. This mitogenome was 16,646 bp in length, which encoded the typical 13 mitochondrial protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Combining with the published mitogenomes of Carabidae and five outgroup species from Trachypachidae, Gyrinidae and Dytiscidae, we performed phylogenetic estimates under maximum likelihood and Bayesian inference criteria to investigate the phylogenetic relationships of carabid beetles. The results showed that the family Carabidae was a non-monophyletic assemblage. The subfamilies Cicindelinae, Elaphrinae, Carabinae, Trechinae and Harpalinae were recovered as monophyletic groups. Moreover, the clade (Trechinae + (Brachininae + Harpalinae)) was consistently recovered in all analyses.

scholarly journals Bar-Coded Pyrosequencing of 16S rRNA Gene Amplicons Reveals Changes in Ileal Porcine Bacterial Communities Due to High Dietary Zinc Intake

2010 ◽  
Vol 76 (19) ◽  
pp. 6689-6691 ◽  
Author(s):  
W. Vahjen ◽  
R. Pieper ◽  
J. Zentek
Keyword(s):  
Zinc Oxide ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Rrna Gene ◽  
Dietary Zinc ◽  
Bacterial Composition ◽  
Zinc Intake ◽  
Gram Negative ◽  
Facultative Anaerobic

ABSTRACT Feeding high levels of zinc oxide to piglets significantly increased the relative abundance of ileal Weissella spp., Leuconostoc spp., and Streptococcus spp., reduced the occurrence of Sarcina spp. and Neisseria spp., and led to numerical increases of all Gram-negative facultative anaerobic genera. High dietary zinc oxide intake has a major impact on the porcine ileal bacterial composition.

scholarly journals Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comté cheese area

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
N. Chemidlin Prévost-Bouré ◽  
B. Karimi ◽  
S. Sadet-Bourgeteau ◽  
C. Djemiel ◽  
M. Brie ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Dairy Farms ◽  
Raw Milk ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Farming Practices ◽  
Organic Fertilization ◽  
Grassland Ecosystems ◽  
Protected Designation Of Origin

AbstractThe specificity of dairy Protected Designation of Origin (PDO) products is related to their “terroir” of production. This relationship needs better understanding for efficient and sustainable productions preserving the agroecological equilibrium of agroecosystems, especially grasslands. Specificity of PDO Comté cheese was related to the diversity of natural raw milk bacterial communities, but their sources need to be determined. It is hypothesized that raw milk indigenous microbial communities may originate from permanent grazed grasslands by the intermediate of dairy cows according to the sequence soil–phyllosphere–teat–milk. This hypothesis was evaluated on a 44 dairy farms network across PDO Comté cheese area by characterizing prokaryotic and fungal communities of these compartments by metabarcoding analysis (16S rRNA gene: V3–V4 region, 18S rRNA gene: V7–V8 region). Strong and significant links were highlighted between the four compartments through a network analysis (0.34 < r < 0.58), and were modulated by soil pH, plant diversity and elevation; but also by farming practices: organic fertilization levels, cattle intensity and cow-teat care. This causal relationship suggests that microbial diversity of agroecosystems is a key player in relating a PDO product to its “terroir”; this under the dependency of farming practices. Altogether, this makes the “terroir” even more local and needs to be considered for production sustainability.

scholarly journals Strategies for Reducing Ruminant Methane Emissions

2022 ◽  
Vol 42 ◽  
pp. 01014
Author(s):  
E. V. Sheida ◽  
S. A. Miroshnikov ◽  
G. K. Duskaev ◽  
K.N. Atlanderova ◽  
V.V. Grechkina
Keyword(s):  
Bacterial Communities ◽  
Ultrafine Particles ◽  
In Vitro Method ◽  
Microbiome Composition ◽  
Rumen Microbiome ◽  
Sequencing Method ◽  
New Generation Sequencing ◽  
New Generation ◽  
Generation Sequencing

The paper studies the effect of additional administration of ultrafine particles on the cattle rumen microbiome composition. The in vitro method was used using the ANKOM Daisy II incubator according to a specialized method. Microflora analysis was performed using MiSeq (Illumina, USA) by a new generation sequencing method with a MiSeq reagent kit. After a detailed analysis of the structure and composition of the microbial community in the contents of the rumen sampled for different diets, it was found that no significant differences were observed in the bacterial communities, with the exception of a slight shift in the Bacteroidetes/Firmicutes ratio. However, we observed numerical differences in the abundance of some representatives, namely, with additional inclusion of Fe and Cr2O3, decrease in the abundance of the methane-forming species Methanobrevibacter, Methanobacterium, Methanosphaera, and Methnaomicrobium was noted regarding the control.

scholarly journals Microbial Community Changes in Response to Ethanol or Methanol Amendments for U(VI) Reduction

2010 ◽  
Vol 76 (17) ◽  
pp. 5728-5735 ◽  
Author(s):  
Tatiana A. Vishnivetskaya ◽  
Craig C. Brandt ◽  
Andrew S. Madden ◽  
Meghan M. Drake ◽  
Joel E. Kostka ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Phylogenetic Diversity ◽  
Sampling Site ◽  
Contaminated Site ◽  
Rrna Gene ◽  
Oak Ridge ◽  
The Family ◽  
Laboratory Microcosm

