There’s life in the deepest part of the ocean. And some of that life is microscopic. It’s not easy to find the world’s tiniest organisms on land and it’s even harder when they live in one of the most out of reach places on Earth. Julie Huber, a marine microbiologist at Woods Hole Oceanographic Institution, specializes in finding these itty bitty lifeforms. She talked to us about operating underwater ROVs, doing research off the side of a ship, how understanding the weirdest forms of life on Earth teaches us new lessons about our planet, and what it’s like to battle seasickness when your career requires you to spend your life among the waves.
AbstractMethane is a product of and substrate for microbial metabolisms in the deep subsurface, but little is known about microbial metabolisms in deep methane hydrate-bearing sediments. We analyzed microbial community diversity and function in subsurface sediments beneath Hydrate Ridge, offshore Oregon (ODP Leg 204 Site 1244). We targeted four geochemically distinct sediment zones: near surface (2 mbsf), sulfate-methane transition zone (4 and 8 mbsf), iron-manganese reduction zone (18 and 20 mbsf) and deep subsurface (35 and 69 mbsf). Reactive iron increased with depth from 2 mbsf (0.4%) to 21 mbsf (1.1%), where dissolved iron and methane concentrations also peaked. The proportion of archaeal sequences decreased with depth, with deeper sediments dominated by Atribacteria and Chloroflexi. There was a resurgence of uncultivated archaeal groups (10% SAGMEG-1 and 16% MBGB) in the iron-manganese reduction zone. Illumina HiSeq metagenomic sequencing of genomic DNA subjected to single cell multiple displacement amplification resulted in 336 million total and 33.7 million coding reads. The taxonomic affiliations of metagenomic sequences corroborated the trend of increasing Atribacteria genes with depth, but a higher percentage of Chloroflexi sequences. ESOM assembly yielded two Atribacteria genomes of ≤5% contaminationfrom 2 vs. 69 mbsf with 55% and 37% completeness, respectively. Genes for amino acid transport and peptide fermentation, as well as Ni-Fe hydrogenases and the Wood-Ljungdahl carbon fixation pathway, were present. This grant entrained two early-career female researchers not previously funded by C-DEBI, and resulted in eight new collaborations and eight research presentations. All data are available at http://www.bco-dmo.org/
AbstractAlthough the subsurface biosphere is now recognized as an important reservoir of life on our planet, until recently the microbial community beneath open-ocean oligotrophic gyres (making up the majority of the seafloor) has not been studied in detail (D’Hondt et al., 2004, 2009). IODP Expedition 329 has taken a first step at characterizing the microbial community beneath the South Pacific Gyre. This region has low biological surface productivity and therefore very low organic carbon burial rates (10-8 and 10-10 moles C cm-1 yr-1), deep oxygen penetration (sediments are oxidized to the basement), and low prokaryotic cell counts (106 cells cm-3 to <103 cells cm-3) (D’Hondt et al., 2009; Fischer et al., 2009, IODP Exp. 329 Preliminary Report, 2011). In these sediments, the dominant fraction of organic carbon may be aggregated or adsorbed to minerals (Arnarson & Kiel 2007). Thus the ability to colonize minerals should be an important ecological adaptation, with those microbes that are able to grow on the minerals creating potential “hotspots” of microbial activity within these oligotrophic sediments. Our project aims to determine whether there is stimulated microbial activity associated in long-term incubations with H13CO3- and 15NO3-. Specific mineral and clay fractions in the oligotrophic South Pacific Gyre sediment system were targeted using combination of magnetic and density separation and SEM-EDS. The bacterial and archaeal community were examined by CARD-FISH, CARD-FISH-nanoSIMS, and 16S rRNA tag sequencing. Overall results from this C-DEBI grant have shown the viability of magnetic separation and identification of single cells in subsurface sediments as a method for investigating mineral association in microbial communities. We have identified putatively viable cells attached to 7 Fe/Mn-rich minerals, potentially representing an unexplored strategy for low-carbon environments. We also have discovered a higher level of diversity in the paramagnetic (Fe/Mn-rich) mineral-associated bacteria and higher number of Marine Group I archaeal OTUs compared to the diamagnetic fraction in the oligotrophic subsurface sediment from the South Pacific Gyre.
I have been invited to sail as a microbiologist and observatory scientist on the 2012 RV Merian cruise with ROV Jason-II to visit the North Pond subsurface observatories installed during IODP Expedition 336 (see letters of support from Dr. Katrina Edwards and Dr. Wolfgang Bach). The purpose of this expedition is to service CORK observatory systems in the ‘North Pond’ location of the Mid-Atlantic Ridge for coupled hydrogeological, geochemical and microbiological analysis. I sailed as a microbiologist and observatory scientist on IODP Expedition 336 and was responsible for assembling the subsurface and seafloor microbial colonization experiments that were a central feature of the observatories. During the 2012 RV Merian cruise, I will be integrally involved in the assembly and installation of seafloor microbial observatory components for these CORKs and also with the collection and processing of sediments and rocks sampled during the cruise. I was chosen for this position based on my previous history of designing the observatory components and participation in 7 research expeditions to deploy, recover, service and analyses these instruments.
The ground beneath your feet is home to a massive, mysterious world of microbes — some of which have been in the earth’s crust for hundreds of thousands of years. What’s it like down there? Take a trip to the volcanoes and hot springs of Costa Rica as microbiologist Karen Lloyd shines a light on these subterranean organisms and shows how they could have a profound impact on life up here.
