ANÁLISE IN SILICO PARA DEFINIÇÃO DE COMMON CORE MICROBIANO ASSOCIADO À DEGRADAÇÃO DE SURFACTANTE ANIÔNICO ALQUILBENZENO LINEAR SULFONADO (LAS)

2021 ◽  
Author(s):  
Isadora Soares de Lima ◽  
Tiago Palladino Delforno ◽  
Iolanda Cristina Silveira Duarte
Keyword(s):  
16S Rrna ◽  
Common Core ◽  
In Silico ◽  
Fumarate Reductase ◽  
Gene 16S Rrna

Introdução: O alquilbenzeno linear sulfonado é o surfactante aniônico de maior interesse econômico, correspondendo a 84% do mercado no Brasil, e 45% no mundo. Sua rota de biodegradação envolve reações de adição de fumarato, β-oxidação, clivagem do anel aromático e dessulfonação. Tratando-se de um processo complexo, o uso de consórcios microbianos possibilita usufruir de diferentes metabolismos para a degradação do LAS. Contudo, nota-se uma escassez na literatura acerca dos microrganismos que desempenham papel fundamental na degradação do surfactante em reatores biológicos. Portanto, o presente trabalho visa preencher esta lacuna por meio do estudo de sequências de gene 16S rRNA obtidas em amostras utilizadas para testar a degradação de LAS, em biorreatores de diferentes configurações e contendo inóculos de origens distintas, presentes na literatura. Objetivos: Definir o common core microbiano associado à degradação do surfactante aniônico Alquilbenzeno Linear Sulfonado (LAS) em biorreatores, por meio da avaliação da diversidade e riqueza microbiana do Domínio Archaea e Bacteria, e predição do perfil funcional das taxonomias obtidas. Material e métodos: Utilizaram-se 52 amostras de sequências de gene 16S rRNA, obtidas de 12 artigos presentes na literatura, que estudaram a remoção biológica de LAS em águas residuárias reais. Para a análise das sequências, utilizou-se a plataforma QIIME 2 e seus plug-ins, a ferramenta Tax4Fun e software R. Resultados: Os filos mais abundantes encontrados foram Proteobacteria e Bacteroidota, e gêneros Methanosaeta e C39. Dentre os common core, o gênero SJA-28 (filo Bacteroidota) foi o mais presente. A enzima fumarate reductase, relacionada à adição de fumarato, foi pouco abundante entre as amostras. Para a reação de β-oxidação, a enzima 3-oxoacyl-acyl- reductase foi predominante. As enzimas relacionadas ao processo de dessulfonação encontradas na literatura foram registradas no presente trabalho. Nenhuma enzima produzida durante a clivagem do anel aromático foi registrada durante a análise. Conclusão: Não foram encontrados gêneros em comum entre todas as amostras analisadas. O perfil funcional relacionado à reação de β-oxidação foi mais abundante, quando comparada às outras reações. Os resultados alcançados pelo presente estudo aumentam o conhecimento sobre a composição taxonômica e funcional existente e compartilhada entre diferentes ambientes associados à degradação do surfactante LAS.

scholarly journals Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Eric J. Raes ◽  
Kristen Karsh ◽  
Swan L. S. Sow ◽  
Martin Ostrowski ◽  
Mark V. Brown ◽  
...  
Keyword(s):  
16S Rrna ◽  
Metabolic Pathways ◽  
Low Cost ◽  
Marker Gene ◽  
South Pacific ◽  
Rrna Gene ◽  
South Pacific Ocean ◽  
Bacterial Marker ◽  
Gene 16S Rrna ◽  
Gene Data

AbstractGlobal oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.

scholarly journals Halomicrococcus hydrotolerans gen. nov., sp. nov., an extremely halophilic archaeon isolated from a subterranean salt deposit

2020 ◽  
Vol 70 (8) ◽  
pp. 4425-4431 ◽  
Author(s):  
Shaoxing Chen ◽  
Yao Xu ◽  
Siqi Sun ◽  
Jingwen Liu ◽  
Feilong Chen
Keyword(s):  
16S Rrna ◽  
In Silico ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Genes ◽  
Salt Deposit ◽  
Halophilic Archaeon ◽  
Content Type ◽  
Link Type ◽  
The Family

