نوع مقاله : مقاله پژوهشی

نویسندگان

1 دکترای میکروبیولوژی ،مؤسسه تحقیقات جنگلها و مراتع ایران، سازمان تحقیقات، آموزش و ترویج کشاورزی، تهران، ایران

2 دانشیار ،گروه میکروبیولوژی، دانشکده علوم زیستی، دانشگاه الزهرا س، تهران، ایران

3 استاد،موسسه تحقیقات جنگلها و مراتع ایران، سازمان تحقیقات، آموزش و ترویج کشاورزی، تهران، ایران

4 استادیار ، گروه علوم گیاهی، دانشکده علوم زیست، دانشگاه الزهرا (س)

10.22051/jab.2021.36477.1428

چکیده

مقدمه: هدف از این مطالعه بررسی تاثیر نوع پرایمر در ارزیابی ساختار جمعیت میکروبی در خاک یک اکوسیستم نیمه خشک بوده است. مواد و روشها: ِDNA نمونه­های خاک پس از استخراج و انجام PCR با دو جفت پرایمر مربوط به نواحی V1-V3 و V4-V5 توالی­یابی و داده­ها با نرم افزار QIME آنالیز شدند. نتایج: آنالیزNext Generation Sequencing  نشان داد پرایمر V4-V5 توانست 97/9 درصد از باکتری­ها را شناسایی کند در حالیکه 90/4 درصد از باکتری­ها با جفت پرایمر V1-V3 شناسایی شدند. جفت پرایمر V1-V3 توانست درصد بیشتری از Proteobacteria (37/8درصد) را شناسایی کند در صورتی­که جفت پرایمر V4-V5 در شناسایی Actinobacteria (33/6 درصد) بهتر عمل کرده است. بعلاوه جفت پرایمر V4-V5 در سطوح تاکسونومیکی راسته، خانواده و جنس تعداد بیشتری را در نمونه­های خاک مطالعه شده در مقایسه با جفت پرایمر V1-V3 شناسایی کرد. بحث: با وجود عملکرد بهتر پرایمر V4-V5 و با توجه به اینکه برخی از اجزای سطوح مختلف تاکسونومیکی با یکی از جفت پرایمرهای استفاده شده شناسایی شدند به نظر می­رسد به منظور ارزیابی دقیق­تر جمعیت­های میکروبی بهتر است از حداقل دو سری پرایمر استفاده شود.

کلیدواژه‌ها

عنوان مقاله [English]

Assay and comparison the impact of primer in evaluation of bacterial community structure in semiarid area by Illumina Miseq

نویسندگان [English]

  • Maryam Teimouri 1
  • Parisa Mohammadi 2
  • Adel Jalili 3
  • Roghaye Zarei 4

1 PhD in Microbiology, Research Institute of Forests and Rangelands, Agriculture, Research, Education and Extension Organization (AREEO) ,Tehran, I.R. Iran.

2 Associate Professor, Associate Professor, Department of Microbiology, Faculty of Biological Sciences,Tehran,, Iran

3 Pirfosor, Research Institute of Forests and Rangelands, Agriculture, Research, Education and Extension Organization (AREEO), Tehran, Iran.

4 Assistant Professor, Department of Plant Sciences, Faculty of Biological Sciences, Alzahra University

چکیده [English]

The aim of this study was to compare the effect of primers in evaluating soil bacterial community structure. For this purpose, soil samples were taken from cold and warm area which grazed (disturbed) or not grazed (undisturbed) in spring and autumn. Microbial DNA was extracted and sequenced after amplification by two primers which amplify V1-V3 and V4-V5 area of 16S rRNA. Next generation sequencing data were analyzed by QIME to determine bacterial community structure. Results showed the effect of area, grazing and season on bacterial community structure. NGS data analysis showed that primers which amplified V4-V5 area identified more bacteria (97.9%) in compared to V1-V3 primers (90.4%). V1-V3 primers had better efficiency to identify Proteobacteria (37.85%) in compared to V4-V5 which identified more Actinobacteria (33.6%). In addition, V4-V5 primers identified more bacteria in class, family and genus taxonomic groups in compared to V1-V3 primer. Although V4-V5 primer had better efficiency in bacteria identification, it is recommended to use both primers to evaluate precisely bacterial community structure.

کلیدواژه‌ها [English]

  • Biodiversity
  • Microbial Community
  • Next generation Sequencing
  • Soil microbiology
  • Taxonomy
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