Deep Subsurface Microbiology
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Deep Subsurface Microbiology
Deep subsurface microbiology is a highly active and rapidly advancing research field at the interface of microbiology and the geosciences; it focuses on the detection, identification, quantification, cultivation and activity measurements of bacteria, archaea and eukaryotes that permeate the subsurface biosphere of deep marine sediments and the basaltic ocean and continental crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and – at best - incompletely understood microbial populations. In spatial extent and volume, Earth's subsurface biosphere is only rivaled by the deep sea water column. So far, no deep subsurface sediment has been found that is entirely devoid of microbial life; microbial cells and DNA remain detectable at sediment depths of more than 1 km; microbial life permeates deeply buried hydrocarbon reservoirs, and is also found several kilometers down in continental crust aquifers. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that have shaped the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical role as long-term organic carbon repository, inorganic electron and energy source, and subduction recycling engine continues to be explored by current research at the interface of microbiology, geochemistry and biosphere/geosphere evolution. This Research Topic addresses some of the central research questions about deep subsurface microbiology and biogeochemistry: phylogenetic and physiological microbial diversity in the deep subsurface; microbial activity and survival strategies in severely energy-limited subsurface habitats; microbial activity as reflected in process rates and gene expression patterns; biogeographic isolation and connectivity in deep subsurface microbial communities; the ecological standing of subsurface biospheres in comparison to the surface biosphere – an independently flourishing biosphere, or mere survivors that tolerate burial (along with organic carbon compounds), or a combination of both? Advancing these questions on Earth’s deep subsurface biosphere redefines the habitat range, environmental tolerance, activity and diversity of microbial life.
Microbiology of the Terrestrial Deep Subsurface
Obtaining and analyzing samples is challenging in subsurface science. This first-of-its-kind reference book addresses accomplishments in this field-from drilling to sample work-up. A collaborative approach is taken, involving the efforts of microbiologists, geochemists, hydrologists, and drilling and mining experts to present a comprehensive view of subsurface research. The text provides practical information about obtaining, analyzing, and evaluating subsurface materials; the current status of subsurface microbial ecology; and describes several applications that will interest a variety of readers, including engineers, physical, and life scientists.
Deep Subsurface Microbiology and Energetics
Author: Alberto Robador
language: en
Publisher: Frontiers Media SA
Release Date: 2025-05-27
The role of deeply buried microbes is far more important than has been previously presumed. Comprehensive studies of deep subsurface microbiology have revealed not only cell abundances that match previous estimates in surface environments, but most importantly, have demonstrated the viability of these microbes and their essential roles in operating and maintaining global biogeochemical cycles. The deep subsurface biosphere refers to the vast ecosystems of microorganisms that exist within marine subseafloor sediments and the oceanic crust, as well as continental subterranean environments. They are estimated to contain a significant portion of the total biomass on Earth and are comprised of diverse microbial taxa including bacteria, archaea, protists, and fungi that survive in environments that are often extremely energy-limited. Due to the unique characteristics of these ecosystems, deep subsurface microorganisms are often distinct from those found in surface environments and laboratory strains. They are becoming a crucial topic of research for their unusual adaptations to energy limitation and their important interactions with the geosphere. Despite its size and significance, however, the deep biosphere remains largely understudied. One of the main gaps in our knowledge is the extent of microbial biogeochemical activity across the physicochemical gradients that characterize deep biosphere extreme ecosystems. This is due, in large part, to the high uncertainty in metabolic rate estimates and unknown systematic biases due to data scarcity. Bioenergetic studies have provided a conceptual framework for understanding the complexity of microbial metabolism within various spatial and temporal scales. However, our knowledge of energy metabolism in the deep biosphere is hindered by inadequate methodology for energy flux quantification and incomplete data of the actual energy parameters associated with subsurface microbes, many of which are novel and uncharacterized species. Despite these gaps, research on the deep biosphere continues to provide new insights into the function of these unique microbial communities and their potential to reach and impact the chemical economy of the overlying ecosystems. The aim of this Research Topic is to open a new perspective on the biotic/abiotic interface in extreme microbiology. We invite contributions from scientists working in diverse disciplines who have a common interest in various aspects of the study of microorganisms that live in energy-limited deep subsurface environments. This can include research on the diversity, activity, genetic repertoire, and expression of subsurface microbial communities and their resulting biogeochemical activity. We encourage the submission of manuscripts focusing on recent advances in deep biosphere studies by using both empirical and theoretical approaches. Articles in this Research Topic are dedicated to commemorating the late Jan Amend, whose pioneering work significantly advanced our understanding of microbial life in deep subsurface environments. Amend's contributions not only challenged existing notions about the limits of life but also provided key insights into the survival strategies of microbes in energy-limited settings, continuing to inspire and guide current research in extreme microbiology.