Judges’ Queries and Presenter’s Replies

  • May 20, 2013 | 10:23 p.m.

    Does a glass slide act as a suitable experimental substrate for the geochemical processes involved? It seems that the rocks in the pools are a much larger source of iron than a glass slide?

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 22, 2013 | 11:16 a.m.

    Dear Dr. Yavitt,

    Thank you for your inquiry and interest in my research. The glass slide (as SiO2) mimics the rhyolitic substratum (which is predominantly SiO2) that these iron oxide microbial mats form on initially when a new geothermal spring source appears. The ferrous iron that is utilized by iron-oxidizing microbes in this geothermal environment originates from the overlying thermal waters. The images on the poster represent mature iron oxide microbial mats that contain significant amounts of accreted iron oxide. You are correct in that iron oxidation and subsequent accretion of Fe oxides is faster on iron oxide surface than on a SiO2 glass slide surface. I hope this answers your question.

    Thanks,

    Jake

  • May 21, 2013 | 12:34 p.m.

    What role do stochastic events and seasonal changes play in the recruitment of taxa on your slides, or are these environments very stable and recruitment well understood?

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 22, 2013 | 12:22 p.m.

    Dear Dr. Bhattacharya,

    Thank you for interest and question. These acidic geothermal springs are relatively stable over time, which has been confirmed by > 10 years of thorough geochemical sampling (e.g., dissolved ions and gases) and analysis by our laboratory. However, it is important to note that we do not have data loggers in the field and stochastic events (e.g., high winds) could produce small temporal changes in aqueous gas concentrations or temperature for instance, which might result in the preferential recruitment of specific microbial taxa. In essence, stochastic events probably do effect the colonization of microbes to the slides but on the time scales we are interested in, I don’t believe that they play a major role or significantly effect the overall pattern of microbial recruitment to the slides.
    I do believe, however, that seasonal changes do effect the recruitment of taxa to the slides. We have preliminary evidence that high UV pressure in the summer months effects the community as well as the function of the community (e.g., iron accretion) most likely due to viral attack (see Fig. 3).
    We are only beginning to understand the formation and assembly of these iron oxide microbial ecosystems. The temporal community dynamics (Fig. 4) is initial data, but I have more time points in sequencing now using iTags (Illumina sequencing) so I believe these will ultimately shed light on the assembly of these ecosystems.
    It is also worth noting that we have metagenomes of these “mature” iron oxide ecosystems from 3 generations of sequencing technology (i.e., Sanger, 454, and Illumina). These metagenomes encompass approximately 7 years of data and have revealed that the mature communities are relatively stable over these time periods (i.e., from year to year or season to season taxon abundances do not significantly change). I hope this addresses your question.

    Thanks,

    Jake

  • May 21, 2013 | 03:53 p.m.

    The observed succession of (1) autotrophic colonizers and (2) subsequent heterotroph colonization does substantiate your conceptual model, in a qualitative sense. I wonder: how will you quantitatively test step (3) niche partitioning? This is a difficult mechanism to “prove” in more well-known systems. How does one approach this in a thermal spring?

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 22, 2013 | 01:48 p.m.

    Dear Dr. McGarvey,

    Thank you for your comments and question. Indeed, you are correct that niche partitioning is difficult to quantitatively determine, even in macroecology and probably even more so in microecology.
    As for your first comment, I completely agree, to an extent, about the qualitative observation of stages 1 and 2 of mat development in the conceptual model. The 16S rRNA gene sequences observed in Fig. 4, 28 days are almost all exclusively related to an autotrophic archaeon, which has been determined by our lab. Currently, I am collaborating with scientists at Lawrence Livermore National Laboratory to better understand autotroph/heterotroph colonization by utilizing natural carbon isotopic fractionation by individual community members in situ (nanoSIMS), which will provide better quantitative support for the conceptual model.
    We hypothesize that depth-wise gradients in dissolved oxygen exist in these microbial mats and that aerobes will be more abundant near the mat/water interface whereas anaerobes will be more abundant further away from the mat/water interface. We approached this question by utilizing Clark-type oxygen microelectrodes specifically designed for these high temperature ecosystems and also careful dissection of the iron oxide mats coupled to taxon specific PCR and reverse transcriptase PCR of a gene that encodes a heme copper oxidase for oxygen respiration (see Bernstein et al., 2013, Environmental Microbiology). We found that 1) oxygen gradients do exist in these microbial mats and oxygen penetrates about 0.5 mm into the mat (10 % of the total mat depth) and 2) aerobic microbes are generally more abundant and active (mRNA expression of an oxygen respiration gene) at the mat/water interface. In the future, I hope to carefully dissect these mats to determine depth-wise distribution of specific taxa in these microbial mats utilizing multiple molecular techniques (e.g., 16S rRNA gene PCR and fluorescence in situ hybridization on mat thin sections) as we have already determined the extent to which oxygen penetrates these iron oxide microbial mats. I hope this brief explanation helped explain how I will determine this conceptual model.

    Thanks,

    Jake

  • May 23, 2013 | 09:26 a.m.

