Geomicrobiology and microbial geochemistry (GMG) investigates the interaction between Earth, environmental systems, and microbial life. Microbes shape their geochemical surroundings through their metabolic and growth needs and thereby exert significant geochemical and mineralogical control on their local environments. In turn, local geochemical conditions dictate what metabolic processes are possible. These mutual influences mean that microbial evolution has occurred in concert with changing geosphere conditions and that microbes have driven major shifts in ocean, continent and atmospheric chemistry. If one wishes to understand element cycling in any system containing water, one must realize that microbes are critical to the story.

The basic premise of geobiochemistry is that life emerged on Earth where there were opportunities for catalysis to expedite the release of chemical energy in water–rock–organic systems. In this framework, life is a planetary response to the dilemma that cooling decreases the rates of abiotic processes to the point that chemical energy becomes trapped. Catalysis via metabolism releases the trapped energy, and life benefits by capturing some of the energy released. Out of necessity, biochemical processes have geochemical origins, and geobiochemistry asserts that these origins can be revealed by mapping reaction mechanisms onto deep time. We propose five principles that should help guide research in the emerging field of geobiochemistry.

The past two decades have witnessed an explosion of DNA sequencing technologies that provide unprecedented insights into genome sequences­—the blueprints of life on Earth. Although initially driven by biomedical research, this revolution offers exciting opportunities in Earth sciences. Analyzing genomes and other biomolecules (“omic” methods) within environmental samples provides new vistas of microbial geochemistry. However, the massive amount of data produced can be hard to decipher, and the resources and infrastructure to train and support geoscientists in omics approaches are lacking. This article summarizes some of the opportunities and challenges in the applications of omic approaches to geochemical problems.

The biogeochemical cycling of major and minor elements in the ocean has direct bearing on the health of the planet and its inhabitants. Reactive intermediates, of both chemical and biological origin, are emerging as important players in these biogeochemical cycles. Due to their rapid production and consumption, these reactive intermediates are short-lived and typically in low concentration. Involvement of these “invisible” species in biogeochemistry may therefore be hidden, or cryptic, with no obvious lingering chemical signature. Here, we highlight reactive intermediates of the oxygen, manganese, and sulfur cycles and how these intermediates are involved in cryptic cross-linkages between marine biogeochemical cycles of global importance.

Microbial processes dominate geochemical cycles at and near the Earth’s surface today. Their role was even greater in the past, with microbes being the dominant life form for the first 90% of Earth’s history. Most of their metabolic pathways originated billions of years ago as both causes and effects of environmental changes of the highest order, such as the first accumulation of oxygen in the oceans and atmosphere. Microbial processes leave behind diverse geochemical fingerprints that can remain intact for billions of years. These rock-bound signatures are now steering our understanding of how life coevolved with the environments on early Earth and are guiding our search for life elsewhere in the universe.

The interdisciplinary field of geomicrobiology and microbial geochemistry (GMG) has provided surprising insights into microbial function and preservation in diverse environments. The emerging frontiers in GMG are driven by recent discoveries in material sciences, economic geology, human health, and paleontology. The length-scales and mechanisms by which organisms can transfer electrons are being redefined, which have implications ranging from the formation of ore deposits to microbial function in the human body. Pathways of biomineralization are a critical control for many fossilization processes. Microbiologically produced materials also exhibit great potential for technological and medical applications.