Bacteria in the Ocean? That Eat Iron??

Lauren Rodgers, Rutgers University

Version 2The problem: Have you ever asked yourself, what is iron? It is an element? A rock? Some weird orange-ish substance? Is it the tool that you use to get the wrinkles out of clothes? And what does iron even do? Does it just sit there? Does anything eat it? Can we make things out of it? Iron is one of the most abundant elements on earth, yet not many people know much about the important role it plays in our lives.

Iron is more than just an element, or something found within a rock. It’s a nutrient, something necessary for the growth and metabolism of almost every living organism on Earth (Hedrich & Johnson, 2011). In the ocean, iron is found in two different forms, ferrous iron or Fe(II), which is soluble in water, and ferric iron or Fe(III), which is insoluble in water (Hedrich & Johnson, 2011). Because ferrous iron is soluble it is the form of iron that can be used by most organisms in the water (Hedrich & Johnson, 2011). This ferrous iron, however, is limited in the ocean despite its abundance in the Earth’s crust. In fact, Fe(II) is present only in incredibly small concentrations, making it a major limiting factor of growth for all of the plants and algae in the ocean. This is important because these plants and algae serve as the base of many food chains, so if there is a limitation on the growth of these organisms, it affects every other organism throughout the food chain. Though iron is an extremely important nutrient for many living organisms, it is still not well understood. One of the least understood aspects is how iron specifically cycles through different marine environments. Does it ever change form? Does anything add iron to the ocean? Does anything take iron out of the ocean? These questions bring us to Zetaproteobacteria.

Zetaproteobacteria is a recently discovered class of iron-oxidizing microbes. This just means that the bacteria eat iron in the form of Fe(II) and produce Fe(III) as a waste product (Emerson et al., 2007; Chiu et al., 2017). In fact, these waste products can take on the form of hollow tubes, also called tubular sheaths, or twisted stalks that you can see under the microscope!


Zetaproteobacteria were initially described in 2007 near hydrothermal vents, utilizing the large concentrations of Fe(II) that were present in the fluid that spewed from the vents (Emerson et al., 2007).

Iron Mat

Iron mat composed of Zetaproteobacteria on a lava rock near the submarine Loihi volcano. (A. Malahoff, Hawaii, Loihi Volcano, July 1988)

How do Zetaproteobacteria relate to the cycling of iron? 

Zetaproteobacteria, with their role in eating iron and transforming it from its soluble Fe(II) state into its insoluble Fe(III) form may have an important role in the cycling of iron through the environment, functioning as an important source of iron removal.

Since their discovery, Zetaproteobacteria have also been observed in many other habitats, including coastal estuarine habitats with lower levels of iron, similar to that of Charleston, SC. (Laufer et al., 2017; Chiu et al., 2017). Our study will try to identify if these Zetaproteobacteria are present in the muddy soils around Charleston, as well as measure the levels of Fe(II) and Fe(III) in the rivers where these bacteria may be found.


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Hopefully, through the study of the distribution of Zetaproteobacteria across the globe, including the chemical characteristics of the different environments that they inhabit, we may get a clearer picture of how iron cycles in aquatic environments and the role that these Zetaproteobacteria play.

I would like to thank my mentor, Dr. Heather Fullerton, for guiding me through this research. I would also like to thank the National Science Foundation for funding this research as well as the College of Charleston and Grice Marine Lab for their support.


Chiu, B. K., Kato, S., McAllister, S. M., Field, E. K., & Chan, C. S. (2017). Novel pelagic iron-oxidizing Zetaproteobacteria from the Chesapeake Bay oxic-anoxic transition zone. Frontiers in Microbiology, 8(JUL), 1–16.

Emerson, D., Rentz, J. A., Lilburn, T. G., Davis, R. E., Aldrich, H., Chan, C. S., & Moyer, C. L. (2007). A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS ONE, 2(8), e667.

Hedrich, S., Schlömann, M., & Johnson, D. B. (2011). The iron-oxidizing proteobacteria. Microbiology,157(6), 1551–1564.

Laufer, K., Nordhoff, M., Halama, M., Martinez, R. ., Obst, M., Nowak, M., … Kappler, A. (2017). Microaerophilic Fe(II)-oxidizing Zetaproteobacteriaisolated from low-Fe marine coastal sediments – physiology and characterization of their twisted stalks. Applied and Environmental Microbiology, 83(February), AEM.03118-16.

Mori, J. F., Scott, J. J., Hager, K. W., Moyer, C. L., Küsel, K., & Emerson, D. (2017). Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. Nov. ISME Journal, 11(11), 2624–2636.


