Where microorganisms meet rocks in the Earth's Critical Zone

Abstract

Abstract. The Critical Zone (CZ) is the Earth's outer shell where all the fundamental physical, chemical, and biological processes critical for sustaining life occur and interact. As microbes in the CZ drive many of these biogeochemical cycles, understanding their impact on life-sustaining processes starts with an understanding of their biodiversity. In this review, we summarize the factors controlling where terrestrial CZ microbes (prokaryotes and micro-eukaryotes) live and what is known about their diversity and function. Microbes are found throughout the CZ, down to 5 km below the surface, but their functional roles change with depth due to habitat complexity, e.g. variability in pore spaces, water, oxygen, and nutrients. Abundances of prokaryotes and micro-eukaryotes decrease from 10 10 or 10 7 cells g soil −1 or rock −1 , or ml water −1 by up to eight orders of magnitude with depth. Although symbiotic mycorrhizal fungi and freeliving decomposers have been studied extensively in soil habitats, where they occur up to 10 3 cells g soil −1 , little is known regarding their identity or impact on weathering in the deep subsurface. The relatively low abundance of microeukaryotes in the deep subsurface suggests that they are limited in space, nutrients, are unable to cope with oxygen limitations, or some combination thereof. Since deep regions of the CZ have limited access to recent photosynthesis-derived carbon, microbes there depend on deposited organic material or a chemolithoautotrophic metabolism that allows for a complete food chain, independent from the surface, although limited energy flux means cell growth may take tens to thousands of years. Microbes are found in all regions of the CZ and can mediate important biogeochemical processes, but more work is needed to understand how microbial populations influence the links between different regions of the CZ and weathering processes. With the recent development of "omics" technologies, microbial ecologists have new methods that can be used to link the composition and function of in situ microbial communities. In particular, these methods can be used to search for new metabolic pathways that are Correspondence to: K. Küsel (kirsten.kuesel@uni-jena.de) relevant to biogeochemical nutrient cycling and determine how the activity of microorganisms can affect transport of carbon, particulates, and reactive gases between and within CZ regions.

How Deep Can Surface Signals Be Traced in the Critical Zone? Merging Biodiversity with Biogeochemistry Research in a Central German Muschelkalk Landscape

“…Traditionally it has been assumed that subsurface microbial processes are dependent on reduced C originating from photosynthesis (represented by "Marilyn" in Figure 4A). Hence the surface would necessarily dictate subsurface characteristics (Culver et al, 1985;Baker et al, 2000;Foulquier et al, 2010;Akob and Küsel, 2011;Foulquier et al, 2011;Pan et al, 2014; Figure 4A). However, reduced carbon can also enter soils via microbial non-photoautotrophic CO 2 fixation (represented by "Elvis" in Figure 4B) and this carbon can be important to soil microenvironments despite its relatively small contribution to fixed C (0.05% of soil organic carbon; Miltner et al, 2004Miltner et al, , 2005.…”

Autotrophic fixation of geogenic CO<sub>2</sub> by microorganisms contributes to soil organic matter formation and alters isotope signatures in a wetland mofette

“…They are characterized by frequently changing redox conditions due to groundwater fluctuations, which might provide sufficient electron donors and acceptors for chemolithoautotrophic microorganisms (Akob and Küsel, 2011). Beulig et al (2014) characterized the microbial community of a reference soil at the same study site.…”

Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages

“…It is the crucial connection between groundwater and surface conditions and the space where fundamental physical, chemical, and biological processes act that are of high importance for sustaining soil and groundwater quality for agricultural and groundwater use (Akob and Küsel, 2011). Assessments of groundwater vulnerability and sustainable groundwater management require a sound knowledge of water movement and carbon transport through the CZ .…”