Visibility is such a great obsession with us, humans! But the world knows little about that. Think about it: how long has the eye--as a biological structure-- been around? And what does it really help with, for all its beautiful and mysterious construction?
For organisms like us, who move in the curiously-ordered universe of meter-scale, specific shapes mean much, often the difference between life and death (think of our acuteness in detecting minor shape changes in someone's face); but for most of life, who operate at time- and space-scales very different to ours? Do they care about the visibility of things?
The Laboratory of Microbial Ecology is focused on a relatively small segment of the very large and disparate group of invisible life forms we call "microbes". We work with eukaryotic microbes, and we are most focused on those eukaryotic microbes living in terrestrial ecosystems. That would mean the unwieldy and multifarious collection of life forms we call fungi. In those terrestrial ecosystems we ask simple questions: where are microbes? How many of them? These are the basic questions of ecology: establishing patterns of abundance and distribution of organisms.
For traditional ecologists, there was no question about the identity of the organism at stake: in a given place, deer are deer and wolves are wolves. Not so for microbes, where a given organism can take multiple shapes (for example filamentous fungi turning into yeasts and viceversa; spores of various kinds can lead to multiple variations on the hyphal theme, and so on), and indistinguishable cellular structures can belie quite different phylogenetic and ecological characters.
Our current attempt to deal with this problem is to develop methods and instrumentation to allow real mapping, at geographical scales, of microbial organisms, with DNA-sequence specificity.
Learn more in our Lab Website.
2004 • Chapela, IH and Garbelotto, M. 2004. Phylogeography and evolution in matsutake and close allies inferred by analyses of ITS sequences and AFLPs. Mycologia, 96(4), 2004, pp. 730-741.
A biogeographical and evolutionary study of what is considered the “flagship” of non-timber forest products in the Pacific Northwest. With this manuscript we establish several new concepts in the field of coevolutionary biology of fungi. First, we resolve long-standing nomenclatural questions in this recalcitrant “species complex”. Second, we show that biogeographical patterning and the evolutionary history of the host play a much more important role in these ectomycorhizal fungi than had previously been assumed from extrapolations of other fungi. Third, using a novel analytical approach to genetic and biogeographical inference, we resolve for the first time the most probable migratory route behind the well-known vicariance pattern observed between the Eastern United States and S-E Asia. Fourth, we provide solid biological data and concepts to inform what has been traditionally a fickle and speculative market which is, nonetheless, very important across the Northern Hemisphere.
• Henn, MH & Chapela, IH. 2004. Isotopic Fractionation during Ammonium Assimilation by Basidiomycete Fungi and Its Implications for Natural Nitrogen Isotope Patterns. New Phytologist 162:771-781.
• Henn, M.R. & Chapela, I.H. 2004. Ecophysiology of 13C and 15N Isotopic Fractionation in Forest Fungi and the Roots of the Saprotrophic-Mycorrhizal Divide. Oecologia 128(4):480-487. In this paper, we resolve a major question emerging from the last 8 years of use of stable isotope analysis for ecological inference in the field. First, on the basis of a study with unprecedented precision in sampling and analysis, we show that a consistent difference between ectomycorrhizal and saprotrophic fungi in terms of stable isotope ratios is due more to substrate than to intrinsic processing. Secondly, we use a meta-analysis approach, using published data from across the Northern Hemisphere, to show that physiological differentiation might exist in all forest basidiomycetes, so that specific physio-ecological groups can be observed. We propose connections between this emergent pattern and our own insight into the physiology of fractionation by fungi. This highly reductionistic work is nonetheless very important for a wide variety of other fields, since the determination of the natural distribution of stable isotopes in the environment has become a tool of choice for studies ranging from nutrient processing to global change. My participation in paper included design of experiments, identification of physiological interpretations and writing.
2003 • Ortiz-García, S., Gernandt, DS, Stone, JK, Johnston, PR, Chapela, IH, Salas-Lizano, R & Alvarez-Buylla, ER. 2003. Phylogenetics of Lophodermium from pine. Mycologia 95(5):846-859.
2002 • Henn MR, Gleixner G, Chapela IH. 2002. Growth-dependent stable carbon isotope fractionation by basidiomycete fungi: delta(13)C pattern and physiological process. Appl Environ Microbiol. Oct;68(10):4956-64.
• Chapela, I.H. 2002. Midcourse evaluation of the Novartis Berkeley agreement. California Monthly (February issue). Commissioned piece in a long-term editorial interest by the University’s alumni magazine to provide insight into the unique relationship between the College of Natural Resources and a transnational company.
2001 • Quist D, & Chapela IH. 2001. Reply. Nature. Nov 29;414(6863):541-3.