ABSTRACT Microbial community responses to ethanol, methanol, and methanol plus humics amendments in relationship to U(VI) bioreduction were studied in laboratory microcosm experiments using sediments and ground water from a uranium-contaminated site in Oak Ridge, TN. The type of carbon source added, the duration of incubation, and the sampling site influenced the bacterial community structure upon incubation. Analysis of 16S rRNA gene clone libraries indicated that (i) bacterial communities found in ethanol- and methanol-amended samples with U(VI) reduction were similar due to the presence of Deltaproteobacteria and Betaproteobacteria (members of the families Burkholderiaceae, Comamonadaceae, Oxalobacteraceae, and Rhodocyclaceae); (ii) methanol-amended samples without U(VI) reduction exhibited the lowest diversity and the bacterial community contained 69.2 to 92.8% of the family Methylophilaceae; and (iii) the addition of humics resulted in an increase of phylogenetic diversity of Betaproteobacteria (Rodoferax, Polaromonas, Janthinobacterium, Methylophilales, and unclassified) and Firmicutes (Desulfosporosinus and Clostridium).

scholarly journals Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

2021 ◽  
Vol 9 (5) ◽  
pp. 1032
Author(s):  
Emily Celeste Fowler ◽  
Prakash Poudel ◽  
Brandon White ◽  
Benoit St-Pierre ◽  
Michael Brown
Keyword(s):  
Striped Bass ◽  
Soybean Meal ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Hybrid Striped Bass ◽  
Bacterial Composition ◽  
Morone Chrysops ◽  
Fish Diets ◽  
Significant Difference

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1–V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

scholarly journals Exploring the Impact of the Biofloc Rearing System and an Oral WSSV Challenge on the Intestinal Bacteriome of Litopenaeus vannamei

2018 ◽  
Vol 6 (3) ◽  
pp. 83 ◽  
Author(s):  
Mariana Pilotto ◽  
André Goncalves ◽  
Felipe Vieira ◽  
Walter Seifert ◽  
Evelyne Bachère ◽  
...  
Keyword(s):  
Litopenaeus Vannamei ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Family ◽  
Biofloc Technology ◽  
Rrna Gene Sequencing ◽  
Abiotic And Biotic Factors ◽  
The Impact ◽  
New Evidence

We provide a global overview of the intestinal bacteriome of Litopenaeus vannamei in two rearing systems and after an oral challenge by the White spot syndrome virus (WSSV). By using a high-throughput 16S rRNA gene sequencing technology, we identified and compared the composition and abundance of bacterial communities from the midgut of shrimp reared in the super-intensive biofloc technology (BFT) and clear seawater system (CWS). The predominant bacterial group belonged to the phylum Proteobacteria, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes. Within Proteobacteria, the family Vibrionaceae, which includes opportunistic shrimp pathogens, was more abundant in CWS than in BFT-reared shrimp. Whereas the families Rhodobacteraceae and Enterobacteriaceae accounted for almost 20% of the bacterial communities of shrimp cultured in BFT, they corresponded to less than 3% in CWS-reared animals. Interestingly, the WSSV challenge dramatically changed the bacterial communities in terms of composition and abundance in comparison to its related unchallenged group. Proteobacteria remained the dominant phylum. Vibrionaceae was the most affected in BFT-reared shrimp (from 11.35 to 20.80%). By contrast, in CWS-reared animals the abundance of this family decreased from 68.23 to 23.38%. Our results provide new evidence on the influence of both abiotic and biotic factors on the gut bacteriome of aquatic species of commercial interest.

scholarly journals High-resolution single-molecule long-fragment rRNA gene amplicon sequencing for uncultured bacterial and fungal communities

2021 ◽  
Author(s):  
Chao Fang ◽  
Xiaohuan Sun ◽  
Fei Fan ◽  
Xiaowei Zhang ◽  
Ou Wang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Second Generation ◽  
Soil Samples ◽  
Full Length ◽  
Fungal Communities ◽  
Read Length ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Second Generation Sequencing ◽  
Generation Sequencing

Although several large-scale environmental microbial projects have been initiated in the past two decades, understanding of the role of complex microbiotas is still constrained by problems of detecting and identifying unknown microorganisms1-6. Currently, hypervariable regions of rRNA genes as well as internal transcribed spacer regions are broadly used to identify bacteria and fungi within complex communities7, 8, but taxonomic and phylogenetic resolution is hampered by insufficient sequencing length9-11. Direct sequencing of full length rRNA genes is currently limited by read length using second generation sequencing or sacrificed quality and throughput by using single molecule sequencing. We developed a novel method to sequence and assemble nearly full length rRNA genes using second generation sequencing. Benchmarking was performed on mock bacterial and fungal communities as well as two forest soil samples. The majority of rRNA gene sequences of all species in the mock community samples were successfully recovered with identities above 99.5% compared to the reference sequences. For soil samples we obtained exquisite coverage with identification of a large number of putative new species, as well as high abundance correlation between replicates. This approach provides a cost-effective method for obtaining extensive and accurate information on complex environmental microbial communities.

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 Differences between Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and Its Mounds

2007 ◽  
Vol 73 (16) ◽  
pp. 5199-5208 ◽  
Author(s):  
Saliou Fall ◽  
Jérôme Hamelin ◽  
Farma Ndiaye ◽  
Komi Assigbetse ◽  
Michel Aragno ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Termite Mound ◽  
Dgge Analysis ◽  
Termite Gut ◽  
Gradient Gel Electrophoresis ◽  
High Level ◽  
Surrounding Soil

ABSTRACT In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.

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