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Is there a good field methods book that covers terrestrial ecology?

Is there a good field methods book that covers terrestrial ecology?


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In the past I have used Limnological Analysis by Wetzel and Likens and Methods in Stream Ecology edited by Hauer and Lamberti to develop labs and research methods for courses and projects with an aquatic focus.

These books detail the standard methods of lotic and lentic ecology with some emphasis on utilizing the methods in undergraduate or graduate level courses.

I am now developing a biogeochemistry course that is not limited to aquatic systems and I am looking for a summary of field methods for terrestrial systems.

Is there a book that summarizes terrestrial field ecology methods similar to Wetzel and Likens and Hauer and Lamberti?


Methods in Ecosystem Science edited by Oswaldo Sala, Rob Jackson, Hal Mooney, and Robert Howarth is a classic standard reference used by many (most?) ecosystem ecologists.


Take a look at Field and Laboratory Methods for General Ecology by James E. Brower, Jerrold H. Zar, and Carl N. von Ende.

If you are only interested in plant sampling techniques, an great resource published by U.S. Bureau of Land Management is Measuring & Monitoring Plant Populations by Caryl L. Elzinga, Daniel W. Salzer, and John W. Willoughby.

Another great resource that covers wildlife research and management techniques (2 volume set) is The Wildlife Techniques Manual published by The Wildlife Society and edited by Nova J. Silvy.


Coenoses

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Field tests of neighborhood population dynamics models of two annual weed
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  • ISBN: STANFORD:36105029402299
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Handbook of Road Ecology

This authoritative volume brings together some of the world’s leading researchers, academics, practitioners and transportation agency personnel to present the current status of the ecological sustainability of the linear infrastructure – primarily road, rail and utility easements – that dissect and fragment landscapes globally. It outlines the potential impacts, demonstrates how this infrastructure is being improved, and how broad ecological principles are applied to mitigate the impact of road networks on wildlife.

Research and monitoring is an important aspect of road ecology, encompassing all phases of a transportation project. This book covers research and monitoring to span the entire project continuum – starting with planning and design, through construction and into maintenance and management. It focuses on impacts and solutions for species groups and specific regions, with particular emphasis on the unique challenges facing Asia, South America and Africa.

  • Contributions from authors originating from over 25 countries, including from all continents
  • Each chapter summarizes important lessons, and includes lists of further reading and thoroughly up to date references
  • Highlights principles that address key points relevant to all phases in all road projects
  • Explains best-practices based on a number of successful international case studies
  • Chapters are "stand-alone", but they also build upon and complement each other extensive cross-referencing directs the reader to relevant material elsewhere in the book

Handbook of Road Ecology offers a comprehensive summary of approximately 30 years of global efforts to quantify the impacts of roads and traffic and implement effective mitigation. As such, it is essential reading for those involved in the planning, design, assessment and construction of new roads the management and maintenance of existing roads and the modifying or retrofitting of existing roads and problem locations. This handbook is an accessible resource for both developed and developing countries, including government transportation agencies, Government environmental/conservation agencies, NGOs, and road funding and donor organisations.

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Об авторе (2015)

Associate Professor Rodney van der Ree has studied the impacts of human activities on biodiversity since the mid 1990s. His current focus includes urban ecology and road ecology, with a strong emphasis on improving research
and monitoring and ensuring evidence-based information contributes to the design and management of infrastructure. Rodney is currently the Deputy Director of the Australian Research Centre for Urban Ecology at the Royal Botanic Gardens Melbourne and The University of Melbourne. He was awarded the Graeme Caughley Travelling fellowship in 2014 to promote and enhance road ecology in developing countries.

Daniel Smith is a research associate and member of the graduate faculty in the Department of Biology at the University of Central Florida and a member of the National Academies Transportation Research Board Subcommittee on Ecology and Transportation. Dr. Smith has 20+ years of experience in the fields of ecology and environmental planning. His primary focus is studying movement patterns and habitat use of terrestrial vertebrates and integrating conservation, transportation and land-use planning. He received the 2014 land
conservation and planning award from the Florida Wildlife Federation for his outstanding contributions to sound use and management of Florida’s natural resources.

