The Trophic-Dynamic Aspect of Ecology Raymond L. Lindeman
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Consistent Responses of Soil Microbial Communities to Elevated Nutrient Inputs in Grasslands Across the Globe
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe Jonathan W. Leffa,b, Stuart E. Jonesc, Suzanne M. Proberd, Albert Barberána, Elizabeth T. Borere, Jennifer L. Firnf, W. Stanley Harpoleg,h,i, Sarah E. Hobbiee, Kirsten S. Hofmockelj, Johannes M. H. Knopsk, Rebecca L. McCulleyl, Kimberly La Pierrem, Anita C. Rischn, Eric W. Seabloomo, Martin Schützn, Christopher Steenbockb, Carly J. Stevensp, and Noah Fierera,b,1 aCooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309; bDepartment of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; cDepartment of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556; dCommonwealth Scientific and Industrial Research Organisation Land and Water Flagship, Wembley, WA 6913, Australia; eDepartment of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108; fSchool of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia; gDepartment of Physiological Diversity, Helmholtz Center for Environmental Research UFZ, 04318 Leipzig, Germany; hGerman Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, D-04103 Leipzig, Germany; iInstitute of Biology, Martin Luther University Halle-Wittenberg, 06108 Halle (Saale), Germany; jEcology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50011; kSchool of Biological Sciences, University of Nebraska, Lincoln, NE 68588; lDepartment of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546; mDepartment of Integrative Biology, University of California, Berkeley, CA 94720; nCommunity Ecology, Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland; oDepartment of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108; and pLancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom Edited by Peter M. -
The Trophic-Dynamic Aspect of Ecology Author(S): Raymond L
The Trophic-Dynamic Aspect of Ecology Author(s): Raymond L. Lindeman Reviewed work(s): Source: Ecology, Vol. 23, No. 4 (Oct., 1942), pp. 399-417 Published by: Ecological Society of America Stable URL: http://www.jstor.org/stable/1930126 . Accessed: 30/01/2012 10:50 Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at . http://www.jstor.org/page/info/about/policies/terms.jsp JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. Ecological Society of America is collaborating with JSTOR to digitize, preserve and extend access to Ecology. http://www.jstor.org THE TROPHIC-DYNAMIC ASPECT OF ECOLOGY RAYMOND L. LINDEMAN OsbornZoological Laboratory,Yale University Recent progressin the studyof aquatic community. A more "bio-ecological" food-cycle relationships invites a re- species-distributionalapproach would appraisal of certain ecological tenets. recognize both the plants and animals Quantitative productivitydata provide as co-constituentsof restricted"biotic" a basis for enunciating certain trophic communities,such as "plankton com- principles, which, when applied to a munities," "benthic communities,"etc., series of successional stages, shed new in which membersof the living commu- light on the dynamics of ecological nity "co-act" with each other and "re- succession. act" with the non-livingenvironment (Clementsand Shelford,'39; Carpenter, "COMMUNITY" CONCEPTS '39, '40; T. Park, '41). -
(Antarctica) Glacial, Basal, and Accretion Ice
CHARACTERIZATION OF ORGANISMS IN VOSTOK (ANTARCTICA) GLACIAL, BASAL, AND ACCRETION ICE Colby J. Gura A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2019 Committee: Scott O. Rogers, Advisor Helen Michaels Paul Morris © 2019 Colby Gura All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Chapter 1: Lake Vostok is named for the nearby Vostok Station located at 78°28’S, 106°48’E and at an elevation of 3,488 m. The lake is covered by a glacier that is approximately 4 km thick and comprised of 4 different types of ice: meteoric, basal, type 1 accretion ice, and type 2 accretion ice. Six samples were derived from the glacial, basal, and accretion ice of the 5G ice core (depths of 2,149 m; 3,501 m; 3,520 m; 3,540 m; 3,569 m; and 3,585 m) and prepared through several processes. The RNA and DNA were extracted from ultracentrifugally concentrated meltwater samples. From the extracted RNA, cDNA was synthesized so the samples could be further manipulated. Both the cDNA and the DNA were amplified through polymerase chain reaction. Ion Torrent primers were attached to the DNA and cDNA and then prepared to be sequenced. Following sequencing the sequences were analyzed using BLAST. Python and Biopython were then used to collect more data and organize the data for manual curation and analysis. Chapter 2: As a result of the glacier and its geographic location, Lake Vostok is an extreme and unique environment that is often compared to Jupiter’s ice-covered moon, Europa. -