A halophilic archaeon, strain H22T, was isolated from a subterranean salt deposit sampled at Yunnan salt mine, PR China. Colonies of strain H22T were light pink-pigmented. Cells were coccus, non-motile, Gram-stain-negative, and did not lyse in distilled water. The strain was aerobic and grew at 20–55 °C (optimum, 37 °C), in the presence of 10–30 % (w/v) NaCl (20 %) and at pH 6.5–9.0 (pH 7.0). Mg2+ was required for growth (optimum, 0.005 M). Major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and sulfated mannosyl-glucosyl-glycerol diether-1. Sequence similarity search based on the multiple 16S rRNA genes (rrnA, rrnB and rrnC) of strain H22T revealed that it was most closely related to species of the genera Haloarchaeobius , Haladaptatus , Halorussus and Halorubellus with relative low sequence similarities (91.9–93.7 %). The strain, however, shared highest rpoB′ gene sequence identities with Halorussus rarus TBN4T (90.8 % rpoB′ gene sequence similarity). Phylogenetic trees based on 16S rRNA and rpoB′ gene sequences revealed a robust lineage of the strain H22T with members of related genera of the family Halobacteriaceae . The DNA G+C content of strain H22T was 62.9 mol%. Genome-based analysis of average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) between strains H22T and its closest relative were equal or lower than 77.7 and 22.4 %, respectively, which were far below the threshold for delineation of a new species. Based on ANI values, in silico DDH, and distinct morphological and physiological differences from the previously described taxa, we suggest that strain H22T represents a novel species of a new genus within the family Halobacteriaceae , for which the name Halomicrococcus hydrotolerans gen. nov., sp. nov. is proposed. The type strain is H22T (=CGMCC 1.16291T=NBRC 113231T).

scholarly journals The Impact of Primer Design on Amplicon-Based Metagenomic Profiling Accuracy: Detailed Insights into Bifidobacterial Community Structure

2020 ◽  
Vol 8 (1) ◽  
pp. 131 ◽  
Author(s):  
Leonardo Mancabelli ◽  
Christian Milani ◽  
Gabriele Andrea Lugli ◽  
Federico Fontana ◽  
Francesca Turroni ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
In Silico ◽  
In Silico Analysis ◽  
Amplification Efficiency ◽  
Rrna Gene ◽  
Test Case ◽  
Bacterial Populations ◽  
Taxonomic Marker ◽  
The Impact

Next Generation Sequencing (NGS) technologies have overcome the limitations of cultivation-dependent approaches and allowed detailed study of bacterial populations that inhabit the human body. The consortium of bacteria residing in the human intestinal tract, also known as the gut microbiota, impacts several physiological processes important for preservation of the health status of the host. The most widespread microbiota profiling method is based on amplification and sequencing of a variable portion of the 16S rRNA gene as a universal taxonomic marker among members of the Bacteria domain. Despite its popularity and obvious advantages, this 16S rRNA gene-based approach comes with some important limitations. In particular, the choice of the primer pair for amplification plays a major role in defining the accuracy of the reconstructed bacterial profiles. In the current study, we performed an in silico PCR using all currently described 16S rRNA gene-targeting primer pairs (PP) in order to assess their efficiency. Our results show that V3, V4, V5, and V6 were the optimal regions on which to design 16S rRNA metagenomic primers. In detail, PP39 (Probio_Uni/Probio_Rev), PP41 (341F/534R), and PP72 (970F/1050R) were the most suitable primer pairs with an amplification efficiency of >98.5%. Furthermore, the Bifidobacterium genus was examined as a test case for accurate evaluation of intra-genus performances at subspecies level. Intriguingly, the in silico analysis revealed that primer pair PP55 (527f/1406r) was unable to amplify the targeted region of any member of this bacterial genus, while several other primer pairs seem to rather inefficiently amplify the target region of the main bifidobacterial taxa. These results highlight that selection of a 16S rRNA gene-based PP should be done with utmost care in order to avoid biases in microbiota profiling results.

scholarly journals Empirical Testing of 16S rRNA Gene PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy Not Suggested by In Silico Analysis

2009 ◽  
Vol 75 (9) ◽  
pp. 2677-2683 ◽  
Author(s):  
Sergio E. Morales ◽  
William E. Holben
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Quantitative Pcr ◽  
In Silico ◽  
In Silico Analysis ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Empirical Testing ◽  
Specific Target ◽  
Silico Analysis

ABSTRACT Phylogenetic and “fingerprinting” analyses of the 16S rRNA genes of prokaryotes have been a mainstay of microbial ecology during the last two decades. However, many methods and results from studies that rely on the 16S rRNA gene for detection and quantification of specific microbial taxa have seemingly received only cursory or even no validation. To directly examine the efficacy and specificity of 16S rRNA gene-based primers for phylum-, class-, and operational taxonomic unit-specific target amplification in quantitative PCR, we created a collection of primers based solely on an extensive soil bacterial 16S rRNA gene clone library containing ∼5,000 sequences from a single soil sample (i.e., a closed site-specific library was used to create PCR primers for use at this site). These primers were initially tested in silico prior to empirical testing by PCR amplification of known target sequences and of controls based on disparate phylogenetic groups. Although all primers were highly specific according to the in silico analysis, the empirical analyses clearly exhibited a high degree of nonspecificity for many of the phyla or classes, while other primers proved to be highly specific. These findings suggest that significant care must be taken when interpreting studies whose results were obtained with target specific primers that were not adequately validated, especially where population densities or dynamics have been inferred from the data. Further, we suggest that the reliability of quantification of specific target abundance using 16S rRNA-based quantitative PCR is case specific and must be determined through rigorous empirical testing rather than solely in silico.

