scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

scholarly journals Spatial Distribution of Total, Ammonia-Oxidizing, and Denitrifying Bacteria in Biological Wastewater Treatment Reactors for Bioregenerative Life Support

2002 ◽  
Vol 68 (5) ◽  
pp. 2285-2293 ◽  
Author(s):  
Yuko Sakano ◽  
Karen D. Pickering ◽  
Peter F. Strom ◽  
Lee J. Kerkhof
Keyword(s):  
Wastewater Treatment ◽  
Spatial Distribution ◽  
16S Rrna ◽  
Life Support ◽  
Denitrifying Bacteria ◽  
Ammonia Removal ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Biological Wastewater Treatment ◽  
Bioregenerative Life Support

ABSTRACT Bioregenerative life support systems may be necessary for long-term space missions due to the high cost of lifting supplies and equipment into orbit. In this study, we investigated two biological wastewater treatment reactors designed to recover potable water for a spacefaring crew being tested at Johnson Space Center. The experiment (Lunar-Mars Life Support Test Project—Phase III) consisted of four crew members confined in a test chamber for 91 days. In order to recycle all water during the experiment, an immobilized cell bioreactor (ICB) was employed for organic carbon removal and a trickling filter bioreactor (TFB) was utilized for ammonia removal, followed by physical-chemical treatment. In this study, the spatial distribution of various microorganisms within each bioreactor was analyzed by using biofilm samples taken from four locations in the ICB and three locations in the TFB. Three target genes were used for characterization of bacteria: the 16S rRNA gene for the total bacterial community, the ammonia monooxygenase (amoA) gene for ammonia-oxidizing bacteria, and the nitrous oxide reductase (nosZ) gene for denitrifying bacteria. A combination of terminal restriction fragment length polymorphism (T-RFLP), sequence, and phylogenetic analyses indicated that the microbial community composition in the ICB and the TFB consisted mainly of Proteobacteria, low-G+C gram-positive bacteria, and a Cytophaga-Flexibacter-Bacteroides group. Fifty-seven novel 16S rRNA genes, 8 novel amoA genes, and 12 new nosZ genes were identified in this study. Temporal shifts in the species composition of total bacteria in both the ICB and the TFB and ammonia-oxidizing and denitrifying bacteria in the TFB were also detected when the biofilms were compared with the inocula after 91 days. This result suggests that specific microbial populations were either brought in by the crew or enriched in the reactors during the course of operation.

scholarly journals Comparative Study of PCR-Based Approaches for the Genetic Characterization of Three Strains of Acidithiobacillus caldus Isolated from Different Sites in China

2013 ◽  
Vol 62 (4) ◽  
pp. 351-358
Author(s):  
Xueling Wu ◽  
Hong Duan ◽  
Hongwei Fan ◽  
Zhenzhen Zhang ◽  
Lili Liu
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Intergenic Spacers ◽  
Acidithiobacillus Caldus ◽  
Pcr Fingerprinting ◽  
23S Rrna Gene

Comparative study of the genetic characteristics among three Acidithiobacillus caldus strains isolated from different typical environments in China was performed using a combination of molecular methods, namely sequencing analysis of PCR-amplified 16S rRNA genes and 16S-23S rRNA gene intergenic spacers (ITS), repetitive element PCR (rep-PCR), arbitrarily primed PCR (AP-PCR) fingerprinting and random amplified polymorphic DNA (RAPD). Both of the 16S rRNA gene and 16S-23S rRNA gene intergenic spacers sequences of the three strains exhibited small variations, with 99.9-100%, 99.7-100% identity respectively. In contrast, according to the analysis of bacterial diversity based on rep-PCR and AP-PCR fingerprinting, they produced highly discriminatory banding patterns, and the similarity values between them varied from 61.97% to 71.64%. RAPD analysis showed that banding profiles of their genomic DNA exhibited obvious differences from each other with 53.44-75% similarity. These results suggested that in contrast to 16S rRNA genes and 16S-23S rRNA gene intergenic spacers sequencing analysis, rep-PCR, AP-PCR fingerprinting and RAPD analysis possessed higher discriminatory power in identifying these closely related strains. And they could be used as rapid and highly discriminatory typing techniques in studying bacterial diversity, especially in differentiating bacteria within Acidithiobacillus caldus.

