Planet of the Microorganisms

This Focus issue on biogeochemistry highlights the metabolic versatility in microbial communities and the significance of microbial contributions to the flow of elements in Earth’s biogeochemical cycles.

Microbial metabolic activity lies at the heart of the in the rhizosphere. On page 291, Poole et al. explore the myriad of interactions between the environment and changes that underlie this transition and the associated microorganisms that shape the dynamics of ecosystems. plant–bacteria interactions.

Earth is a closed system with a finite amount of matter Bacteria contribute to the fixation of CO2 to provide that cycles between the lithosphere (rocky surface), organic carbon that is necessary to support hetero- atmosphere, hydrosphere and biosphere, and microbial trophic life, and BMCs have a role in this fixation. metabolism drives biogeochemical cycling between these BMCs are self-assembling organelles (consisting of an spheres. This Focus issue explores microbial metabolism enzymatic core that is encapsulated by a selectively per- in the context of wider ecosystems. It comprises Reviews meable protein shell) that enhance metabolic flux and that discuss the microbial nitrogen cycling network, the protect bacteria from potentially toxic metabolites. The role that bacterial microcompartments (BMCs) have in first BMC that was isolated was found to enclose Rubisco atmospheric carbon fixation, the symbiotic exchange of — an enzyme that catalyses the first major step in car- nitrogen and carbon compounds between rhizobia and bon fixation and is the most abundant enzyme on Earth. legumes, and the function of hopanoid lipids, which Since then, numerous BMCs that are involved in vari- are important components of bacterial membranes and ous metabolic pathways have been identified, revealing affect interactions with other organisms. their functional diversity in the biosphere. On page 277, The six most common elements that are found in Kerfeld and colleagues review our understanding of the organic molecules — carbon, hydrogen, nitrogen, oxygen, role of BMCs in microbial metabolism, their structure, phosphorus and sulfur — exist in various chemical assembly and functional diversity. They discuss appli- forms, and the redox cycling of these elements by cations for engineered BMCs in biotechnology and pro- microorganisms substantially influences biogeochemi- pose that they could be used to program the metabolism cal cycling and the functions of ecosystems on a global of microbial communities in an approach known as scale. Nitrogen is the most abundant element in the synthetic ecology. atmosphere and is essential for all life on Earth. A com- Finally, on page 304, Newman and colleagues discuss plex network of nitrogen-transforming microorganisms hopanoids — a class of bacterial membrane lipids that facilitates the interconversion between organic and resemble eukaryotic sterols. They were first discovered inorganic forms of nitrogen while it cycles between the by petroleum geologists in ancient sedimentary rocks, atmosphere and terrestrial and marine ecosystems. On but since then they have been found in numerous envi- page 263, Kuypers and colleagues take us on a journey ronments. In this Review, the authors explore the biology through the microbial nitrogen cycle, highlighting new and biochemistry of hopanoids and discuss how they pathways and the vast diversity of nitrogen-transforming may promote beneficial interactions between bacteria, microorganisms and their enzymes. They discuss how in particular nitrogen-fixing species, and plants. these microorganisms form complex nitrogen cycling This Focus issue highlights the metabolic diversity on networks in different environments and posit on here- Earth and the significance of microbial contributions to tofore undiscovered nitrogen-transforming reactions biogeochemical cycles. An important future consider- that are thermodynamically feasible. ation is how the impact of changes in climate and land

The fixation of atmospheric N2 by rhizobia that live in use will influence the relationship between microbial microbial symbiosis with leguminous plants such as alfalfa, beans communities and the environment. Could increasing metabolism and soy provides a substantial proportion of nitrogen temperatures, greenhouse gas emissions or changing soil to the biosphere. During the transition from free-living humidity impact microbial ecosystems, for example, by drives soil microbiota to plant-associated endosymbionts, accelerating human-caused climate change, with broad biogeochemical rhizobia undergo drastic lifestyle and developmental implications for geological systems and human health? cycling between changes to become bacteroids — the N2-fixing form of For now, this remains an open question. Nevertheless, rhizobia. Historically, rhizobia research has focused on providing evidence of the microbial regulation of bio [Earth’s] specific interactions with legumes, without considering geochemical cycles is vital for predicting ecosystem spheres the complexity of the microbial communities that exist functions under current and future climate scenarios.