The BMA of Today

Christine Hart, Clemson University

2017-06-22 10.29.36

In previous blog posts I described the sand-dwelling microalgae, also known as benthic microalgae (BMA), which are essential to estuary ecosystems. Not only do they produce the air we breathe and food we eat, they also inform us about the subtle changes that are occurring in our environment. Changes that otherwise may go unnoticed.

How do BMA show these environmental changes? By forming the foundation of estuarine energy, they provide a snapshot of how the estuary is functioning as a whole. If changes occur in BMA patterns, this may indicate changes in the overall ecosystem. BMA are also easily characterized and compared using modern molecular approaches. These qualities make BMA living indicators, or bioindicators, that are important in monitoring future ecosystem health.

BMA become visible in the upper layers of sediment at low tide. Later, they decrease in density—or biomass—as the tide rises. Our project studied the mechanism for the increase of biomass during low tide. Previous studies suggested that the mechanism for biomass increase is vertical migration of BMA from lower layers to upper layers of sediment. We also tested whether BMA growth due to high light exposure contributes to the biomass increase.

Our results indicated that both vertical migration and growth due to sunlight exposure were important to the increase in biomass. This is the first contribution to literature that recognizes a multifaceted approach to BMA biomass changes.

Additionally, we studied in how the biomass increase was connected to patterns in the type of BMA in Charleston Harbor. Previous studies suggested that increasing biomass was connected to changes in the abundance of BMA species; therefore, we expected to see the amount of certain BMA species change based on their exposure to migration and sunlight.

We were surprised by our findings. In this study, we found that BMA did not vary over short time periods (by tidal stage or by exposure to migration and sunlight). Instead, we found that BMA varied spatially and over a period of 6 years. In fact, only one of the dominant species of BMA remained the same from 2011 to 2017 (Figure 1).  The long-term change in community coincides with geological changes in the sampling site (Figure 2).


Figure 1. The relative abundance of each dominant BMA species from 2011 to 2017 is shown immediately after sediment exposure (T0) and 3 hours later (TF). Only one species—Halamphora coffeaeformis—remains dominant in 2017. This is evidence of a dramatic change in the dominant type of BMA in Grice Cove.

These are positive results for the use of BMA as bioindicators. If types of BMA are invariable over short periods of time, measurements of BMA will be more precise. Bioindicators must be capable of showing changes that are occurring on a larger environmental scale; therefore, it would be a good sign if the change in BMA community reflects the changing geological environment (Figure 2). Still, more studies on the temporal and spatial patterns of BMA communities should be conducted before BMA can be used as bioindicators.

Changes in Grice Cove

Figure 2. Aerial view of Grice Cove sampling site over time. The approximate location of the sampling site is shown by the white line. Sampling sandbar has changed over time, possibly contributing to community changes. Source: “Grice Cove” 32 degrees 44’58”N 79 degrees 53’45”W. Google Earth. January 2012 to March 2014. June 20, 2017.

This study contributed new information to the studies of BMA biomass during low tide, and showed that the BMA of today in Grice Cove are significantly different than in previous years.


Thank you to my mentor, Dr. Craig Plante, and my co-advisor, Kristina Hill-Spanik, for their support and guidance. This project is funded through the National Science Foundation and supported by College of Charleston’s Grice Marine Laboratory.


Literature Cited:

Holt, E. A. & Miller, S. W. (2010) Bioindicators: Using Organisms to Measure Environmental Impacts. Nature Education Knowledge 3(10):8.

Lobo, E. A., Heinrich, C. G., Schuch, M., Wetzel, C. E., & Ector, L. (n.d.). Diatoms as Bioindicators in Rivers. In River Algae (pp. 245-271). Springer International Publishing. doi:10.1007/978-3-319-31984-.

MacIntyre, H.L., R.J. Geider, and D.C. Miller. 1996. Microphytobenthos: the ecological role of
 the “Secret Garden” of unvegetated, shallow-water marine habitats. I. Distribution, abundance and primary production. Estuaries 19:186-201.

Rivera-Garcia, L.G., Hill-Spanik, K.M., Berthrong, S.T., and Plante, C. J. Tidal Stage Changes in Structure and Diversity of Intertidal Benthic Diatom Assemblages: A Case Study from Two Contrasting Charleston Harbor Flats. Estuaries and Coasts. In review.