Spatial Ecology of Territorial Populations
Spatial ecology of territorial populations Benjamin G. Weinera, Anna Posfaib, and Ned S. Wingreenc,1 aDepartment of Physics, Princeton University, Princeton, NJ 08544; bSimons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; and cLewis–Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 Edited by Nigel Goldenfeld, University of Illinois at Urbana–Champaign, Urbana, IL, and approved July 30, 2019 (received for review July 9, 2019) Many ecosystems, from vegetation to biofilms, are composed of and penalize niche overlap (25), but did not otherwise struc- territorial populations that compete for both nutrients and phys- ture the spatial interactions. All these models allow coexistence ical space. What are the implications of such spatial organization when the combination of spatial segregation and local interac- for biodiversity? To address this question, we developed and ana- tions weakens interspecific competition relative to intraspecifc lyzed a model of territorial resource competition. In the model, competition. However, it remains unclear how such interactions all species obey trade-offs inspired by biophysical constraints on relate to concrete biophysical processes. metabolism; the species occupy nonoverlapping territories, while Here, we study biodiversity in a model where species interact nutrients diffuse in space. We find that the nutrient diffusion through spatial resource competition. We specifically consider time is an important control parameter for both biodiversity and surface-associated populations which exclude each other as they the timescale of population dynamics. Interestingly, fast nutri- compete for territory. This is an appropriate description for ent diffusion allows the populations of some species to fluctuate biofilms, vegetation, and marine ecosystems like mussels (28) or to zero, leading to extinctions. -
Chapter 4: PROKARYOTIC DIVERSITY
Chapter 4: PROKARYOTIC DIVERSITY 1. Prokaryote Habitats, Relationships & Biomes 2. Proteobacteria 3. Gram-negative and Phototropic Non-Proteobacteria 4. Gram-Positive Bacteria 5. Deeply Branching Bacteria 6. Archaea 1. Prokaryote Habitats, Relationships & Biomes Important Metabolic Terminology Oxygen tolerance/usage: aerobic – requires or can use oxygen (O2) anaerobic – does not require or cannot tolerate O2 Energy usage: phototroph – uses light as an energy source • all photosynthetic organisms chemotroph – acquires energy from organic or inorganic molecules • organotrophs – get energy from organic molecules • lithotrophs – get energy from inorganic molecules …more Important Terminology Carbon Source: autotroph – uses CO2 as a carbon source • e.g., photoautotrophs or chemoautotrophs heterotroph – requires an organic carbon source • e.g., chemoheterotroph – gets energy & carbon from organic molecules Oligotrophs require few nutrients, the opposite of eutrophs or copiotrophs Facultative vs Obligate (or Strict): facultative – “able to, but not requiring” • e.g., facultative anaerobes can survive w/ or w/o O2 obligate – “absolutely requires” • e.g., obligate anaerobes cannot survive in O2 Symbiotic Relationships Symbiotic relationships (close, direct interactions) between different organisms in nature are of several types: • e.g., humans have beneficial bacteria in their digestive tracts that also benefit from the food we eat (mutualism) Microbiomes All the microorganisms that inhabit a particular organism or environment (e.g., human or -
Casamino Acids Slow Motility and Stimulate Surface Growth in an Extreme Oligotroph
