کاربرد روش PCR-DGGE در مطالعه‌ی اثر فعالیت‌های زراعی بر جوامع میکروبی خاک

نوع مقاله : مقاله کامل علمی - مروری

نویسندگان

استادیار، گروه گیاهپزشکی، دانشگاه رازی، دانشکده کشاورزی، کرمانشاه، ایران

چکیده

کشاورزی فشرده سبب کاهش حاصلخیزی خاک شده و اثرهای زیان‌باری بر سلامت انسان و محیط‌زیست داشته است؛ بنابراین، استفاده از شیوه‌های کشاورزی کم‌نهاده و سازگار با محیط‌زیست نظیر کشاورزی پایدار برای رسیدن به پایداری لازم جهت تأمین مواد غذایی، ضروری است. از راهبردهای مهم کشاورزی پایدار، حفظ و تقویت جوامع میکروبی مفید موجود در خاک است. این موجودات با فعالیت‌های گوناگون خود (نظیر تجزیه بقایا، معدنی نمودن و تثبیت مواد غذایی برای رشد گیاه، تولید هورمون‌های گیاهی، تجزیه آلاینده‌ها، تقویت رشد گیاه و مهار زیستی بیمارگرهای گیاهی)، نقش‌های بسیار مهمی در عملکرد و پایداری بوم‌نظام‌های خشکی‏زی ایفا می‌کنند. شناخت عوامل مؤثر بر این جوامع، به‌ویژه شیوه‌های مختلف مدیریت زمین‌های کشاورزی، کمک می‌کند تا آن‌ها را به سمت بهبود حاصلخیزی خاک، رشد و سلامت مطلوب گیاه و افزایش بهره‌وری و ثبات بوم‌نظام‌های کشاورزی مدیریت نماییم. برای انتخاب مناسب‌ترین روش‌های کشاورزی که موجب حفظِ تنوع و تقویت جوامع میکروبی مفید خاک می‌شوند و نیز اجتناب از اقداماتی که نابودی و کاهش تنوع میکروارگانیسم‌های آن را به دنبال دارند، به روش‌هایی سریع، قابل‌اعتماد، حساس و اختصاصی نیاز است که اطلاعات جامعی در مورد اثر فعالیت‌های زراعی مختلف بر ساختار و تنوع این جوامع از جمله بخش غیر قابل‌کِشت آن ارائه نمایند. در میان تکنیک‌های مولکولی، روش‌های بر پایه واکنش زنجیره‌ای پلیمراز به‌طور گسترده برای بررسی تنوع و ساختار میکروارگانیسم‌های خاک مورد استفاده قرار گرفته‌اند و polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)، یکی از شناخته‌شده‌ترین و پرکاربردترین این روش‌ها به شمار می‌آید. بیش از دو دهه است که روش PCR-DGGE، با موفقیت برای بررسی اثر عملیات زراعی مختلف بر تنوع و ساختار میکروارگانیسم‌های موجود در خاک‌های مختلف یا در یک خاک تحت مدیریت‌های زراعی مختلف به‌کار رفته است. با وجود در دسترس بودن نسل جدید فن‌آوری‌های توالی‌یابی دارای توان بالا در مطالعه جوامع میکروبی خاک، روش PCR-DGGE به دلیل مزیت‌های مختلف و نیاز به زحمت، هزینه و زمان کمتر و ارائه فوری مؤلفه‌ها به دو صورت کیفی و نیمه‌کمی، هم‌چنان روشی مهم برای بررسی تأثیر اقدامات و مدیریت‌های مختلف کشاورزی بر جوامع میکروبی به شمار می‌آید. با کمک یافته‌های حاصل از این تکنیک می‌توان بهترین روش‌های مدیریتی را در کشاورزی انتخاب کرد و راه را برای تحقق کشاورزی پایدار و امنیت تأمین مواد غذایی هموار نمود. در این نوشته به برخی منابع و پژوهش‌هایی که در آن‌ها از قابلیت PCR-DGGE جهت بررسی تأثیر مدیریت‌های کشاورزی و فعالیت‌های زراعی گوناگون بر ترکیب و تنوع جوامع میکروبی خاک استفاده شده و نیز بخشی از نتایج حاصل از آن‌ها اشاره گردیده است. همچنین ویژگی‌ها، مزیت‌ها، محدودیت‌ها و اصول انجام این روش ذکر شده‌اند.

کلیدواژه‌ها


عنوان مقاله [English]

Application of PCR-DGGE technique in studying the effect of agricultural activities on soil microbial communities

نویسندگان [English]

  • Nahid Moarrefzadeh
  • Hadi Khateri
Member of the scientific staff, Razi University
چکیده [English]

Intensive agriculture has reduced soil fertility and has had harmful effects on human health and the environment. Therefore, the use of low-input and environmentally-friendly agricultural methods such as sustainable agriculture is necessary to achieve the required sustainability in food supply. Preservation and revitalization of beneficial microbial communities in the soil, is one of the important strategies of sustainable agriculture. These microorganisms with diverse activities (such as residue decomposition, mineralization and fixation of nutrients for plant growth, production of plant hormones, decomposition of pollutants, plant growth and biological control of plant pathogens), play very important roles in the function and sustainability of terrestrial ecosystems. Understanding the factors affecting these communities particularly the different methods of managing agricultural lands helps to manage them towards improving soil fertility, optimal plant growth and health, and increasing the productivity and stability of agricultural ecosystems. For selecting the best cultivation methods that preserve the diversity and strengthen microbial communities as well as avoiding activities that lead to the destruction and reduction of its diversity of microorganisms, fast, reliable, sensitive and specific methods are needed that provide comprehensive knowledge about the effect of different agricultural activities on the structure and diversity of these communities, including its unculturable part. Among molecular techniques, polymerase chain reaction-based methods have been widely used to study the diversity and structure of soil microorganisms, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) is one of the most well-known and widely used methods. PCR-DGGE has been used successfully for more than two decades to investigate the effect of different crop managements on the diversity and structure of microorganisms in different soils or in a soil under different crop managements. Despite the availability of new generation of high-throughput sequencing technologies in the study of soil microbial communities, PCR-DGGE method due to various advantages with less hassle, cost and time and immediate presentation of components in both qualitative and semi-quantitative form is still an important way to study the impact of various agricultural practices and managements on microbial communities. With the help of the findings of this technique, the best management methods in agriculture could be selected and the way can be paved for the realization of sustainable agriculture and stable food supply. In this review, some researches and references that have used the efficacy of PCR-DGGE in studying the impact of various agricultural managements and activities on the composition and diversity of soil microbial communities and some of their results have been mentioned. The features, advantages, limitations, and principles of this method have also been outlined.

کلیدواژه‌ها [English]

  • Sustainable Agriculture
  • Microorganisms
  • Population Structure
  • Diversity
  • Ecosystem
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