The Institute for Chemistry and Biology of the Marine Environment (ICBM) at the School of Mathematics and Natural Sciences invites applications for the position of a Professorship (W3) in Benthic Microbiology commencing as soon as possible. The appointed professor is expected to cover the complete field of teaching microbiology in the Bachelor’s and Master’s programs of the School of Mathematics and Natural Sciences. We seek a microbiologist with distinct expertise in physiology and diversity of prokaryotes, preferentially with anaerobic organisms. The appointed professor should investigate fundamental questions in marine microbiology, combining classical-microbiological and modern OMICS-driven approaches, and bearing the potential for modern and innovative microbiome research. It is expected that the appointed professor will contribute to future interdisciplinary, process-oriented research projects of the ICBM (see collaborative research at www.icbm.de) and participate in joint research cruises. Prerequisites for employment include a dissertation of superior quality, a habilitation or an equivalent scientific achievement, and pedagogical aptitude proven by practical experience. Excellence in research is expected as well as international experience, generally attained by a research stay abroad. Successful acquisition of third-party funds is required. Applications should be submitted by no later than January 15, 2019.
How deep into the Earth can we go and still find life? Marine microbiologist Karen Lloyd introduces us to deep-subsurface microbes: tiny organisms that live buried meters deep in ocean mud and have been on Earth since way before animals. Learn more about these mysterious microbes, which refuse to grow in the lab and seem to have a fundamentally different relationship with time and energy than we do.
What’s it like to travel right down to the bottom of the ocean? Deep sea microbiologist Julie Huber should know. Her group, at the Marine Biological Laboratory in Massachusetts, USA, is trying to uncover more about the microbes living in the deepest darkest depths of the ocean. But that’s not all – there are even microbes living thousands of metres beneath the ocean floor itself, within the rocks and sediment. This is an environment that couldn’t be more different to our world on land – no light, huge pressures, underwater volcanoes and hardly any nutrients. So what kind of microbes do we see living there, and how do they manage to make a living?
The bottom of the ocean is one of the most mysterious places on the planet, but microbiologist Karen Lloyd of the University of Tennessee, Knoxville, wanted to go deeper than that. In 2010, she was a postdoc at Aarhus University in Denmark, and Lloyd wanted to see what microbes were living more than 400 feet beneath the sea floor.
AbstractPat Harcourt and Mark Friedman presented a session on the C-DEBI project and subseafloor microbes for teachers in grades 7 – 12 at the National Marine Educators Association annual conference held in Anchorage, Alaska in June 2012. The C-DEBI research and technology served as an engaging and exciting focal area for teachers who want to incorporate marine science into their curricula. Pat worked with C-DEBI education specialist Cindy Joseph to develop lessons and activities that integrated marine biology, geology, technology, and the process of science. This session highlighted three classroom lessons. In an activity on the discovery of microbes below the sea floor, participants were required to construct a timeline of events based on reading excerpts from “Is Life Thriving Deep Beneath the Seafloor?” (Carl Wirsen, Oceanus, 2004) and track the evidence for microbial life in extreme marine environments. A size and scale activity required participants to place images of familiar objects along a greatly magnified size scale, then add images of newly discovered marine microbes to the scale to provide a sense of their sizes. A demonstration activity was presented to illustrate the work of microbiologist Richard Lenski on bacterial evolution and use of resources, and participants discussed how microbes could evolve to exploit new and extreme environments. Participants shared teaching ideas and strategies for using these lessons as well as resources from the C-DEBI web site.
I have been invited to sail as a Microbiologist on IODP Expedition 336 (X336). The purpose of this expedition is to install CORK observatory systems in the ‘North Pond’ location of the Mid-Atlantic Ridge for coupled hydrogeological, geochemical and microbiological analysis. This expedition is one of the three current focus sites of C-DEBI for deep biosphere research. During this cruise, I will be integrally involved in the assembly and installation of the microbial observatory components for these CORKs – a critical component of these experiments. I was chosen for this position based on my previous history of designing the observatory components and participation in 6 research expeditions to deploy, recover, service and analyses these instruments. I have hands-on experience with microbiology experiments in CORKs based on my participation in the recent IODP Expedition 327 to the Juan de Fuca Ridge flank.
A cruise is scheduled for December 5-23, 2013 to visit the Dorado Outcrop, a new Major Program focus site of C-DEBI, with Geoff Wheat from the University of Alaska, Fairbanks as Chief Scientist. I have been given the opportunity to participate aboard this expedition as a shipboard microbiologist. In collaboration with the microbiology team (lead by Dr. B. Orcutt), I will part take in routine microbial and geochemical analyses, which will contribute to the following primary expedition objectives: To determine the ecological and biogeochemical nature of microbial communities in cool crustal fluids from the Dorado Outcrop, and determine the degree to which the communities and chemistry vary by comparison to ridge axis systems; and to determine the influence of cool crustal fluid circulation on sediment and hard-rock microbial ecology and biogeochemistry. These objectives will be further fulfilled post-expedition by various shore-based scientists, using samples that I will help to collect and preserve onboard. As a shipboard scientist, I am also entitled to, and responsible for, contributing to post-expedition research. My specific research plan is to employ single cell genomic techniques to identify the biogeochemical potential of uncultivable heterotrophic organisms present within aerobic marine sediment of the Dorado Outcrop. Revealing the potential functions and life requirements of uncultured organisms will greatly benefit our understanding of elemental cycling in the marine subsurface biosphere.