scholarly journals Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
Carolina Chiellini ◽  
Renato Iannelli ◽  
Franco Verni ◽  
Giulio Petroni
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Biology ◽  
16S Rrna ◽  
Bacterial Communities ◽  
In Silico ◽  
Pollution Levels ◽  
High Pollution ◽  
Seabed Sediments ◽  
Bacterial Groups ◽  
Different Levels

Seabed sediments of commercial ports are often characterized by high pollution levels. Differences in number and distribution of bacteria in such areas can be related to distribution of pollutants in the port and to sediment conditions. In this study, the bacterial communities of five sites from Leghorn Harbor seabed were characterized, and the main bacterial groups were identified. T-RFLP was used for all samples; two 16S rRNA libraries andin silicodigestion of clones were used to identify fingerprint profiles. Library data, phylogenetic analysis, and T-RFLP coupled within silicodigestion of the obtained sequences evidenced the dominance ofProteobacteriaand the high percentage ofBacteroidetesin all sites. The approach highlighted similar bacterial communities between samples coming from the five sites, suggesting a modest differentiation among bacterial communities of different harbor seabed sediments and hence the capacity of bacterial communities to adapt to different levels and types of pollution.

scholarly journals Molecular Detection of Borrelia Bacteria in Cerebrospinal Fluid-Optimisation of Pre-Analytical Sample Handling for Increased Analytical Sensitivity

Diagnostics ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2088
Author(s):  
Malin Lager ◽  
Peter Wilhelmsson ◽  
Andreas Matussek ◽  
Per-Eric Lindgren ◽  
Anna J. Henningsson
Keyword(s):  
Cerebrospinal Fluid ◽  
16S Rrna ◽  
Clinical Diagnostics ◽  
Systematic Evaluation ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Analytical Sensitivity ◽  
Gene 16S Rrna ◽  
Pcr Targeting ◽  
The 16S Rrna Gene

The main tools for clinical diagnostics of Lyme neuroborreliosis (LNB) are based on serology, i.e., detection of antibodies in cerebrospinal fluid (CSF). In some cases, PCR may be used as a supplement, e.g., on CSF from patients with early LNB. Standardisation of the molecular methods and systematic evaluation of the pre-analytical handling is lacking. To increase the analytical sensitivity for detection of Borrelia bacteria in CSF by PCR targeting the 16S rRNA gene, parameters were systematically evaluated on CSF samples spiked with a known amount of cultured Borrelia bacteria. The results showed that the parameters such as centrifugation time and speed, the use of complementary DNA as a template (in combination with primers and a probe aiming at target gene 16S rRNA), and the absence of inhibitors (e.g., erythrocytes) had the highest impact on the analytical sensitivity. Based on these results, a protocol for optimised handling of CSF samples before molecular analysis was proposed. However, no clinical evaluation of the proposed protocol has been done so far, and further investigations of the diagnostic sensitivity need to be performed on well-characterised clinical samples from patients with LNB.

scholarly journals Phân lập và tuyển chọn một số dòng vi khuẩn từ lá thực vật có khả năng kích thích sinh trưởng cây trồng

2021 ◽  
Vol 57 (2) ◽  
pp. 94-103
Author(s):  
Thanh Nhàn Ung ◽  
Thị Kiều Oanh Nguyễn ◽  
Nguyễn Khởi Nghĩa
Keyword(s):  
16S Rrna ◽  
Mineral Salt ◽  
Rosa Chinensis ◽  
Arachis Pintoi ◽  
Coccinia Grandis ◽  
Gene 16S Rrna

