# Microbial Bioremediation and Biodegradation of Petroleum Products--A Mini Review
## 3 Microbial Diversity and Ecology  
Microbial ecology is critical to research in microbiology, which helps ascertain the organisms present in a specific habitat. Moreover, it helps to detect which kinds of microbes may be present within the particular site where samples were collected during the sequencing of DNAs of the microorganisms. Recently, researchers have adopted DNA-based technologies in analyzing microbial communities in organic compounds or petroleum hydrocarbon (PH) contaminated sediments, water, and soils [20]. This field of science is known as \"community genomics\", \"economics\" or \"environmental genomics\" [21]. It is, therefore, a study of genetic materials which are directly recuperated from samples of the environment. In its early years of study, new environmental gene sequencing cloned specific genes (16S or 18S rRNA genes), and cultivated clonal cultures were utilized to manufacture a diversified profile in a biological sample. A broad spectrum of microbial diversity used cultivation-based methods [22]. Nevertheless, recent studies have also shown that environmental samples could contain a smaller number of cultivable microorganisms than non-cultivable ones [21]. Thus, studies that focus on either polymerase chain reaction (PCR), or \"shotgun\" directed sequencing tend to have primarily objective sampled genes from all the sampled communities included in the study [23]. Because metagenomics can reveal the hitherto hidden diversity of microbial life, it allows microbial ecology to be scrutinized comprehensively and at a grander scale than before as DNA sequencing prices continue to decrease [21]. In analyzing the community structure of the microbes in PH-contaminatedwater, sediment/soil, the total chromosomal DNA is isolated using one of numerous accessible viable DNA kits. The isolated DNA is then kept at a temperature of \(-20\)\({}^{\circ}\)C for future usage. Thereafter, in a bid to analyze the microbial community structure, 16S rRNA genes are PCR amplified from the chunk DNA by utilizing PCR reaction mixture [21]. The mixture usually contains template DNA with a volume of PCR mixture between 20-50 \(\mu\)L, polymerase enzyme (pfu or Taq polymerases), polymerase enzyme buffer, and universal primers (e.g., 1492R/27F) each of four dNTPs [24]. Similarly, by PCR using the forward and reverse primers of 27F (5-AGA GTT TGA TCC TGG CTC AG-3) and 1492R (5-CGG CTA CCT TGT TAC GAC TT-3), respectively, the 16S rRNA region is amplified [25]. Principally, the amplification of DNA is performed under the prescribed cycling conditions. First, it starts with 1 cycle of 2 min at 94 \({}^{\circ}\)C. After that, it moves to 25 cycles of 30 s at 94 \({}^{\circ}\)C, followed by 30 s at 55 \({}^{\circ}\)C, then 1 min at 72 \({}^{\circ}\)C, and finally with the last cycle of 10 min at 72 \({}^{\circ}\)C [21]. After DNA amplification, PCR products, also known as 'amplicons', are tested to ascertain the particular length of the DNA PCR or DNA amplicons by a 2% agarose gel [26]. They are then purified to sequence cloned specific genes. Combo kits, which are used for the extraction and purification of gel, are commercially ubiquitous. In a single step, the combo kits can perform both purification and gel extraction of amplicons. ITS (internal transcribed spacer) regions of their complete DNA are augmented by using ITS1 and ITS2 primers in the event of analyzing the fungal community structure [27]. The purified PCR products are then utilized in the sequencing process. Myriad 'next-generation' now high-throughput methods come in handy in sequencing the genome. They include nanopore DNA sequencing, single-molecule real-time (SMRT) sequencing, Heliscope single-molecule sequencing, DNA nano ball sequencing, Ion Torrent semiconductor sequencing, solid sequencing, Illumina (Solexa) sequencing, 454-Pyrosequencing, colony sequencing and massively parallel signature sequencing (MPSS) [28; 29].