The difference of the gut microbiota of gastric cancer in relation to Helicobacter pylori negativity and positivity.

2019 ◽  
Vol 37 (4_suppl) ◽  
pp. 10-10
Author(s):  
Mijin Seol ◽  
Yu Ra Lee ◽  
Kyung Mi Kim ◽  
Cheol Min Shin ◽  
Hyuk Yoon ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Helicobacter Pylori ◽  
Relative Abundance ◽  
Fecal Sample ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacillus Species ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Microbial Composition

10 Background: Helicobacter pylori (HP) is a major risk factor for gastric cancer, however, only 1-2% of HP(+) people develop adenocarcinoma. In this study, we have compared the intestinal microbiota composition related to HP status among gastric cancer patient using 16SrRNA gene-based metagenomic sequencing analysis and culture-based method. Methods: Stool samples were collected from 18 gastric cancer patients. 16S rRNA genes were sequenced on the Illumina Miseq platform and further analyzed to evaluate the gut bacterial community. The bacteria strains of fecal sample were isolated in aerobic and anaerobic condition. Results: Metagenomics analysis of fecal sample showed four major phyla; Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were dominant. Firmicutes were the most dominant phylum. Within this phylum, the relative abundance of Clostridiales including Ruminococcus was higher in the HP(-) group, whereas Lactobacillales including streptococcus was higher in HP(+) group. In addition the relative abundance of Bacteroidetes in HP(-) group and Actinobacteria (especially, genus Bifidobacterium) in HP(+) group was observed highly. In the bacterial culture-based approach, bacteria strains belonged to Clostridiales such as Clostridium perfringens, Ruminococcus feacis, Blautia sp., Coprococcus comes were isolated in HP(-) sample. In HP(+) sample, Klebsiella, Bacteroides, Bifidobacterium were isolated. Bacillus species, Escherichia/Shigella was enriched regardless of HP exist. Streptococcus was not cultivated in HP(+) group, but isolated in HP(-) group in contrast with metagenome data. Conclusions: We found the intestinal bacterial diversity in the HP(+) group was lower than those in the HP(-) and the microbial composition was different between HP(+) and HP(-). Metagenome analysis showed the order Clostridiales of the phylum Firmicutes were enriched in the HP(-) group while the order Lactobacillales (specially, Streptococcus) were enriched in the HP(+) group. Compared to isolates between two groups, bacteria species belonged to the order Clostridiales such as Clostridium, Ruminococcus , Blautia , Coprococcus were cultivated particularly in HP(-) sample.

scholarly journals Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle

2010 ◽  
Vol 76 (14) ◽  
pp. 4858-4862 ◽  
Author(s):  
Lisa M. Durso ◽  
Gregory P. Harhay ◽  
Timothy P. L. Smith ◽  
James L. Bono ◽  
Todd Z. DeSantis ◽  
...  
Keyword(s):  
Food Safety ◽  
16S Rrna ◽  
Beef Cattle ◽  
Microbial Diversity ◽  
Intestinal Microbiota ◽  
Animal Health ◽  
Methane Emissions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Health Food

ABSTRACT The intestinal microbiota of beef cattle are important for animal health, food safety, and methane emissions. This full-length sequencing survey of 11,171 16S rRNA genes reveals animal-to-animal variation in communities that cannot be attributed to breed, gender, diet, age, or weather. Beef communities differ from those of dairy. Core bovine taxa are identified.

scholarly journals Identification by molecular techniques of halophilic bacteria producing important enzymes from pristine area in Campeche, Mexico

2023 ◽  
Vol 83 ◽  
Author(s):  
L. A. Can-Herrera ◽  
C. D. Gutierrez-Canul ◽  
M. A. A. Dzul-Cervantes ◽  
O. F. Pacheco-Salazar ◽  
J. D. Chi-Cortez ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Microbial Community ◽  
16S Rrna ◽  
Relative Abundance ◽  
Halophilic Bacteria ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pristine Area ◽  
Blast Program