    Interesting, Jake. Thanks for the thoughtful reply!

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 23, 2013 | 12:32 p.m.

    Thanks again for your interest and comments Dr. McGarvey!

  • May 21, 2013 | 08:49 p.m.

    Hi Jake,

    Thanks for your video and poster. You did a really nice job explaining what you do, and I was very impressed by that, and learned a lot. What I wasn’t quite as clear about is “why should I care?” I’m not asking that question in a confrontational manner, I just would like to hear (or read) from you how this would be relevant beyond the system that you study?

    Thanks,
    Volker

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 22, 2013 | 08:03 p.m.

    Dear Volker,
    Thank you for your comments and question. Your question is completely valid and I often encounter this question in other situations as well and it may be difficult to envisage other applications other than the geothermal system presented here or in similar geothermal habitats.
    These geothermal ecosystems contain a few dominant community members or “ecotypes” as compared to a microbial assemblage in a mesophilic stream channel that could contain upwards of hundreds to thousands of “ecotypes”. These differences in the number of taxa present is due to the phyiscochemical constraints that exist in geothermal environments. This allows us to begin to understand community assembly in more detail because we are only dealing with a few taxa as compared to hundreds or perhaps thousands of taxa. Thus, it makes studying these communities “easier” due to the low amount of taxa present. I guess basically what I am getting at is that these geothermal ecosystems provide excellent case studies and techniques and hypotheses built around the assembly of these communities can be utilized and is directly applicable to all environments (e.g., a mesophilic stream channel). Furthermore, the field of microbial ecology is in its infancy and determining how microbial communities assemble is fundamental to our understanding of ecosystem processes as it is for macroecology. So it stands to reason that studying the ecological succession of any microbial community (in this case in a geothermal environment) will begin to shed light on the factors controlling community assembly in any given environment. I could go on forever, but it basically boils down to laying down a foundation for future studies on the ecological succession of microbial communities. I hope I addressed your question (and I didn’t find it confrontational at all).
    Thanks,
    Jake

  • May 22, 2013 | 02:10 a.m.

    Biofilms are so interesting and those in hot springs are fascinating to look at in Yellowstone Park. Your poster objectives were very clear and made the great graphics easy to follow.Can you tell me if members of the new candidate phylum “Geoarchaeota” have been found to exhibit quorum sensing?

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 22, 2013 | 08:12 p.m.

    Dear Dr. Anderson,
    Thank you for your comments and question. I’m glad that you found my poster easy to follow and understood the objectives clearly.
    Your question is very interesting, and as much as I know, quorum sensing in the domain Archaea hasn’t been studied in much detail. As for the “Geoarchaeota”, I am not aware of any mechanisms that they may use to signal to themselves or other thermophiles. Keep in mind too that the “discovery” of the “Geoarchaeota” was only made very recently by our laboratory (see Kozubal et al., 2013, ISME J) and the genomic analysis performed didn’t include an exhaustive search on all potentially functional attributes. However, I would hypothesize that not only do the “Geoarchaeota” have mechanisms of signalling one another, but other thermophiles in these communities would have similar mechanisms of signalling reminiscent of bacterial quorum sensing. Would be very interesting to study in these communities and is potentially an important mechanism of microbial recruitment to the glass slides. Thanks you for the idea, it is not something I had thought of previously.
    Thanks,
    Jake

  • May 22, 2013 | 08:40 p.m.

    Thank you for your candid answer and it was a premature question. I will read the article you suggested. The MSU Center for Bioengineering has strong ties and excellent resources for those of us who teach introductory microbiology. I use BIOFILMS:THE HYPERTEXTBOOK for research background with undergrads.

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 23, 2013 | 12:31 p.m.

    Hi Dr. Anderson,
    I don’t think it was a premature question at all. Yes, the Center for Biofilm Engineering at MSU has great resources and wonderful people to collaborate with, some of whom are working on this project with me. They also have great user facilities at the CBE, which I often take advantage of. Thanks again for your interest and comments, they are much appreciated!
    Jake

  • Further posting is closed as the competition has ended.

Presentation Discussion

  • Icon for: Hannah Birge

    Hannah Birge

    Trainee
    May 21, 2013 | 08:52 a.m.

    Acidic geothermal outflow sounds like an extreme environment!

    There’s a lot of work floating around attempting to link microbial community structure/genetics to microbial functioning. From the looks of it, the microbial community you studied changes after 169 days of exposure.

    I did something vaguely similar for my MS work and found that microbial community structure isn’t consequential for carbon mineralization (arguably a broader process that yours). Do you think your work is evidence for a structure to function linkage? Could extremophiles be a simple enough system to show this, once and for all?

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 23, 2013 | 11:49 a.m.

