The DEEP lab studies how microbes bridge the gap between non-living matter and living ecosystems in dark habitats and at chemical interfaces. We use a combination of cutting-edge tools to study how microbes make a living in a wide range of habitats, from estuarine mud to icy moons.

Understanding how microbes transform the “stuff of life” will help us solve important issues like climate change and pollution, and also help us find life on other planets.

Ghost Towns in the New Jersey Pine Barrens

The New Jersey Pine Barrens is the largest remaining example of the Atlantic coastal pine barrens ecosystem and a distinguishing feature of the coastal plain of southern New Jersey. The region is characterized by its nutrient-poor soil and acidic, iron-rich waterways. The delivery of reduced iron from underlying anoxic aquifers to the oxygenated surface leads to the precipitation of oxidized “bog iron” deposits, which supported a thriving ironworks industry in the 18th and early 19th centuries. While bog iron formation in the Pine Barrens is a well-documented phenomenon, the biogeochemical processes driving iron oxidation and iron cycling in this environment are poorly characterized.

The biogeochemical cycling of iron is a crucial component of many environmental processes, including carbon capture and storage, greenhouse gas emissions, and the fate of nutrients and toxic metals/metalloids. However, the bioenergetic pathways involved in iron cycling remain enigmatic, and the environmental conditions that shape iron-cycling microbial communities are currently poorly understood. Bog iron seeps in the New Jersey Pine Barrens offer a unique and understudied habitat in which to explore microbial communities sustained by iron redox cycling. 

The DEEP Lab studies the processes driving bog iron formation using a multi-pronged approach, including DNA and RNA sequencing, enrichment culturing, scanning electron microscopy, and geochemical monitoring. Using these tools, we aim to not only better understand the mechanisms of microbial iron cycling, but also to address fundamental questions concerning the role that redox conditions play at the crossroads between biological and geological systems- in other words, how electron transfer links life to rock.

Buried in Blue Mud

Salt marshes store carbon at higher rates than any other terrestrial system. Primary productivity generally exceeds the rate of decomposition in these systems, as oxygen is rapidly depleted within the first few millimeters of sediment. This, combined with the ability to trap and bury transient planktonic particles, allows salt marshes to bury organic matter at an exceptionally high rate, where it may be stored on geologic timescales- making these habitats vital to the regulation of the Earth’s temperature. The metabolic capabilities of the highly diverse microbial communities inhabiting salt marsh sediments remain poorly understood.

Our research at Stockton examines microbial activity in deeply buried salt marsh sediment, using a combined approach of stable isotope probing, metagenomics, and metatranscriptomics. These techniques make it possible to assess the genetic capability of the microbes that incorporate specific carbon substrates of interest, answering not only “who” is doing “what” but also “how.” This research describes the roles that the microbial community plays in the generation and decomposition of organic matter, and their impact on carbon storage at the ecosystem scale.

Ancient Life in the Dark Ocean

Greater than 90% of the ocean’s biomass consists of microorganisms, and about 70% of these microbes live in the dark open ocean. These microorganisms include archaea- ancient organisms that resemble bacteria but are genetically very distinct. Once thought to solely survive at very high temperatures, or in the guts of ruminant animals, we now know that archaea live and thrive in any environment where bacteria may be found.

The turnover of organic matter and the cycling of nutrients in marine environments is driven by a complex consortium of microbial activity known as the microbial loop. The impact of archaeal activity on the microbial loop remains poorly understood, partly because they resist laboratory culturing. Yet, planktonic archaea can comprise nearly half of the marine microbial community, particularly at depths below 1,000 meters– the majority of the ocean’s volume. At these depths, microbial life depends on food produced via chemical energy, and sinking organic compounds produced at the sunlit surface, in order to survive.

Currently our lab is using stable isotope probing experiments to explore archaeal and bacterial uptake of complex carbon sources in deep ocean samples taken on a research cruise in the Caribbean Sea. We are also planning a cruise to the Atacama Trench in 2024, to explore microbial diversity in sediment, methane cold seeps, and deep seawater.

Europa, Enceladus, and Ganymede

In collaboration with investigators at the NASA Jet Propulsion Laboratory and Goddard Space Flight Center, we are developing culturing platforms that support conditions resembling those hypothesized to exist at the origin of life, and which may support life on icy moons in our solar system. This project will utilize custom-made flow reactors mimicking early mineral catalytic systems in hydrothermal chimneys/sediments to compare biogenic and abiogenic outputs from these systems, and uses molecular/organic geochemical techniques to characterize the metabolic processes that occur in this environment in relation to abiotic reactions occurring in tandem. The project represents a novel system for culturing microbes with ancient metabolisms, in order to observe microbial populations and the products and kinetics of biochemical and geochemical pathways in an early life scenario.