Microbial activity in the marine deep biosphere: progress and prospects

Abstract

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).

Metagenomics of extreme environments

“…Interestingly, the majority of the cDNA transcripts were of bacterial origin, with fungal and archaeal transcripts formally minor components. What this study, and others, does confirm is that deep subsurface microbial communities are indeed active [55,57,59,60] and that metabolic activity and growth is apparently limited by energy and not the availability of carbon and nitrogen compounds [59]. It remains unclear, however, which archaea or bacteria mediate key trophic functions.…”

“…environmental parameters), or how these organisms survive (and function) under apparent conditions of extreme oligotrophy [54]. Unsurprisingly, given the technical difficulties associated with sample acquisition, very few explorations of deep subterranean habitats have been undertaken [55,56].…”

Impact of Photooxidation and Biodegradation on the Fate of Oil Spilled During the Deepwater Horizon Incident: Advanced Stages of Weathering

“…42 The heterotrophic respiration of aerobic microbial communities was monitored as the impact of sand patties on the endogenous rate of oxygen utilization, while the corresponding anaerobic respiration activity was measured as a rate of sulfide formation ( Table 1).…”

Ship space to database: emerging infrastructures for studies of the deep subseafloor biosphere

“…The first is constraints on scientists' ability to pursue their field's immediate research objectives, which are to characterize deep subseafloor microbial communities in terms of the quantity and types of microbes that exist, how these microbes interact with the physical environment they inhabit, and how microbial communities vary between geographic sites on the seafloor (Orcutt et al, 2013). As a C-DEBI report stated, ''Evidence for microbial alteration [of the physical environment] exists, yet scientists lack robust molecular, biochemical, or physiological data so needed'' (Center for Dark Energy Biosphere Investigations, 2011, p. 11).…”

“…As no comparable set of standards exists for the microbiological properties, cruises neither conduct nor report basic microbiological descriptions of cores. Many of the C-DEBI-affiliated scientists interviewed mentioned this lack of agreement around standardized methods as a serious constraint on their scientific progress (Orcutt et al, 2013). Instead, individual scientists devote much effort to basic microbiological analyses in their home laboratories.…”