scholarly journals Assessment of microbial community diversity in lakes of İğneada floodplain forest by metabarcoding approach

2021 ◽  
Vol 4 (4) ◽  
pp. 304-312
Author(s):  
E. Gözde Özbayram ◽  
brahim Halil Miraloğlu ◽  
Bahar İnce
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
Floodplain Forest ◽  
Community Diversity ◽  
Rrna Gene ◽  
Community Patterns ◽  
Biotechnological Potential ◽  
Sequencing Platform ◽  
The Family

This paper aims to contribute to the understanding of bacterial community patterns of the lakes of İğneada Floodplain Forest by metabarcoding approach. Within this scope, surface water samples were collected from three lakes located in the area namely Mert Lake, Hamam Lake, and Saka Lake, and the bacterial diversity was assessed by a high throughput sequencing of the 16S rRNA gene. Chao1 richness and Shannon diversity were higher in Saka Lake indicated a more diverse bacterial community. Proteobacteria was by far the most abundant phyla in all lakes. Although Bacteroidetes and Actinobacteria also dominated the community, their abundances differed in each lake. While the family Burkholderiaceae represented 25% of the bacterial community in Saka Lake, the abundances were 9% and 4% in Hamam Lake and Mert Lake, respectively. This study is one of the first investigations specifically focused on the bacterial communities in three lakes of İğneada Floodplain by next-generation sequencing platform and gave a prescreening of the bacterial diversity. Further studies are required to determine the biotechnological potential of this unique habitat.

scholarly journals Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

2021 ◽  
Vol 12 ◽  
Author(s):  
Larissa Frühe ◽  
Verena Dully ◽  
Dominik Forster ◽  
Nigel B. Keeley ◽  
Olivier Laroche ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Environmental Dna ◽  
Community Diversity ◽  
Rrna Gene ◽  
Local Conditions ◽  
Global Trends ◽  
Bacterial Taxon ◽  
Metabolic Properties

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

scholarly journals Effects of a Superabsorbent Resin with Boron on Bacterial Diversity of Peat Substrate and Maize Straw

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Yuxin Wang ◽  
Chaonan Wang ◽  
Yanan Zhao ◽  
Pingzhi Wang
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Original Structure ◽  
Strengthening Effect ◽  
Theoretical Support ◽  
Maize Straw ◽  
New Type ◽  
Superabsorbent Resin

As a chemical water-saving material, superabsorbent resin is often applied to improve soil physicochemical properties for the purpose of promoting crop growth. In this study, a new type of superabsorbent resin with boron (SARB) was used as a functional material mixed with peat substrate and maize straw in percentages (mass ratio) of 0.05%, 0.1%, 0.15%, and 0.2%, respectively, and high-throughput sequencing technology was used to test bacterial diversity, analyzing and exploring ecological safety of the superabsorbent resin with boron (SARB) in order to provide theoretical support for field applications. The research results show that the superabsorbent resin with boron (SARB) can promote bacterial community diversity in the maize straw. In ten treatments, Proteobacteria accounted for the absolute advantage of the bacterial population in the CT group and in the JG group. However, the superabsorbent resin with boron (SARB) synthesized in the laboratory cannot change the original structure of the bacterial community and has scarcely any toxic effect on the bacterial community in both peat substrate and maize straw, and, indeed, it has a strengthening effect on Proteobacteria and Actinobacteria and a weakening effect on Acidobacteria and Firmicutes to some extent.

scholarly journals Temporal Bacterial Community Diversity in the Nicotiana tabacum Rhizosphere Over Years of Continuous Monocropping

2021 ◽  
Vol 12 ◽  
Author(s):  
Lang Yan ◽  
Wenyou Zhang ◽  
Wangjun Duan ◽  
Yizheng Zhang ◽  
Wen Zheng ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Underlying Mechanism ◽  
Development Stage ◽  
Community Diversity ◽  
Rrna Gene ◽  
Bacterial Community Diversity ◽  
Microbial Network ◽  
Tobacco Production ◽  
Occurrence Patterns

Long-term continuous monocropping negatively influences the physicochemical and biological characteristics of cultivated soil, especially for the economically important crop of flue-cured tobacco that is intolerant to continuous monocropping. The underlying mechanism of soil sickness under continuous monoculture and the temporal dynamic changes over the tobacco life cycle among different monoculture time spans remain poorly characterized. In this study, high-throughput sequencing targeting the 16S rRNA gene phylogenetic marker was performed on 60 soil samples of rhizosphere soil from flue−cured tobacco in the replanting, growth and harvest period across 5, 10, and 20 years of a continuous monocropping system. Bacterial community diversity decreased with the increase in duration of continuous monocropping, and the rhizosphere microbiota was highly dynamic in the harvest period. The random forests algorithm identified 17 taxa as biomarkers and a model was established to correlate root microbiota with continuous monocropping time of flue-cured tobacco. Molecular ecological network analysis elaborated the differences and interactions in bacterial co-occurrence patterns under different monocropping systems. The co-occurrence microbial network was larger in size but there were fewer interactions among microbial communities with the increase in continuous monocropping duration. These results provide insights into the changes of flue−cured tobacco root microbiome diversity in response to continuous monocropping and suggest a model for successional dynamics of the root-associated microbiota over continuous monocropping time and development stage. This study may help elucidate the theoretical basis underlying obstacles to continuous monocropping and could contribute to improving guidance for tobacco production.

