Approaches to Unmask Functioning of the Uncultured Microbial Majority From Extreme Habitats on the Seafloor

Abstract

Researchers have recognized the potential of enzymes and metabolic pathways hidden among the unseen majority of Earth’s microorganisms for decades now. Most of the microbes expected to colonize the seafloor and its subsurface are currently uncultured. Thus, their ability and contribution to element cycling remain enigmatic. Given that the seafloor covers ∼70% of our planet, this amounts to an uncalled potential of unrecognized metabolic properties and interconnections catalyzed by this microbial dark matter. Consequently, a tremendous black box awaits discovery of novel enzymes, catalytic abilities, and metabolic properties in one of the largest habitats on Earth. This mini review summarizes the current knowledge of cultivation-dependent and -independent techniques applied to seafloor habitats to unravel the role of the microbial dark matter. It highlights the great potential that combining microbiological and biogeochemical data from in situ experiments with molecular tools has for providing a holistic understanding of bio-geo-coupling in seafloor habitats and uses hydrothermal vent systems as a case example.

Genomic insight and physiological characterization of thermoacidophilic Alicyclobacillus isolated from Yellowstone National Park

“…Isolating pure cultures of certain microorganisms from complex microbial consortia requires special cultivation strategies based on an understanding of growth requirements, metabolic characteristics and microbial interactions. Commonly, unintentional isolation of untargeted microorganisms or contamination of DNA occurs during cultivation for the purpose of microbial isolation ( Kawanishi et al, 2011 ), especially from extreme environments with low microbial diversity ( Delavat et al, 2012 ; Böhnke and Perner, 2022 ; Kim et al, 2022 ). In our study, Alicyclobacillus was inadvertantly co-cultured during the original isolation of a methanotroph from the Yellowstone Hot Spring samples.…”

Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications

“…Consequently, it is highly likely that among the uncultured microbial majority (81% of microbial cells on earth) numerous, currently inaccessible CODH (-like) enzymes are hidden (Lloyd et al 2018 ). Targeting, identifying and characterizing this tremendous potential of CODH (-like) biocatalysts must be one of the key strategies used in future research approaches (Böhnke and Perner 2022 ).…”

Meta‐omics assisted microbial gene and strain resources mining in contaminant environment

“…Additionally, microbial‐based bioremediation technologies (e.g., activated sludge, biofilm, and bioleaching) are often considered to be an efficient and environmentally safe alternative for pollutant removal [ 7 , 8 , 9 ]. In earlier studies, many microorganisms (e.g., Alcaligenes , Cellulosimicrobium , Sphingobium , and Flavobacterium ) and enzymes (e.g., oxidoreductases, hydrolases, and amidohydrolases) have been applied in environmental bioremediation and industrial production [ 6 , 10 ].…”