Microbial Diversity in the Era of Omic Technologies

Abstract

Human life and activity depends on microorganisms, as they are responsible for providing basic elements of life. Although microbes have such a key role in sustaining basic functions for all living organisms, very little is known about their biology since only a small fraction (average 1%) can be cultured under laboratory conditions. This is even more evident when considering that >88% of all bacterial isolates belong to four bacterial phyla, the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Advanced technologies, developed in the last years, promise to revolutionise the way that we characterize, identify, and study microbial communities. In this review, we present the most advanced tools that microbial ecologists can use for the study of microbial communities. Innovative microbial ecological DNA microarrays such as PhyloChip and GeoChip that have been developed for investigating the composition and function of microbial communities are presented, along with an overview of the next generation sequencing technologies. Finally, the Single Cell Genomics approach, which can be used for obtaining genomes from uncultured phyla, is outlined. This tool enables the amplification and sequencing of DNA from single cells obtained directly from environmental samples and is promising to revolutionise microbiology.

Biogeography of aquatic hyphomycetes: Current knowledge and future perspectives

“…NGS technologies will continue to improve both accuracy and throughput and, in the near future, benchtop sequencers will become standard equipment in individual labs. Amplicon analyses are expected to become a rapid screening technique in preparation for more detailed metagenomic studies, rather than representing the final stage in ecological analysis (Nikolaki and Tsiamis, 2013). While NGS technologies may inform us that different geographic regions harbour different aquatic fungal communities, they will not reveal much about their function.…”

“…New approaches exploiting NGS technologies and single cell genomics (characterizing genomes of uncultured phyla from single cells obtained directly from the environment; Lasken, 2007) may target genomes and associate them with quantitative measurements in particular geographic regions. This approach potentially targets all active members (abundant and rare) of a given ecosystem, quantifies the transcribed genes, and obtains complete genomes (Nikolaki and Tsiamis, 2013). Single cell genomics have been employed to investigate the biogeographic distribution of uncultured marine Flavobacteria and marine bacterioplankton (Mason et al, 2012;Woyke et al, 2009).…”

Unveiling PHA-storing populations using molecular methods

“…NGS platforms perform massively parallel sequencing, where millions of fragments of DNA from a single sample are sequenced simultaneously (Nikolaki and Tsiamis 2013). The sequencing is steered either in a continuous real-time manner or in a stepwise iterative process, where each clonal template or single molecule is independently sequenced and can be counted among the total sequences generated (Fig.…”

“…The sequencing is steered either in a continuous real-time manner or in a stepwise iterative process, where each clonal template or single molecule is independently sequenced and can be counted among the total sequences generated (Fig. 3) (Mardis 2013;Nikolaki and Tsiamis 2013). This allows for quickly sequencing an entire genome.…”

Bacterial Diseases of Crops

“…On the other hand, the use of nonselective medium could equally be a problem for an effective diagnosis given that some of these species (P. fluorescens, Pectobacterium atrosepticum, and P. carotovorum) grow very rapidly thereby masking the presence of other slow-growing species. Although several advanced culture-independent techniques, such as next-generation sequencing, allow identification of bacterial species without being isolated on the media (Nikolaki and Tsiamis, 2013), the isolations of such microbes result essential to perform the pathogenicity tests.…”