Going to Antarctica!

So as expected, I didn’t continue blogging. I will not be taking my comprehensive exam this fall, instead I’ll take them in April. But for good reason, this warm-desert rat is going to Antarctica!

Lake Vanda in Wright Valley.

I will be in the McMurdo Dry Valleys from October 19 to January 10th. I will be collecting water samples from several of the lakes to study. I will be analyzing the waters for my own dissertation chapter along with collecting samples for Tina Takacs-Vesbach. I’m excited and appreciative to have this opportunity!

The McMurdo Dry Valleys (MCM) are part of the Long-Term Ecological Research (LTER) Network. Research at MCM is interdisciplinary and revolves around the aquatic and terrestrial ecosystems in the iceless valleys in Antarctica. MCM is along the coast of McMurdo Sound and has perennially ice-covered lakes (which I’ll be studying). I will have to take a helicopter to the Dry Valleys from the McMurdo station.

So during that time I will work my butt off, study for comps, enjoy the vistas, try not to be home sick (or lose a toe), and most of all learn from living there. I’ll probably inundate everyone with photos of the same places everyone else that visits takes. But they’ll be my photos.

Simple Science: Soil Carbon

Soils are the largest active, terrestrial pool of carbon, with 2500 Pg of carbon. A petagram (Pg) is 1 quadrillion grams or 1.1 billion tons, which is equivalent to the weight of 143 million elephants. In the Earth’s crust there’s 90,000,000 Pg of carbon.

Soil carbon is either organic (from organisms) or inorganic (rocks). Organic carbon is dynamic and can be influenced by human environmental changes, such as cutting down forests for farms or burning fossil fuels. Soil organic carbon (SOC) is controlled by soil forming factors called “CLORPT”, which is a mnemonic for CLimate, Organisms, Relief, Parent Material, and Time (Jenny 1941).

The carbon cycle begins with photosynthesis (plants take in CO2) and ends up in soil through humification, aggregation, and illuviation. Humification is when hummus is formed from dead plants. Hummus (Latin- soil) is the organic material in soil that is stable and causes the dark brown coloration of soil. Aggregation is when soil granules clump and aggregate, creating pores between them and leading to soil structure– influencing water movement, root growth, and other biological activities. Aggregation is conditioned by the coating of colloids (clays) and soil cementing substances (carbonates etc). Illuviation is the soaking of water into the layers of soil, which then deposits colloids along with organic carbon to lower levels of soil.

Article Summary: N-fixation in Karst Caves (Frasassi Caves, Italy)

Here’s another nitrogen fixation in caves article, but this time from Desai et al. (2013) in Frasassi caves, Italy. These caves are karst caves, which were formed through sulfuric acid speleogenesis (SAS). During SAS, H2S is transformed to sulfuric acid, which then reacts with the limestone to form gypsum that dissolves and creates caverns over time. H2S serves as an energy source to bacteria. Chemoautotrophs, organisms that can use reduced compounds to fix inorganic carbon, are found in caves.

Prior to this study, we didn’t know for sure nitrogen fixation, the transformation of N2 to NH3, occured in the Frasassi Caves. Desai et al. approached it by using acetylene reduction assays, isotope analysis of 15N2, and sequencing for nifH genes. Samples were from amphipods, biofilms, and sediments; which all had evidence for N-fixation. nif-H was found in the biofilm samples and some of which were Desulfovibrio related and Beggiatoa spp. They also found low 15N values on the caves walls, suggesting ammonia degassing. They did not follow it up to check for ammonia oxidase (AMO) or nitric oxide synthase (NOS) genes, along with nitrate concentrations. But it would be interesting to continue studying the rest of the nitrogen cycle in the caves.

---

Desai MS, Assig K, Dattagupta S. 2013. Nitrogen fixation in distinct microbial niches within a chemoautrotrophy-driven cave ecosystem. The ISME Journal 1-13. doi:10.1038/ismej.2013.126

Article Summary: Larger and metabolically diverse genomes = soil bacteria ubiquity

Microbial metabolism strategies are diverse; which can be broken down into how they obtain: carbon, reducing compounds, or energy. But we cannot grow the majority of bacteria, ~99% cannot be grown in labs. And on top of that, soils are highly heterogeneous environments yet certain microbes can be found across a broad range of conditions. But we should use genomic information (opposed to phylogeny) to understand the distribution of bacteria throughout soil, as proposed by Barberan et al. 2014. They sampled soil from Central Park, NYC and analyzed the distribution of bacteria and archaea across different areas. They found that bacteria with larger genomes had greater habitat breadth. Also, ubiquitous bacteria had greater amounts of genes associated with amino acid metabolism and xenobiotic degradation.  So larger, metabolically diverse genomes are common among abundant bacteria.