Edinburgh Research Explorer Casamino acids slow motility and stimulate surface growth in an extreme oligotroph Citation for published version: Samuels, T, Pybus, D & Cockell, CS 2019, 'Casamino acids slow motility and stimulate surface growth in an extreme oligotroph', Environmental microbiology reports, vol. 12, no. 1, pp. 63-69. https://doi.org/10.1111/1758-2229.12812 Digital Object Identifier (DOI): 10.1111/1758-2229.12812 Link: Link to publication record in Edinburgh Research Explorer Document Version: Peer reviewed version Published In: Environmental microbiology reports Publisher Rights Statement: This is the peer reviewed version of the following article: Samuels, T., Pybus, D. and Cockell, C.S. (2019), Casamino acids slow motility and stimulate surface growth in an extreme oligotroph. Environmental Microbiology Reports. doi:10.1111/1758-2229.12812], which has been published in final form at https://doi.org/10.1111/1758- 2229.12812. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. -
Aquatic Microbial Ecology 78:51
Vol. 78: 51–63, 2016 AQUATIC MICROBIAL ECOLOGY Published online December 15 doi: 10.3354/ame01801 Aquat Microb Ecol Contribution to AME Special 6 ‘SAME 14: progress and perspectives in aquatic microbial ecology’ OPENPEN ACCESSCCESS REVIEW Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere Ryan J. Newton1, Ashley Shade2,* 1School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E. Greenfield Avenue, Milwaukee, WI 53204, USA 2Department of Microbiology and Molecular Genetics and Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, 567 Wilson Road, East Lansing, MI 48824, USA ABSTRACT: There are patterns in the dynamics of rare taxa that lead to hypotheses about their lifestyles. For example, persistently rare taxa may be oligotrophs that are adapted for efficiency in resource-limiting environments, while conditionally rare or blooming taxa may be copiotrophs that are adapted to rapid growth when resources are available. Of course, the trophic strategies of microorganisms have direct ecological implications for their abundances, contributions to commu- nity structure, and role in nutrient turnover. We summarize general frameworks for separately considering rarity and heterotrophy, pulling examples from a variety of ecosystems. We then inte- grate these 2 topics to discuss the technical and conceptual challenges to understanding their pre- cise linkages. Because much has been investigated especially in marine aquatic environments, we finally extend the discussion to lifestyles of rarity for freshwater lakes by offering case studies of Lake Michigan lineages that have rare and prevalent patterns hypothesized to be characteristic of oligotrophs and copiotrophs. To conclude, we suggest moving forward from assigning dichotomies of rarity/prevalence and oligotrophs/copiotrophs towards their more nuanced con- tinua, which can be linked via genomic information and coupled to quantifications of microbial physiologies during cell maintenance and growth. -
Oligotrophy and Pelagic Marine Bacteria: Facts and Fiction
AQUATIC MICROBIAL ECOLOGY Published April 10 Aquat Microb Ecol l REVIEW Oligotrophy and pelagic marine bacteria: facts and fiction Frits Schutl, Rudolf A. prins2,*,Jan C. Gottscha12~** 'Microscreen b.v., Zernikepark 8, 9747 AN Groningen, The Netherlands *Department of Microbiology. University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands ABSTRACT: Oligotrophy, or the inability of bacterial cells to propagate at elevated nutrient concentra- tions, is a controversial phenomenon in microbiology. The exact cause of the unculturability of many indigenous marine bacteria on standard laboratory media has still not been resolved. Unfortunately, the physiology of such cells is difficult to investigate as long as high cell density cultures cannot be obtained. An extensive evaluation of experiments relating to oligotrophy and the cultivation of marine bacteria is presented in this review. When incorporating the findings of studies performed with molec- ular biological methods, the picture emerges that indigenous marine bacteria can be cultivated under certain cond~tionsand that the 'ohgotrophic way of life' is a transient characteristic. Although strong generalisations should not be made w~threspect to a biological system as diverse as the world's oceans, it should be anticipated that cells with unique physiological characteristics appear to exist in the oceanic system. When combining conventional physiological approaches with molecular biological techniques it is feasible to unveil the phenotypes that go with the encountered genotypes. In view of the enormous complexity of the oceanic system this will prove an ambitious, yet resourceful under- taking. KEY WORDS Oligotrophy Unculturable bacteria . Uptake kinetlcs . Marine bacteria . Isolation procedures 1. BACTERIA IN THE MARINE FOOD WEB belong to the smallest of all living cells. -
PERSPECTIVE What Is Microbial Community Ecology?
