The Fuchsman lab focuses on linking microbes and biogeochemical cycles in low oxygen waters.
At the moment our lab is particularly focused on the role of organic particles in Oxygen Deficient Zones. Oxygen Deficient Zones are hot spots of N loss from the ocean by N2 production. The microbes mediating this N2 production must either consume organic matter or use by products of organic matter degradation as energy. Thus fluxes of organic C and N2 production are closely linked. Organic particles and the water column are also quite different niches for microbes. Organic particles are rich in organics and reduced N but are transient. The open ocean water column is organic and reduced N poor but stable. Microbes must adapt to respire and reproduce quickly on particles and to acquire scarce resources and reproduce slowly in the water column. Not surprisingly the communities in these two niches are often different. To examine these systems, we combine field work, lab work and bioinformatics.
For more information contact Clara Fuchsman: https://www.umces.edu/clara-fuchsman
Eastern Tropical North Pacific Oxygen Deficient Zone Cruises
There are three naturally occuring regions in the ocean with no oxygen (and no measurable sulfide), the Eastern Tropical North Pacific (ETNP), the Eastern Tropical South Pacific (ETSP) and the Arabian Sea. The Fuchsman lab was involved in three completed cruises in Mexican waters to study the ETNP Oxygen Deficient Zone
- January 2017 (R/V Sikuliaq) cruise blog: https://hohohomz.wordpress.com
- April 2018 (R/V Revelle) cruise blog: https://springatsea2018.wordpress.com
- September 2019 (R/V Kilo Moana)
These cruises have a goal of understanding the microbial community, and biogeochemical rates associated with organic particles in anoxic conditions. In collaboration with Rick Keil (UW), Allan Devol (UW) and Gabrielle Rocap (UW), we examining meta-genomics, meta-proteomics, in situ rates, sediment trap fluxes, and N2 gas concentrations and isotopes. The offshore Oxygen Deficient Zone is organic matter limited. One question we are interested in answering is how alternative sources of organic matter, such as primary productivity by cyanobacteria in the Oxygen Deficient Zone or migration of zooplankton, affects organic C fluxes and the activity of the microbial community.
Oxygen Deficient Zone Microbial Community
Our lab studies the microbial community in oxygen deficient water using meta-genomics, with particular interest in the N cycle and sinking particles.
What biogeochemical processes occur on sinking particles and which bacteria mediate these processes? and which processes and microbes occur strictly in the water column? and how does this affect the biogeochemistry of the Oxygen Deficient Zone? In the following paper we examine depth distributions of phylotypes of functional genes involved in N cycling both on particles and in the water column: https://www.frontiersin.org/articles/10.3389/fmicb.2017.02384/full
Currently, we are examining potential sources of organic matter fueling activity in the Oxygen Deficient Zone, including fluxes from the euphotic zone, cyanobacterial primary production in the Oxygen Deficient Zone or micronekton migration into the Oxygen Deficient Zone. This work has implications for predicting microbial activity in the Oxygen Deficient Zone in a changing ocean. Our paper on the addition of organic matter from cyanobacteria photosynthesizing in the Oxygen Deficient Zone can be seen here: https://www.nature.com/articles/s41396-019-0452-6.
At the moment, we, in conjuction with Michael C.G. Carlson and Debbie Lindell (Technion, Israel), are examining how viruses may mediate the organic matter transfer from cyanobacteria to denitrifying microbes using the polony method to count cyanophage in the water column and the iPolony method to count the number of cyanobacteria infected with viruses.
Evolution and Horizontal Gene Transfer in Low Oxygen Environments
Horizontal gene transfer can increase the fitness of a microbe to its environment. We are interested in the amounts and types of genes acquired by horizontal gene transfer under low oxygen conditions. In our paper, https://peerj.com/articles/3865/, we show increased horizontal transfer between anaerobic archaea and anaerobic bacteria.
Viruses are one vector for horizontal gene transfer because viruses sometime acquire genes from their host. We have been working to examine host genes specific to cyanobacterial viruses in the ETNP Oxygen Deficient Zone. We find that the genes aquired by cyanobacterial viruses from their hosts change with depth in the euphotic zone. https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.1.... These viruses are also a way for cyanobacteria to die and become organic particles. https://www.nature.com/articles/s41396-019-0452-6.
To understand what viral host genes are specific to Oxygen Minimum Zones, we also have to examine depth profiles in the oxic ocean. Right now we are examining depth profiles of cyanophage and pelagiphage (SAR11 viruses) and their viral host genes across the world's oceans.
Stable Isotopes of N2
In situ stable isotopes are one way to track microbial activity in the environment. In our lab, we track the production of N2 gas under anoxic conditions as seen here:
https://www.sciencedirect.com/science/article/pii/S0967064517301194
In this paper we determine the apparent isotope effect for N2 production in the Eastern Tropical North Pacific and Arabian Sea Oxygen Deficient Zones. The isotope effect is particularly large, which may be explained by the fact that denitrifying bacteria live on organic particles. The isotope effect can then be used in ocean models to determine the amount of N2 production occuring in the entire ocean. We now have much more unpublished N2 gas concentration and isotope data from transects across the ETNP.