    Hi Hannah,
    Thanks for checking out my presentation and poster!
    Your MS works sounds very interesting and it might be possible to draw parallels between the two, could you direct me to your MS work?
    I believe we are coming closer to the structure to function linkage in these ecosystems as well as understanding the assembly of these communities as they relate to their physicochemical environment. Yes, you are correct in your assessment of the simplicity of these ecosystems as compared to say a soil microbial assemblage that may contain upwards of thousands of taxa whereas these acidic geothermal environments contain a few dominant taxa. I believe this is one of the strengths of this part of my research project because I only have to track a few community members instead of hundreds, which can make the final analysis and interpretation cumbersome or difficult to link structure to function.
    Thanks!
    Jake

  • Icon for: Brian Drayton

    Brian Drayton

    Faculty
    May 23, 2013 | 07:04 a.m.

    Very interesting study. I have to say that the video narrative was a little challenging for a nonspecialist, such as myself, a humble plant ecologist.
    A question: What are some typical disturbances in this system? From your poster, some of the early-successional species (Metallosphaera app and Sulfolobus spp) remain part of the community late into the series. What happens under disturbance — do the early-successional app. increase in importance again (as in classical terrestrial series) or are the dynamics different in these communities?

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 23, 2013 | 01:06 p.m.

    Dear Dr. Drayton,
    Thank you for viewing my presentation and poster. I can see how the video may have been difficult to understand for a nonspecialist as the field of microbial ecology is advancing at such a fast pace (technology, analysis, etc.), it is often challenging for myself to stay on top of all the recent advancements.
    That is a great question. Typically, these ecosystems are relatively free from “extreme” perturbations that one might encounter in a temperate forest soil microbial assemblage, for instance, where the soil assemblage would experience prolonged dry or wet periods and extremes in temperature (i.e, winter versus summer months), which would significantly change the various ecological guilds present. These acidic geothermal springs are like chemostats. Our lab has monitored and sampled these springs for > 10 years and the chemical and physical makeup has been more or less the same. However, there are short term, episodic events (e.g., high winds producing short term temperature swings) that may affect community structure, although on the time scale that I am sampling on, it would not be possible to “know” if we were witnessing such an event. So yes, these systems are different than the classical terrestrial series. I do always try to use examples from classical ecology studies and I am trying to model this study following the series presented in Odum’s 1969 paper in Science on the successional dynamics of ecosystems.
    Thanks,
    Jake

  • Icon for: Graham Fogg

    Graham Fogg

    Faculty
    May 23, 2013 | 01:16 p.m.

    Very interesting project. As a hydrogeologist, I wonder how the hydrogeochemical processes of the groundwater systems that sustain these springs affect the microbial phenomena that you are studying. Furthermore, it might be interesting to explore whether during times of extreme drought (or groundwater overdraft by pumping) in which springs dry up, would the subsequent reversal of flow (from spring back into the groundwater system) potentially populate the deeper groundwater system with microbial communities.

  • Icon for: Jake Beam

    Jake Beam

    Presenter
    May 23, 2013 | 04:36 p.m.

    Dear Dr. Fogg,
    Thank you for your interest and question. The hydrology and underground water-rock interactions ultimately control the various types of springs present in any given region in Yellowstone. The geological setting in this region of the park (Norris Geyser Basin) more often than not produces acidic hot springs. The water-rock interactions and hydrology also control the structure and function of the microbial assemblages.
    These particular geothermal springs have never seen a prolonged period of drought or groundwater overdraft. They are like chemostats and have gone relatively unchanged, geochemically and hydrologically speaking, for >10 years that our laboratory has monitored them. With that said though, I think that it would be interesting to explore how these “extreme” perturbations would affect the surface communities as well as their recession to an underground habitat.
    Thanks,
    Jake

  • Further posting is closed as the competition has ended.

Icon for: Jake Beam

JAKE BEAM

Montana State University
Years in Grad School: 5

Biogeophysical interactions control the formation of iron oxide mat microbial communities in acidic geothermal springs

Ecological succession of microbial communities in their natural environment is a complex process that is not well understood. Microbial ecosystems are difficult to examine in part due to the small size of microbial cells and small scale of key biogeochemical processes, where microscopy and molecular techniques must be employed to track the activities microorganisms in their environment. However, modern molecular (e.g., community genomics) and microscopy techniques (e.g., fluorescence in situ hybridization) have allowed for microbial communities to be studied in greater detail. This study focused on the successional development of iron oxide mat microbial ecosystems that occur within high temperature (65-75° C), acidic (pH ~ 3), geothermal spring outflow channels in Yellowstone National Park. These iron oxide microbial communities contain both microorganisms from the domains Archaea and Bacteria that either use inorganic sources of energy (e.g., iron) and fix carbon dioxide (lithoautotrophs) or utilize organic sources of energy and do not fix carbon dioxide (organoheterotrophs). Glass microscope slides were placed in the outflow channel to provide a substrate for microbial growth and total iron deposited was measured as well as community development by using 16S rRNA genes. Results suggest inter-spring variation of iron deposition likely caused by differences in flow and seasonal variations due to increases UV radiation causing an increase in viral pressure in summer months. Lithoautotrophs were often found to be more dominant in early stages of community development, whereas organoheterotrophs were more abundant when the community reached a pseudo-steady state. Thus, iron oxide microbial community development is a dynamic process.