• Quist, D. & Chapela, IH. 2001. Transgenic DNA introgressed into traditional maize landraces in Oaxaca, Mexico. Nature 414:541-543.
A paper which, despite simple statements, has acquired much notoriety even before its publication. In this article, we provide molecular evidence of the presence of transgenic DNA in genomes and geographical regions where it was not supposed to occur. This discovery, which challenges many accepted assumptions about the ecology of transgenic organisms, is the first publication where my interests in both the science as well as the policy of microbial ecology become crystalized. We applied simple methods typical of microbial ecology to a critical question of policy relevance. The consequence has been an exceptional public attention and media coverage for the story. Among others, this story has so far appeared as front-page item in LeMonde (France) and El País (Spain), among many others. It has been covered in newscasts over six months in many countries, made the cover story for Newsweek (Latin America edition, Jan 21), and was listed by the New York Times Sunday Magazine as one of the 80 stories that “made a difference” in 2001. My role in this paper was to conceive of the project, implement the necessary field capacity (over the last 15 years), and write. Laboratory work was mostly performed by graduate student David Quist.
• Chapela, I.H., Osher, L.J., Horton, T.R. and Henn, M.R. 2000. Ectomycorrhizal fungi introduced with exotic plantations induce soil carbon depletion. Soil Biology and Biochemistry 33:1733-1740. This paper describes ecophysiological changes associated with the introduction of exotic plantations into grasslands due to the “portmanteau” fungal flora accompanying the introduced trees. The methods used (a combination of traditional soil analysis, stable- and radioactive isotope analysis and DNA-based microbial community characterization), and indeed the concepts behind this manuscript are novel and of very large significance, since plantations of this type are now being planted over extremely large areas globally. Because of its novelty, and because of its potential impact on the economy of plantations, this paper has received a very deep level of scrutiny and challenge. Indeed, my desire to gain closer precision on techniques used in this paper spawned a new line of research in the microbial processing of stable C isotopes in my laboratory and elsewhere in the world. After much debate and eight rounds of review, the manuscript was accepted.
2000 • Pinto-Scherer, T.J. Chapela, I.H. Ecology and evolution in Hypoxylon sensu lato: a perspective from DNA analysis. Submitted to Mycologia. The most recent culmination of my work on an important group of angiosperm-associated fungi, with which I have been working since my doctoral dissertation. In this paper, we take a biogeographical and evolutionary approach to questions of coevolution, host-specificity and adaptation. Principles emerging from this study include the lack of lineage-tracking in this important group, and its directed evolution and adaptive radiation towards drying environments. We also provide a solid grounding for a revaluation of nomenclature within this important group, which has remained elusive for analyses based only on morphological and histochemical methods.
• Henn, M.R. and Chapela, I.H. 2000. Differential C Isotope Discrimination by Fungi during Decomposition of C3- and C4-Derived Sucrose. Applied and Environmental Microbiology 66(10): 4180-4186. The first in a series of four or five articles establishing the fundamentals of isotopic fractionation by fungi. This research was first conceived to resolve open questions raised by our “exotic plantations” work (see below), but has been praised in its own right, and has opened a whole line of future research. One reviewer refered to this work as “one of the most interesting articles I have reviewed in a long time”. My participation in this manuscript included the design of experiments, identification of C3- C4- differential fractionation, production of the explanatory model proposed here and writing.
• Chapela, I.H. 2000. Global bodies won't save the environment: it needs grass-roots efforts. Nature 403 (6766): 129 (13-Jan-2000). A response to a proposed initiative for global conservation. This response draws from my work and experience with Latin American conservation reality on the ground.
• Scholz, A. and Chapela, I.H. 1999. Biodiversity - cornucopia of knowledge. In: Posey, D.A. (ed.): Cultural and Spiritual Values of Biodiversity. Intermediate Technology, London: 525-526. As part of the Global Biodiversity Assessment, this is the first contribution from my work together with ERG’s doctoral candidate Astrid Scholz. This short note marks the published beginning of a project I have been developing since 1990 as a comparative approach to valuation of biological resources. The underlying basis of this project, of which Ms Scholz’s work is only a part, is that we can usefully utilize a comparative approach (as in comparative biology) to study the market for “biodiversity products”, and that a useful comparative model for this market is the market for art items. This is an original concept derived from my experience in the field of drug discovery, together with my understanding of microbial ecology and the needs of conservation practice.
- 6 - Environmental Biology
- 98 - DIRECTED GROUP STDY
- 99 - SUPERV INDEP STUDY
- 134 - FOR ECOSYS DISRUPT
- 194 - SEM IN C RES ST
- H196 - HONORS RESEARCH
- 197 - FIELD STUDY
- 198 - DIRECTED GROUP STDY
- 199 - SUPERV INDEP STUDY
- 299 - INDIVIDUAL RESEARCH
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