Catch of the Day(s)

Melanie Herrera, University of Maryland College Park

South Carolina is known for its iconic southern cuisine, including a staple of fresh seafood which fuels the buckets of shrimp & grits and “catch of the day”. In order to support this huge industry (and fill the bellies of every South Carolinian), I am conducting an experiment to figure out where this seafood is holing up prior to its demise. Dr. Harold, his graduate student, Mary Ann McBrayer, and I are out on Grice Beach collecting fishes, crabs, shrimps, and much more in order to figure what exactly is there… And what they are using to survive.

Using a seine net, we encircle marine animals in dense and sparse patches of an invasive sea grass, Gracilaria, for collection. We hypothesize that Gracilaria is helping the local economy (a surprising contribution from an invasive species) by creating refuge for young animals. On the beach, we submerge separate samples of animals (from dense versus sparse areas of Gracilaria) into a euthanizing solution to bring them up to the lab for preservation and analysis (Figure 1).

Dense v Sparse.png

Figure 1: An example of animals caught in separate habitats at Grice Cove. The left exhibits animals caught in a dense area of Gracilaria and the right exhibits animals caught from a sparse area of Gracialaria. Credit: Melanie Herrera

In the lab, separate samples (dense versus sparse) undergo a few transfers into different fixatives (10% seawater formalin, 25% isopropyl, and 50% isopropyl consecutively) to keep the fish from decaying. After this preserving process, fish and other animals are separated and categorized by family, genus, and species. This categorization enables us to identify and analyze what types of animals and how many of each are using different habitat. Our analysis will give us insight on what type of habitat, either patches dominated by Gracilaria or areas with more open water, benefits fish. Specifically, we will be able to identify if Gracilaria is more advantageous to young fish or if their survivorship is independent from their habitat.

So far, we have collected lots of pipefish, narrow skinny fish that resemble a hair strand-size snake, Atlantic Silversides, a fish that looks exactly like it sounds, and more shrimp than anyone needs (Figure 2). Although some of these animals do not directly contribute to the seafood industry, its presence in the Charleston Harbor can tell us a lot of things. For example, we have seen some fishes that usually stay in warmer waters in the Southern U.S. Their expanding habitat can lead us to some more hypotheses on climate change and warm weather moving northward. In addition, we can find out if Gracilaria has a stake in rearing economically important fish in the future.

Pipefish, Silversides, Grass Shrimp.png

Figure 2: (From left to right) Pipefish, Atlantic Silversides, and Grass Shrimp caught for analysis.Credit: Melanie Herrera

Thank you so much to my mentor Dr. Tony Harold and his lab for his advice and guidance. Thank you to Mary Ann McBrayer for helping me facilitate this project. This research is funded through the National Science Foundation and College of Charleston’s Grice Marine Lab.


Searching in the Sand

Christine Hart, Clemson University

Interim report picture

In “Exploring the Secret Garden” I discussed our studies of the benthic microalgae (BMA) that inhabit the intertidal regions of beaches. The goal of our study is to identify the mechanisms involved in the visually noticeable increase of BMA during low tide. This mechanism will be linked to changes in the type of BMA dominating the sand flat. To accomplish these goals our study will incorporate field work, molecular techniques, and DNA analysis.

During field work we will collect and manipulate sediment to distinguish between an increase in BMA by either vertical migration or growth mechanisms. The sediment will be collected on a sand flat in Grice Cove (Figure 1). Sand will be sampled using corers, which pick up a layer of sand without disturbing the vertical organization. The collected sand will be split between measurements of biomass, or BMA density, and DNA analysis. Biomass is measured by finding the concentration of chlorophyll a in the sediment. BMA synthesize chlorophyll a; therefore, the concentration of chlorophyll a is proportional to the density of BMA.

Sampling Site.png

Figure 1. Aerial view of Grice Cove sampling site with the approximate location of the 50 m sand flat transect site. Sampling sand flat is open to the Charleston Harbor. Source: “Grice Cove” 3244’58”N 7953’45”W. Google Earth. March 20, 2017. June 20, 2017.

The methods for field work are represented in Figure 2. There are two vertical migration treatments: filter and mesh. Filter treatments prevent vertical migration between cored and surrounding sediment. Mesh treatments permit vertical migration. If migration is important to the biomass increase, biomass measurements in mesh will be greater than in filter treatments. Filter and mesh treatments will also be exposed to shade and light conditions to interpret the impact of growth on biomass. Sunlight provides the energy necessary for BMA growth. Without sunlight growth will be limited. If growth is the mechanism of biomass increase, the shaded samples will have a lower biomass than the light exposed samples.