Nghiên cứu thực hiện nhằm phân lập vi khuẩn kích thích sinh trưởng cây trồng từ lá thực vật. Môi trường nuôi cấy ammonium mineral salt (AMS) được sử dụng để phân lập vi khuẩn. Kết quả đã phân lập được 28 dòng vi khuẩn từ lá của 6 loài thực vật khác nhau gồm mồng tơi (Basella rubra L.), hoa hồng (Rosa chinensis Jacq.), chiều tím (Ruellia brittoniana), cỏ đậu (Arachis pintoi), cơm nguội (Ardisia quinquegona Blume) và bình bát dây (Coccinia grandis (L) Voigt) dựa trên hình thái và màu sắc của khuẩn lạc. Các chỉ tiêu về tỉ lệ nảy mầm, chiều dài rễ, chiều cao chồi và số rễ của hạt bắp được khảo sát để đánh giá khả năng kích thích sinh trưởng của các dòng vi khuẩn phân lập. Các dòng vi khuẩn phân lập có hình thái khuẩn lạc và tế bào rất đa dạng. Hai dòng vi khuẩn ký hiệu HH5 và MT6 làm gia tăng tỉ lệ nảy mầm và sinh trưởng của hạt bắp tốt nhất trong các dòng vi khuẩn phân lập. Bên cạnh đó, nghiên cứu còn cho thấy ở mật số 106 CFU.mL-1 cả hai dòng vi khuẩn giúp gia tăng tỉ lệ nảy mầm và sinh trưởng của cây bắp tốt hơn so với mật số 107, 108 và 109 CFU.mL-1. Kết giải mã trình tự đoạn gene 16S rRNA cho thấy hai dòng vi khuẩn HH5 và MT6 lần lượt có mối quan hệ gần...

scholarly journals Isolamento de linhagens bacterianas degradadoras de hidrocarbonetos BTEX proveniente do setor petroquímico

2017 ◽  
Vol 13 (9) ◽  
Author(s):  
Tielly De Mattos Padilha ◽  
Jamilla Sampaio ◽  
Letícia Longoni ◽  
Anelise Beneduzi
Keyword(s):  
16S Rrna ◽  
Pseudomonas Sp ◽  
Gene 16S Rrna

O petróleo e seus derivados são responsáveis por impactos ambientais significativos e a fração dos hidrocarbonetos aromáticos BTEX é amplamente utilizada, mesmo sendo considerada altamente tóxica. Sabendo que áreas com histórico de contaminação de hidrocarbonetos possuem microrganismos capazes de sobreviver ao contaminante e que a biodegradação pode ser utilizada para minimizar ou remover estes poluentes do ambiente, o objetivo deste trabalho foi isolar e identificar linhagens bacterianas degradadoras de hidrocarbonetos do tipo BTEX, provenientes de um solo com histórico de vinte e dois anos de contaminação do setor petroquímico em Triunfo/RS. Para isso foram coletadas amostras de solo em células de landfarming, com histórico de disposição de compostos derivados do petróleo e estas foram preparadas em três concentrações de BTEX (0,5%; 1%; 1,5%) como única fonte de carbono. Foram obtidos 122 isolados e estes foram testados quanto à sua capacidade de biodegradação de 5%, 10% e 20% do contaminante, sendo selecionados onze isolados promissores (linhagens 8, 10, 15, 17, 23, 24, 62, 64, 99, 126 e 128), destacando-se a linhagem 62 (Pseudomonas sp.) que cresceu em 20% de BTEX. Através do sequenciamento do gene 16S rRNA foi possível identificar principalmente isolados dos gêneros Bacillus (linhagens 8, 10, 15, 17 e 23), Pseudomonas (linhagens 24,62, 64, 99 e 128) e um isolado de Paenibacillus jamilae (linhagem 126).O petróleo e seus derivados são responsáveis por impactos ambientais significativos e a fração dos hidrocarbonetos aromáticos BTEX é amplamente utilizada, mesmo sendo considerada altamente tóxica. Sabendo que áreas com histórico de contaminação de hidrocarbonetos possuem microrganismos capazes de sobreviver ao contaminante e que a biodegradação pode ser utilizada para minimizar ou remover estes poluentes do ambiente, o objetivo deste trabalho foi isolar e identificar linhagens bacterianas degradadoras de hidrocarbonetos do tipo BTEX, provenientes de um solo com histórico de vinte e dois anos de contaminação do setor petroquímico em Triunfo/RS. Para isso foram coletadas amostras de solo em células de landfarming, com histórico de disposição de compostos derivados do petróleo e estas foram preparadas em três concentrações de BTEX (0,5%; 1%; 1,5%) como única fonte de carbono. Foram obtidos 122 isolados e estes foram testados quanto à sua capacidade de biodegradação de 5%, 10% e 20% do contaminante, sendo selecionados onze isolados promissores (linhagens 8, 10, 15, 17, 23, 24, 62, 64, 99, 126 e 128), destacando-se a linhagem 62 (Pseudomonas sp.) que cresceu em 20% de BTEX. Através do sequenciamento do gene 16S rRNA foi possível identificar principalmente isolados dos gêneros Bacillus (linhagens 8, 10, 15, 17 e 23), Pseudomonas (linhagens 24,62, 64, 99 e 128) e um isolado de Paenibacillus jamilae (linhagem 126).<w:LsdException Locked="false" Priority="72" Na

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