scholarly journals Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8430
Author(s):  
Jia Bie ◽  
Qing Tong ◽  
Xiaoning Liu ◽  
Xianhao Zhang ◽  
Hongbin Wang
Keyword(s):  
Bacterial Community ◽  
Beta Diversity ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Recovery Period ◽  
Alpha Diversity ◽  
Community Diversity ◽  
Control Group ◽  
Rrna Gene ◽  
Rana Dybowskii

Introduction Pathogenic bacteria limit the success of Rana dybowskii breeding. Gentamicin is used to treat R. dybowskii disease. To understand the effects of gentamicin on the composition and structure of the cutaneous bacterial community of R. dybowskii, three groups (control, gentamicin and recovery) were established in this study. Materials & Methods The V3–V4 hypervariable region of the 16S rRNA gene was analyzed in samples by high-throughput sequencing. Alpha diversity and beta diversity were evaluated to compare the cutaneous bacterial community diversity. Results A total of 1,159,668 valid sequences and 3,132 operational taxonomic units (OTUs) were obtained from these three experimental groups. The number of OTUs obtained in the control group, gentamicin group and recovery group were 2,194, 2,288, and 2,047, respectively, and the number of shared OTUs was 1,313. The alpha diversity of the cutaneous bacterial community was not significantly affected by gentamicin, while beta diversity was significantly affected. Discussion & Conclusions The effect of a gentamicin bath on relative species abundance was greater than the effect on the species composition. The changes in Proteobacteria, Acinetobacter, and Chryseobacterium were significant, and reductions were observed after the recovery period. Six potentially pathogenic genera were detected, including Aeromonas, Citrobacter, Chryseobacterium, Pseudomonas, Staphylococcus, and Streptococcus. Among them, Aeromonas and Chryseobacterium were significantly inhibited by the gentamicin bath. The results of this study provide a theoretical basis for the application of gentamicin in R. dybowskii breeding.

scholarly journals Bacterial diversity in the gastrointestinal tracts of Rhinolophus luctus and Murina leucogaster in Henan Province, China

2019 ◽  
Vol 69 (13) ◽  
pp. 1407-1414 ◽  
Author(s):  
Yan Sun ◽  
Zhimin Yuan ◽  
Yuming Guo ◽  
Yuanzhao Qin ◽  
Yongtian Ban ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
High Throughput ◽  
Disease Transmission ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Human Pathogens ◽  
Sequencing Platform ◽  
Bacterial Phyla ◽  
Gastrointestinal Bacteria

Abstract Purpose Previous studies have assessed the diversity of gastrointestinal bacteria in bats and reported that some of the strains are pathogenic to humans; therefore, bats are considered to be potential reservoirs of zoonotic pathogens. However, the bacterial diversity and types of pathogenic bacteria in the gastrointestinal tracts of Rhinolophus luctus and Murina leucogaster have not yet been determined. Humans frequently come into contact with these species; therefore, assessments of their gut microbiota, especially potential pathogens, are essential for public health. In the present study, MiSeq high-throughput sequencing was used to address this research gap, and the results were compared with those reported previously. Methods The V3–V4 regions of the 16S rRNA gene were sequenced using the MiSeq high-throughput sequencing platform to determine the bacterial community of the stomach and the intestines of R. luctus and M. leucogaster. Results The bacteria in the gastrointestinal tracts of R. luctus and M. leucogaster were classified into three and four main bacterial phyla, respectively. In both R. luctus and M. leucogaster, the dominant phylum was Proteobacteria (stomach 86.07% and 95.79%, intestines 91.87% and 88.78%, respectively), followed by Firmicutes (stomach 13.84% and 4.19%, intestines 8.11% and 11.20%, respectively). In total, 18 and 20 bacterial genera occurred in a relative abundance of 0.01% or more in the gastrointestinal tracts of R. luctus and M. leucogaster, respectively. In R. luctus, the dominant genera were Lactococcus (10.11%) and Paeniclostridium (3.41%) in the stomach, and Undibacterium (28.56%) and Paeniclostridium (4.69%) in the intestines. In M. leucogaster, the dominant genera were Undibacterium (54.41%) and Burkholderia (5.28%) in the stomach, and Undibacterium (29.67%) and Enterococcus (7.19%) in the intestines. Among the detected gastrointestinal tract flora of R. luctus and M. leucogaster, 12 bacterial genera were pathogenic or opportunistic pathogens. Conclusion A high number of human pathogens were detected in the gastrointestinal tracts of R. luctus and M. leucogaster, which demonstrates the urgency for increased efforts in the prevention and management of bat-to-human disease transmission from these species.