---

Barberan A, Ramirez KS, Leff JW, Bradord MA, Wall DH, and Fierer N. 2014. Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecology Letters 17: 794-802. doi: 10.1111/ele.12282

Simple Science: Some Cave Research

In the Northup lab, I study microbiology in cave environments. My project is on nutrient cycling within a few New Mexican caves. Caves offer a great laboratory to study bacteria without the influences of the elements, such as solar radiation and wind erosion. Inside caves, bacteria can live off of limited nutrients found on the cave walls or floor. We know bacteria help facilitate the break down of dead organisms, but in caves some bacteria can break down rock and promote cave enlargement.

Let me take a step back—way back. Bacteria have dominated Earth since life first evolved between 3.5-4 bya. They were alone for 3 billion years until multicellular life evolves 3 billion years later (2.1 bya). Just to add perspective,  Homo sapiens evolved 0.2 mya. Bacteria are the most diverse domain of life and can be found almost every possible place on Earth, such as deep-sea thermal vents and clouds. The study of this microbial diversity and how they interact with the environment is called microbial ecology.

Today the Northup lab is interested in metagenomics of caves, which is a tool to capture the entire microbial community’s genetic material from environmental samples. Jason Kimble and Ara Kooser both study nitrogen fixation genes among the communities, including the nifH and amoA genes. My research hasn’t moved to metagenomics yet, I’m still looking at the presence of enzymes responsible for decomposition. But with their shit-load of data, I can possibly mine to look for genes responsible for making the enzymes I’m interested in.

N-Cycling Genes in Caves: amoA & nifH Genes in Azorean Lava Caves

My mentor, Diana Northup, studies lava caves in Azores, Portugal. Lava caves are great places to study bacterial communities, which may produce antibiotics; and are model systems for Martian caves that may host microbial life.

Hathaway et al. (2014) examined Azorean lava caves for two genes that encode for enzymes responsible for nitrogen transformation. Nitrogen is a nutrient critical for living organisms. The nitrogen cycle allows for the conversion of N₂ into bioavailable forms, such as ammonia (NH₃). The two genes were nitrogen fixation (nifH) and ammonia monooxygenase (amoA); they’re responsible for N-fixation and nitrficiation (fig. 1).

Figure 1. Nitrogen Cycle & Enzymes

nifH encodes for nitrogenase, which helps convert N₂ to NH₃. Ammonia can be a source of energy for chemolithotrophic organisms; they obtain energy from redox reactions of inorganic compounds. amoA converts NH₃ to hydroylamine (NH₂OH)– the limiting step in nitrification. They collected samples from bacterial mats in 11 lava caves that were beneath different land use: pasture, forest, and urban. Prior to this study, the genes were not studied in caves along with analyzing soil and water chemistry.

Hathaway found no difference among caves under different land use for water and soil chemistries, but lava caves below forested land had greater diversity of ammonia-oxidizing bacteria and an abundance of nifH genes. They suggested there might be other abiotic influences over bacterial communities. However, the study didn’t explain the statistics and did not determine if the genes are being expressed.  But this was the first study of its kind.

---

Article:
Jennifer J. Marshall Hathaway , Robert L. Sinsabaugh , Maria De Lurdes N. E. Dapkevicius & Diana E. Northup (2014) Diversity of Ammonia Oxidation (amoA) and Nitrogen Fixation (nifH) Genes in Lava Caves of Terceira, Azores, Portugal, Geomicrobiology Journal, 31:3, 221-235, DOI: 10.1080/01490451.2012.752424

Intro & Goals

Hello! I’m Noelle, a 3rd year PhD student that enjoys writing and talking to the public about science. I’m still finding my voice and learning how to share my love for caves & soils without being cheesy.

My comprehensives are coming up this autumn and I will be using this space as a way to summarize my thoughts, journal articles, and books. I may pepper in postings that are non-science related (NSR).

Goals:

• At least 3 entries per week: Monday, Wednesday, and Friday posts
• One entry per book or article(s)- articles if they’re related so I may connect them together
• Entry shall be less than 250 words

Topics

• Cave microbiology
• Soil ecology/ microbiology/ biogeochemistry
• Plant-microbe interactions
• Locations: Arches; Duke Forest; Chihuahua Desert; Spider Cave, NM; Lechuguilla Cave, NM

* Me collecting moonmilk in a cave. Photo courtesy of Kenneth Ingham.