Abstract Isla Arena is located in the coordinate 20° 70´ N - 90° 45´ W, from Campeche, Mexico. In these estuaries, the ocean mixes with fresh water, and ecosystems are concentrated where petenes and pink flamingos proliferate. Crustaceans and mollusks abound in the sea. Despite its enormous marine wealth, there are no studies carried out on which halophilic microorganisms are present in these waters. In this work, the diversity and structure of the microbial community was investigated through a metagenomics approach and corroborated for sequencing of 16S rRNA genes. It was found that the phylum Fimicutes predominates with more than 50%, in almost the same proportion of the class Bacilli and with almost 41% of relative abundance of the order Bacillales. The sequencing results showed that one of the samples presented a high percentage of similarity (99.75%) using the Nucleotide BLAST program with a peculiar microorganism: Bacillus subtilis. This microorganism is one of the best characterized bacteria among the gram-positive ones. Our results demonstrate that B. subtilis can be an efficient source of proteases, lipases and cellulases, from halophilic microbial communities located in poorly explored areas.

scholarly journals Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome

2009 ◽  
Vol 75 (23) ◽  
pp. 7519-7526 ◽  
Author(s):  
Carola Simon ◽  
Arnim Wiezer ◽  
Axel W. Strittmatter ◽  
Rolf Daniel
Keyword(s):  
16S Rrna ◽  
Phylogenetic Diversity ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Metabolic Potential ◽  
Data Set ◽  
Glacial Ice ◽  
Microbial Life ◽  
Derived Data

ABSTRACT The largest part of the Earth's microbial biomass is stored in cold environments, which represent almost untapped reservoirs of novel species, processes, and genes. In this study, the first metagenomic survey of the metabolic potential and phylogenetic diversity of a microbial assemblage present in glacial ice is presented. DNA was isolated from glacial ice of the Northern Schneeferner, Germany. Pyrosequencing of this DNA yielded 1,076,539 reads (239.7 Mbp). The phylogenetic composition of the prokaryotic community was assessed by evaluation of a pyrosequencing-derived data set and sequencing of 16S rRNA genes. The Proteobacteria (mainly Betaproteobacteria), Bacteroidetes, and Actinobacteria were the predominant phylogenetic groups. In addition, isolation of psychrophilic microorganisms was performed, and 13 different bacterial isolates were recovered. Analysis of the 16S rRNA gene sequences of the isolates revealed that all were affiliated to the predominant groups. As expected for microorganisms residing in a low-nutrient environment, a high metabolic versatility with respect to degradation of organic substrates was detected by analysis of the pyrosequencing-derived data set. The presence of autotrophic microorganisms was indicated by identification of genes typical for different ways of carbon fixation. In accordance with the results of the phylogenetic studies, in which mainly aerobic and facultative aerobic bacteria were detected, genes typical for central metabolism of aerobes were found. Nevertheless, the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Numerous characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by the incorporation of unsaturated fatty acids, were detected. Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments.

scholarly journals Axillary Microbiota Compositions from Men and Women in a Tertiary Institution-South East Nigeria: Effects of Deodorants/Antiperspirants on Bacterial Communities

2020 ◽  
Author(s):  
Kingsley C Anukam ◽  
Victoria Nmewurum ◽  
Nneka R Agbakoba
Keyword(s):  
16S Rrna ◽  
Relative Abundance ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sample Collection ◽  
Tertiary Institution ◽  
Male And Female ◽  
Significant Difference ◽  
Microbial Taxonomy ◽  
Male Subjects