Field Work Diagram.png

Figure 2. Field work methods visualization. Locations of replicates along the 50 m transect are chosen using a random number generator and marked with flags. Random coordinates and a quadrat of 50 cm by 50 cm are used to determine where sediment will be sampled and treatments will be placed. Three controls (T0, TM, and TF) are taken at time intervals 1.5 hours apart after sand exposure. During TM and TF time points, samples are taken from the 4 treatments shown above: filter, mesh, filter + shade, and mesh + shade. Filter treatments prevent vertical migration, while mesh treatments permit vertical migration. Shaded and non-shaded filter and mesh treatments will be important in determining the role of sun exposure in biomass increase.

To link the mechanism of biomass increase to the BMA composition, we will use molecular techniques and analyze the DNA found in the sediment. DNA will be extracted from the sediment and amplified using a polymerase chain reaction (PCR). The DNA will be sequenced using High Throughput Ion Torrent technology. The results from sequencing will identify the BMA present at each time point and within each treatment. This information will link the mechanism of biomass increase to the changes in BMA composition. Our understanding of BMA dynamics will establish a basis for the BMA ecology in the Charleston Harbor. In the future, BMA dynamics could be compared to our study to assess changes caused by human influences in Charleston estuaries.


Thank you to my mentor, Dr. Craig Plante, and my co-advisor, Kristina Hill-Spanik, for their support and guidance. This project is funded through the National Science Foundation and supported by College of Charleston’s Grice Marine Laboratory.


Literature Cited:

Lobo, E. A., Heinrich, C. G., Schuch, M., Wetzel, C. E., & Ector, L. (n.d.). Diatoms as Bioindicators in Rivers. In River Algae (pp. 245-271). Springer International Publishing. doi:10.1007/978-3-319-31984-.

MacIntyre, H.L., R.J. Geider, and D.C. Miller. 1996. Microphytobenthos: the ecological role of
 the “Secret Garden” of unvegetated, shallow-water marine habitats. I. Distribution, abundance and primary production. Estuaries 19: 186-201.

Invasive Species: Friend or Foe

Melanie Herrera,  University of Maryland – College Park

Invasive species…. Haunting, domineering, and downright evil. Or are they? Unlike the infamous Zebra Mussels, dominating the Great Lakes, or Fire Ants, constantly wreaking havoc, Gracilaria Vermiculophylla, are giving invasive species a good name. Don’t get me wrong, invasive species infuriate me just as much as the next guy; but Dr. Tony Harold and I are here to draw out the benefits of this invasive sea grass to baby fish.

Unlike the native, simpler sea grass previously occupying Charleston Harbor, Gracilaria is characterized by coarse branching structures that appeal to many species of fish as protective homes. We are particularly interested in fishes in the larval and juvenile stages (the young ones) that associate with these complex habitats. Having access to more protective sea grass, such as this invasive, in these vulnerable life stages can help determine how many of these little guys make it into adulthood. Similar macro-algae to Gracilaria, such as seaweeds, have been known to be preferable hideouts for larvae and juveniles, reducing the pressures of predation. Since Gracilaria is on the rise in our local estuary, the Charleston Harbor, it’s important to find out the role they play in keeping our fish alive and well.

Our project is designed to better understand the level of association of local fish such as Gobies, Atlantic Menhaden, Atlantic Silversides, and other estuary-occupying fishes, with Gracilaria. We will compare abundance and distribution of young fish in dense patches of Gracilaria to sparse patches. Maybe these young fishes prefer the familiarity that native sea grass and open water brings. Or maybe Gracilaria’s “new and improved” design is too advantageous to resist. After we figure this out, we can go on sustainably managing local fish critical to commercial and recreational use and condemning the rest of the invasive species.

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An example of a collection site characterized as a “dense” habitat of Graclaria vermiculophylla.  Photo Credit: Melanie Herrera

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An example of a collection site characterized as a “sparse” habitat of Gracilaria vermiculophylla. Photo Credit: Melanie Herrera


Thank you so much to my mentor Dr. Tony Harold and his lab for his advice and guidance. Thank you to Mary Ann McBrayer for helping me facilitate this project. This research is funded through the National Science Foundation and College of Charleston’s Grice Marine Lab.


Works Cited

Munari, N. Bocchi & M. Mistri (2015) Epifauna associated to the introduced Gracilaria vermiculophylla (Rhodophyta; Florideophyceae: Gracilariales) and comparison with the native Ulva rigida (Chlorophyta; Ulvophyceae: Ulvales) in an Adriatic lagoon, Italian Journal of Zoology, 82:3, 436-445, DOI: 10.1080/11250003.2015.1020349