The ISME Journal (2009) 3, 1223–1230 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej PERSPECTIVE What is microbial community ecology? Allan Konopka Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property. The ISME Journal (2009) 3, 1223–1230; doi:10.1038/ismej.2009.88; published online 6 August 2009 Keywords: microbial community; functional redundancy; microbial interactions; emergent properties Introduction will deepen our understanding of how ecosystems function. In turn, this understanding may elucidate Analyses of 16S rRNA gene sequences from -
Impacts of Seasonality and Nutrients on Microbial Mat Community Structure and Function
MARINE ECOLOGY PROGRESS SERIES Vol. 123: 207-216. 1995 Published July 20 Mar Ecol Prog Ser Impacts of seasonality and nutrients on microbial mat community structure and function J. Pinckney, H. W. Paerl, M. Fitzpatrick University of North Carolina at Chapel Hill, Institute of Marine Sciences, 3431 Arendell Street. Morehead City, North Carolina 28557, USA ABSTRACT. To understand the mechanisms responsible for seasonal fluctuations in growth and N2 fixation in intertidal microbial mat communties, we quantified seasonal changes in mat community composition, related these changes to die1 and seasonal N2 fixation rates, and evaluated community responses (growth, N2 fixation, composition) to long-term (22 d) nutrient addition bioassays. A tem- perate intertidal cyanobacterial mat community, located in coastal North Carolina, USA, was sampled at monthly intervals for 1 yr (1993-94) to determine changes in community composition. The abun- dances of major phototrophic groups were quantified based on the relative concentrations of taxa- specific photopigments (chlorophylls and carotenoids). The most abundant phototrophs were cyano- bacteria, diatoms, and photosynthetic bacteria. Mat blomass and community composition underwent marked changes on both monthly and seasonal scales and corresponded with seasonal shifts in the dlel patterns of N2 fixation. Diatom biomass increased during periods of low N2 fixation. Nutnent (nitrate and phosphate) addition bioassays indicated that both cyanobacterial and diatom growth were N limited. Cyanobacteria were able to circumvent N llmltation by N2 fixation. The addition of high con- centrations of N (100 ,pM NaNO,) in combination with P (100 ~JMNaH2P04) resulted In an Increase (163'Y") in the relative abundance of diatoms The addition of P alone more than doubled N2 fixation rates and cyanobacterial abundance increased (+34'h) relative to diatoms. -
Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater
sustainability Article Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater Tamara Nazina 1,2,* , Tamara Babich 1, Nadezhda Kostryukova 1, Diyana Sokolova 1, Ruslan Abdullin 1, Tatyana Tourova 1, Vitaly Kadnikov 3, Andrey Mardanov 3, Nikolai Ravin 3, Denis Grouzdev 3 , Andrey Poltaraus 4, Stepan Kalmykov 5, Alexey Safonov 6, Elena Zakharova 6, Alexander Novikov 2 and Kenji Kato 7 1 Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] (T.B.); [email protected] (N.K.); [email protected] (D.S.); [email protected] (R.A.); [email protected] (T.T.) 2 V.I. Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] 3 Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] (V.K.); [email protected] (A.M.); [email protected] (N.R.); [email protected] (D.G.) 4 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] 5 Chemical Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; [email protected] 6 Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] (A.S.); [email protected] (E.Z.) 7 Faculty of Science, Department of Geosciences, Shizuoka University, 422-8529 Shizuoka, Japan; [email protected] -
Metabolic Evolution and the Self-Organization of Ecosystems
Metabolic evolution and the self-organization PNAS PLUS of ecosystems Rogier Braakmana,b,1, Michael J. Followsb, and Sallie W. Chisholma,c,1 aDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; bDepartment of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; and cDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 Contributed by Sallie W. Chisholm, February 22, 2017 (sent for review November 28, 2016; reviewed by Ron Milo and John A. Raven) Metabolism mediates the flow of matter and energy through the Results and Discussion biosphere. We examined how metabolic evolution shapes ecosys- Metabolism Provides Clues About Large-Scale Evolutionary Driving tems by reconstructing it in the globally abundant oceanic phy- Forces. To examine the driving forces shaping the evolution of toplankter Prochlorococcus. To understand what drove observed Prochlorococcus, we reconstructed (Fig. 2) the evolution of its evolutionary patterns, we interpreted them in the context of metabolic core (SI Appendix, Fig. S1). Because all biosynthetic its population dynamics, growth rate, and light adaptation, and pathways originate there, its evolution is highly constrained, and the size and macromolecular and elemental composition of cells. any innovations likely reflect major driving forces (5). Previ- This multilevel view suggests that, over the course of evolu- ous studies identified some unique presence/absence patterns for