The details of this research, led by the Institut de Ciències del Mar (ICM-CSIC) and the Universitat Autònoma de Barcelona (UAB), are reported in an article published recently in the prestigious journal ISME Communications.
A team of researchers led by the Institut de Ciències del Mar (ICM-CSIC) of Barcelona and the Universitat Autònoma de Barcelona (UAB) has unveiled that abundant deep ocean bacteria can be retrieved in pure culture in the laboratory, thus questioning the idea that the majority of the cultivated taxa belong to species normally present in very low abundances in the environment. The details of this research are reported in an article published recently in the prestigious journal ISME Communications.
Traditionally, marine microbial diversity, especially in the deep ocean, was considered challenging to cultivate, making it difficult to study in the laboratory. Isolation of microorganisms constitutes a valuable tool for testing ecological hypotheses and understanding the role of key bacteria in the ocean. Thanks to a large-scale comparative analysis of isolated bacteria and environmental sequences we are reshaping our understanding of deep-sea bacteria.
To carry out the study, researchers compared genetic sequences from a collection of over 2,000 cultured heterotrophic marine bacteria obtained through oceanographic campaigns including Tara Oceans and Malaspina expeditions, which covered various ocean layers, from surface waters to some of the deepest parts of the ocean.
“This study is key because there is a lack of studies focusing on the isolation of marine bacteria from different ocean depths including surface, mesopelagic, and bathypelagic waters and covering wide oceanographic regions, from Atlantic, Pacific, Indian as well as southern Oceans. Moreover, the results reveal that heterotrophic bacteria isolates represent a significant fraction of the total diversity”, explains the ICM-CSIC researcher Silvia G. Acinas, one of the leading authors of the study. Besides, adds Acinas, “the research allowed to retrieve some of the most abundant taxa in the deep ocean using marine standard media”. Finally, the researcher stresses the huge effort that is needed to obtain such a collection of marine bacteria.
From her side, Isabel Sanz Sáez, (ICM-CSIC), the first author of the study, points out that “the use of traditional culture techniques together with modern bioinformatic approaches allowed us to obtain a more comprehensive view of the cultivability of bacteria present in different ocean depths and oceanographic regions”. In particular, Sanz Sáez states, “the combination of these approaches has revealed that the cultivability of heterotrophic bacteria in the deep ocean is higher compared to the surface ocean”. In fact, adds the expert, “we have isolated some of the top 10 most abundant species found in the bathypelagic ocean that corresponded to the genera Sulfitobacter, Halomonas and Erythrobacter”.
Cultivable heterotrophic marine bacteria
The access to samples and data from different oceanographic campaigns has been key to explore in detail if cultivable bacteria have a preference to live as free-living bacteria or attached to particles of different sizes. According to Olga Sánchez, researcher at the Department of Genetics and Microbiology of the UAB and co-author of the study, this reveals that “particles are resource-rich habitats for microbes, and make them hot-spots for heterotrophic bacteria that can be cultivated under laboratory conditions”.
“This is an important matter because it is known that free-living and particle-attached bacterial communities are different in terms of taxonomic composition but also metabolic activity. Therefore, most of the isolates retrieved in the study would present a metabolic activity different than those present only in the free-living fraction, a fact that hints at different implications in the biogeochemical cycles of the ocean”, adds Sánchez.
In the authors' opinion, future studies should focus on using alternative isolation methods in order to help us to bring to the laboratory key taxa that are still uncultivated, as well as to explore the potential of these isolates from culture collections by combining genome sequencing with transcriptomic analyses to test hypothesis under different experimental scenarios of temperature, pressure or particle-association. All this, conclude the authors, “would enhance our understanding of these major taxa in the deep ocean”.