AbstractBuilding on the synthesis of carbon reservoirs in Earth's subsurface, this chapter focuses on the forms, cycling, and fate of the carbon supporting microbial life in the terrestrial and marine subsurface. As the subsurface is estimated to host a vast reservoir of life on Earth, identifying the carbon compounds that life uses for energy and growth is key to understanding ecosystem functioning in the past and at present, and also for extrapolating these findings to the search for life in the universe. This chapter highlights advances in quantifying small carbon compounds, measuring rates of carbon turnover, and the fate of carbon in the deep biosphere.
AbstractRecent studies reveal that life in the terrestrial and marine subsurface exists on far less energy flux than is commonly understood from laboratory incubations with isolated organisms. This has profound implications for understanding the development of life on Earth, as well as for the search for life in the universe. Similarly, several recent research efforts have also addressed other limits to life, such as high temperature. This chapter presents an overview of the current understanding of the energetic limits of life on Earth.
AbstractRecent advances in nucleic acid extraction and sequencing have changed and expanded our understanding of the diversity of life in the terrestrial and marine subsurface. This chapter highlights recent developments in sequencing genetic material from the deep biosphere (spurred in part by the Census of Deep Life) and new bioinformatics approaches to present a synthesis of our current understanding of the biogeography of life in the deep biosphere. Building from this data framework, this chapter also explores emerging trends in understanding the ecology and evolution of subsurface life.
AbstractMarine shallow-water hydrothermal vents are defined as occurring at less than ~ 200 m below sea level, and are often found off the coasts of island arc volcanoes, which provide the necessary heat source to drive circulation. Recent research suggests that marine shallow-water hydrothermal vents, also known as “shallow-sea” vents (SHVs), are abundant across the Earth. While they have many similarities to deep-sea hydrothermal vents (DHVs), they also have many important differences, primarily due to their occurrence at shallower depths. Here we introduce SHVs and describe some of the processes which influence their geochemistry. This information is summarized from Price and Giovannelli (2017), and is complementary to Giovannelli and Price (2018), which describes the microbiology of shallow-sea vents.
AbstractOrganic matter degradation and preservation play a key role in global biogeochemical cycles and climate. The degradation of OM generally proceeds via multiple enzymatic reactions involving millions of different organisms, billions of organic compounds, and a number of different oxidants, as well as intermediate compounds. As a result, OM degradation and preservation is controlled by a dynamic and complex interplay of different environmental factors. Attempts to isolate the impact of a single variable on the rate of OM degradation have often led to contradictory results. It is therefore becoming increasingly clear that OM degradability is not an intrinsic property of the organic matter itself but an ecosystem property. Correspondingly, the likelihood that a given organic compound will be degraded by a microbial community or be preserved will depend on the chemical formula and structure of that compound, in addition to the metabolic capabilities of the resident microorganisms in response to environmental factors such as electron acceptor and intermediate metabolite concentrations, temperature, and physical associations with minerals or other organic compounds.
In 1973, Christian Anfinsen and coworkers noted that accelerated protein folding in intact cells and cell extracts suggested that a “disulfide interchange enzyme” might be present in vivo. This concept of catalyzed folding foreshadowed the discovery of ubiquitous protein chaperones. The chaperonin GroEL/GroES was identified serendipitously when GroE mutants of E. coli failed to grow bacteriophage λ and were also temperature sensitive. The GroEL/GroES proved to be a ubiquitous chaperone and heat shock protein in bacteria and eukaryotic organelles, with two back-to-back rings of seven subunits each, forming a cavity that enclosed nonnative proteins, capped by the separate GroES lid complex. Group II chaperonins were subsequently discovered in all of the Archaea and in the Eukaryote cytoplasm with a similar cage-like shape, only with a “built-in” lid instead of the GroES module of Group I chaperonins. These chaperones have been intensely studied for three decades and have provided deep insights into protein-folding mechanisms. Despite this, some aspects of chaperonin-induced protein folding remain controversial.
The shared architecture and sequence similarity of two classes of chaperonins implies that they share a common ancestor. A recently identified, deeply branching clade of archaeal-like chaperonins encoded in bacteria may shed light on the early history of chaperonins. This clade shares many molecular properties with Group II chaperones; however, their phylogeny suggests that they arose early in prokaryotic evolution and may represent a vestige of the common ancestor of Group I and Group II chaperonins.