scholarly journals Comparison of Respiratory Microbiome Disruption Indices to Predict VAP and VAE risk at LTACH Admission

2020 ◽  
Vol 41 (S1) ◽  
pp. s179-s180
Author(s):  
Erik Clarke ◽  
Kathleen None Chiotos ◽  
James Harrigan ◽  
Ebbing Lautenbach ◽  
Emily Reesey ◽  
...  
Keyword(s):  
Critical Illness ◽  
Bacterial Community ◽  
16S Rrna ◽  
Respiratory Tract ◽  
Predictive Performance ◽  
Community Diversity ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Antibiotic Exposure ◽  
Shannon Diversity

Background: Healthcare exposure results in significant microbiome disruption, particularly in the setting of critical illness, which may contribute to risk for healthcare-associated infections (HAIs). Patients admitted to long-term acute-care hospitals (LTACHs) have extensive prior healthcare exposure and critical illness; significant microbiome disruption has been previously documented among LTACH patients. We compared the predictive value of 3 respiratory tract microbiome disruption indices—bacterial community diversity, dominance, and absolute abundance—as they relate to risk for ventilator-associated pneumonia (VAP) and adverse ventilator-associated events (VAE), which commonly complicate LTACH care. Methods: We enrolled 83 subjects on admission to an academic LTACH for ventilator weaning and performed longitudinal sampling of endotracheal aspirates, followed by 16S rRNA gene sequencing (Illumina HiSeq), bacterial community profiling (QIIME2) for diversity, and 16S rRNA quantitative PCR (qPCR) for total bacterial abundance. Statistical analyses were performed with R and Stan software. Mixed-effects models were fit to relate the admission MDIs to subsequent clinically diagnosed VAP and VAE. Results: Of the 83 patients, 19 had been diagnosed with pneumonia during the 14 days prior to LTACH admission (ie, “recent past VAP”); 23 additional patients were receiving antibiotics consistent with empiric VAP therapy within 48 hours of admission (ie, “empiric VAP therapy”); and 41 patients had no evidence of VAP at admission (ie, “no suspected VAP”). We detected no statistically significant differences in admission Shannon diversity, maximum amplicon sequence variant (ASV)–level proportional abundance, or 16S qPCR across the variables of interest. In isolation, all 3 admission microbiome disruption indices showed poor predictive performance, though Shannon diversity performed better than maximum ASV abundance. Predictive models that combined (1) bacterial diversity or abundance with (2) recent prior VAP diagnosis and (3) concurrent antibiotic exposure best predicted 14-day VAP (type S error < 0.05) and 30-day VAP (type S error < 0.003). In this cohort, VAE risk was paradoxically associated with higher admission Shannon diversity and lower admission maximum ASV abundance. Conclusions: In isolation, respiratory tract microbiome disruption indices obtained at LTACH admission showed poor predictive performance for subsequent VAP and VAE. But diversity and abundance models incorporating recent VAP history and admission antibiotic exposure performed well predicting 14-day and 30-day VAP.Disclosures: NoneFunding: None

scholarly journals Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

2021 ◽  
Vol 11 (3) ◽  
pp. 918
Author(s):  
Lingzi Mo ◽  
Augusto Zanella ◽  
Xiaohua Chen ◽  
Bin Peng ◽  
Jiahui Lin ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Negative Impact ◽  
Bacterial Community Composition ◽  
N Deposition ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Soil Dna ◽  
Urban Green ◽  
Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

scholarly journals Interaction between typical sulfonamides and bacterial diversity in drinking water

2018 ◽  
Vol 16 (6) ◽  
pp. 914-920 ◽  
Author(s):  
Qing Wu ◽  
Shuqun Li ◽  
Xiaofei Zhao ◽  
Xinhua Zhao
Keyword(s):  
Drinking Water ◽  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Microbial Community Structure ◽  
Antibiotic Use ◽  
Community Diversity ◽  
Wide Range ◽  
Growth Of Bacteria

Abstract The abuse of antibiotics is becoming more serious as antibiotic use has increased. The sulfa antibiotics, sulfamerazine (SM1) and sulfamethoxazole (SMZ), are frequently detected in a wide range of environments. The interaction between SM1/SMZ and bacterial diversity in drinking water was investigated in this study. The results showed that after treatment with SM1 or SMZ at four different concentrations, the microbial community structure of the drinking water changed statistically significantly compared to the blank sample. At the genus level, the proportions of the different bacteria in drinking water may affect the degradation of the SM1/SMZ. The growth of bacteria in drinking water can be inhibited after the addition of SM1/SMZ, and bacterial community diversity in drinking water declined in this study. Furthermore, the resistance gene sul2 was induced by SM1 in the drinking water.

scholarly journals Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Matteo Daghio ◽  
Francesca Ciucci ◽  
Arianna Buccioni ◽  
Alice Cappucci ◽  
Laura Casarosa ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Growth Performance ◽  
Community Composition ◽  
Lipid Composition ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Daily Weight Gain ◽  
Rrna Gene ◽  
Rumen Microbiota ◽  
Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

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