Methods for Analyzing Diversity of Microbial Communities in Natural Environments

Abstract

Difficulties in cultivating most of the microorganisms limit our ability to study microbial ecosystems. Molecular methods are valuable tools for investigating the diversity and structure of bacterial communities. These techniques can be used on culturable as well as non-culturable bacteria. Cultivation independent techniques based on nucleic acids extracted from the environment provide information on community structure and diversity. Analyses of DNA can determine the numbers of different genomes. Ribosomal RNA (rRNA) or rDNA (genes coding for rRNA) fingerprinting, probing and sequencing can be used to detect and identify organisms. The combination of different methods that complement each other is a useful strategy for monitoring changes of microbial communities in natural ecosystems.

A comparative study on microbiota from the intestine of Prussian carp (Carassius gibelio) and their aquatic environmental compartments, using different molecular methods

“…; Wu et al . ; Fakruddin and Mannan ). It is known that it is impossible to culture and identify over 70% of intestinal microbiota (Trust and Sparrow ; Sugita et al .…”

Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake

“…It is considered that the bacterial communities are the basis of a trophic pyramid that is, on one side being utilized as a source of food by other animals, whereas from the other side they hydrolyse the organic compounds in aquatic ecosystems (Ugolev 1985) thereby modifying their surroundings. The metabolic plasticity of bacteria has allowed them to adapt to different habitats and occupy various ecological niches (Hugenholtz et al 1998;Fakruddin and Mannan 2013). One such niche, the focus of this study, is the fish gut.…”

Effects of postharvest Irvingia fruit wastes on soil microbial diversity and physico-chemical properties

“…The term species diversity consists of two components which are species richness and evenness. Species richness simply means the total number of species (Fakruddin and Mannan, 2013). The term Operational Taxonomic Units was often interchangeably used to represent this phenomenon in this work.…”

“…Firstly, soil microbial community is diverse, and heterogeneous (Singh et al, 2004). Secondly, microorganisms exist in high numbers in natural ecosystems and there are several thousands of microbial species that have not yet been described (Fakruddin and Mannan, 2013). For example, an estimated 1.5 million fungal species are considered to inhabit natural ecosystems, but only 5 to 10% have been described formally (Hawksworth, 2001;Wang et al, 2008).…”