ABSTRACTThe axillary skin microbiota compositions of African populations that live in warm climate is not well studied with modern next-generation sequencing methods. To assess the microbiota compositions of the axillary region of healthy male and female students, we used 16S rRNA metagenomics method and clustered the microbial communities between those students that reported regular use of deodorants/antiperspirants and those that do not. Axillary skin swab was self-collected by 38 male and 35 females following uBiome sample collection instructions. Amplification of the V4 region of the 16S rRNA genes was performed and sequencing done in a pair-end set-up on the Illumina NextSeq 500 platform rendering 2 × 150 base pair. Microbial taxonomy to species level was generated using the Illumina Greengenes database. 26 phyla were identified in males with Actinobacteria as the most abundant (60%), followed by Firmicutes (31.53%), Proteobacteria (5.03%), Bacteroidetes (2.86%) and others. Similarly, 25 phyla were identified in females and Actinobacteria was the most abundant (59.28%), followed by Firmicutes (34.28%), Proteobacteria (5.91%), Bacteroidetes (0.45%) and others. A total of 747 genera were identified, out of which 556 (74.4%) were common to both males and females and 163 (21.8%) were exclusive to males while 28 (3.8%) were exclusive to females. Corynebacterium (53.89% vs 50.17%) was the most relative abundant genera in both male and female subjects, followed by Staphylococcus (19.66% vs 20.90%), Anaerococcus (4.91% vs 7.51%), Propionibacterium (1.21% vs 1.84%). There was a significant difference (P=0.0075) between those males that reported regular use of antiperspirant/deodorants and those that reported non-use of antiperspirants/deodorants in the relative abundance of Corynebacterium (68.06% vs 42.40%). Higher proportion of Corynebacterium was observed in male subjects than females, while more relative abundance of Staphylococcus was found in females than males. This study detected Lactobacilli in the axilla of over 82% of female and over 81% of male subjects, though in low relative abundance which suggests that Lactobacillus taxa might be considered as part of the normal axillary bacterial community. The study also revealed that the relative abundance of Corynebacterium (68.06% vs 42.40%) was higher in those that reported regular use of deodorants/antiperspirants.

scholarly journals Simulated Winter Incubation of Soil With Swine Manure Differentially Affects Multiple Antimicrobial Resistance Elements

2020 ◽  
Vol 11 ◽  
Author(s):  
Daniel N. Miller ◽  
Madison E. Jurgens ◽  
Lisa M. Durso ◽  
Amy M. Schmidt
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
Relative Abundance ◽  
Resistance Genes ◽  
Swine Manure ◽  
The United States ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Manure Application ◽  
Background Soil

Gastrointestinal bacteria that harbor antibiotic resistance genes (ARG) become enriched with antibiotic use. Livestock manure application to cropland for soil fertility presents a concern that ARG and bacteria may proliferate and be transported in the environment. In the United States, manure applications typically occur during autumn with slow mineralization until spring planting season. A laboratory soil incubation study was conducted mimicking autumn swine manure application to soils with concentrations of selected ARG monitored during simulated 120-day winter incubation with multiple freeze-thaw events. Additionally, the effects of two soil moistures [10 and 30% water holding capacity (WHC)] and two manure treatments [raw versus hydrated lime alkaline stabilization (HLAS)] were assessed. Fourteen tetracycline resistance genes were evaluated; tet(D), tet(G), and tet(L) were detected in background soil while swine manure contained tet(A), tet(B), tet(C), tet(G), tet(M), tet(O), tet(Q), and tet(X). By day 120, the manure-borne tet(M) and tet(O) were still detected while tet(C), tet(D), tet(L), and tet(X) genes were detected less frequently. Other tet resistance genes were detected rarely, if at all. The sum of unique tet resistance genes among all treatments decreased during the incubation from an average of 8.9 to 3.8 unique tet resistance genes. Four resistance elements, intI1, blactx–m–32, sul(I), erm(B), and 16s rRNA genes were measured using quantitative PCR. ARG abundances relative to 16S abundance were initially greater in the raw manure compared to background soil (−1.53 to −3.92 log abundance in manure; −4.02 to &lt;−6.7 log abundance in soil). In the mixed manure/soil, relative abundance of the four resistance elements decreased (0.87 to 1.94 log abundance) during the incubation largely because 16S rRNA genes increased by 1.21 log abundance. Throughout the incubation, the abundance of intI1, blactx–m–32, sul(I), and erm(B) per gram in soil amended with HLAS-treated manure was lower than in soil amended with raw manure. Under low initial soil moisture conditions, HLAS treatment reduced the abundance of intI1 and resulted in loss of blactx–m–32, sul(I), and erm(B)] compared to other treatment-moisture combinations. Although one might expect antibiotic resistance to be relatively unchanged after simulated winter manure application to soil, a variety of changes in diversity and relative abundance can be expected.

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