Marine genomics: at the interface of marine microbial ecology and biodiscovery

Abstract

The composition and activities of microbes from diverse habitats have been the focus of intense research during the past decade with this research being spurred on largely by advances in molecular biology and genomic technologies. In recent years environmental microbiology has entered very firmly into the age of the ‘omics’– (meta)genomics, proteomics, metabolomics, transcriptomics – with probably others on the rise. Microbes are essential participants in all biogeochemical processes on our planet, and the practical applications of what we are learning from the use of molecular approaches has altered how we view biological systems. In addition, there is considerable potential to use information about uncultured microbes in biodiscovery research as microbes provide a rich source of discovery for novel genes, enzymes and metabolic pathways. This review explores the brief history of genomic and metagenomic approaches to study environmental microbial assemblages and describes some of the future challenges involved in broadening our approaches – leading to new insights for understanding environmental problems and enabling biodiscovery research.

Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia

“…These and other studies have placed microbes (used in this sense to include archaea, bacteria and viruses) as essential participants in most biogeochemical processes. However, studies of the diversity and activities of microbial eukaryotic (protistian) assemblages have lagged behind in this and other systems (Caron et al, 2009; Heidelberg et al, 2010). Consequently, the ecological importance that microbial eukaryotes have in food web dynamics in hypersaline systems is poorly understood (Pedrós-Alió et al, 2000; Elloumi et al, 2009).…”

Comparative Analysis of Eukaryotic Marine Microbial Assemblages from 18S rRNA Gene and Gene Transcript Clone Libraries by Using Different Methods of Extraction

“…Since the late 1980s, culture-independent PCR-amplified clone libraries that target the small subunit (SSU) 16S rRNA taxonomic genes have served as a proxy for the diversity and composition of natural microbial bacterial and archaeal populations (15, 16, 33a). However, studies of microbial eukaryotic populations have lagged behind those of their generally smaller prokaryote counterparts (7,25). More recently, natural assemblages of microbial eukaryotes have been assessed and compared using the SSU 18S rRNA gene.…”

How mutualisms arise in phytoplankton communities: building eco‐evolutionary principles for aquatic microbes

“…Despite the considerable information that can be gained from studies of environmental samples, inferring and characterising interactions is at best correlativea process once described as 'akin to boiling dinner leftovers in a pot for 24 h, pureeing heavily and then trying to attribute any spice or stew fragment back to the original dish or constituent from which it derived' (Heidelberg et al 2010). To gain real mechanistic understanding of interactions it is necessary to study defined or model systems that can be co-cultured under controlled conditions, enabling identification of the metabolic foundations for the ecology, demonstrating directly the compounds that are exchanged, and studying the molecular machinery involved in the associations.…”