Clara Grilo obtained her doctorate in Conservation Biology from the University of Lisbon (Portugal). Her primary
interest is applied ecological research in support of active conservation projects. Over the last years, much of her research has focused on the impact of anthropogenic changes to the landscape and effects on wildlife. Currently,
she is coordinating research projects on road ecology, namely the effects of roads on the abundance, spatial behavior, population genetic structure and risk of mortality on owls and mammals and the effectiveness of measures to reduce the negative effects of roads on wildlife.


Databases

BIOSIS Previews [via Web of Science] [via Clarivate Analytics]
Zoological Record [via Clarivate Analytics / Web of Science]
Aquatic Sciences and Fisheries Abstracts (ASFA) [via ProQuest] [via ProQuest]
Agricultural & Environmental Science Database [via ProQuest]
National Technical Reports Library
Wildlife & Ecology Studies Worldwide [via EBSCO]

Indexes literature on wild mammals, birds, reptiles, and amphibians covering all aspects of wildlife and wildlife management. Database producer from South Africa with excellent coverage of African publications.

Fish, Fisheries & Aquatic Biodiversity Worldwide [via EBSCO]

More than 1 million records. Covers fish, fisheries and aquaculture, including biology, genetics, natural history, behavior, diseases, parasites, limnology and oceanography, habitat management, culture, propagation, fish processing, marketing, and fisheries management. Merged content from thirteen databases including records from the now ceased database Aquatic Biology, Aquaculture, & Fisheries Resources (ABAFR), and from FISHLIT, Aquatic Biology Citations (ABC), the Fishing Industry Research Index (FIRI), Fisheries Review, and a database from the Worldfish Center’s Library. Database producer from South Africa — excellent coverage of African publications.

Web of Science Core Collection [via Clarivate Analytics]
JSTOR: The Scholarly Journal Archive

JSTOR provides Full-Text access to back files of hundreds important scholarly journals in nearly 50 disciplines spanning the arts, humanities, social sciences and the sciences. Current issues are now included for selected titles. Holdings vary by journal. JSTOR is a not-for-profit organization established with the assistance of the Andrew W. Mellon Foundation.

Africa-Wide Information [via EBSCO]
ECOTOX (ECOTOXicology)

Provides single chemical toxicity information for aquatic and terrestrial life which is useful for examining impacts of chemicals on the environment. Peer-reviewed literature is the primary source for the database including information on the species, chemical, test methods, and results. Another source of test results is independently compiled data files (such as the Pesticide Ecotoxicity database) provided by various United States and International government agencies. ECOTOX is a unified interface providing access to three U.S. Environmental Protection Agency (U.S. EPA) ecological effects databases: AQUIRE (all aquatic species including freshwater and marine) TERRETOX (terrestrial animal mainly wildlife) and PHYTOTOX (terrestrial plant). Ecology, Toxicology.

Faculty Opinions [via Faculty Opinions Limited, Sciwheel Limited]
WorldCat [via OCLC]
ProQuest Dissertations & Theses Database [via Proquest]

Abstract

Outdoor recreation is a known source of disturbance to many wildlife populations. We systematically reviewed 126 relevant papers that study the impact of outdoor recreation on wildlife, focusing on terrestrial wildlife (birds excluded) to assess the different methodological approaches adopted by researchers. We characterised the research methods into seven categories (direct observation, indirect observation (field-based), telemetry, camera traps, physiological measurement, trapping, and simulation). We find that direct observation is the most commonly used method to capture human-wildlife interactions, followed by the use of telemetry, and camera traps. The animals most commonly studied were ungulates, and the orders Carnivora and Rodentia. Studies typically captured data over longer periods (median 54 months) when using trapping methods other methods exhibited shorter study durations (median 22 months). The size of the animal under study appears to influence how methods are chosen, with larger species often being studied using telemetry methods. We highlight advantages and disadvantages of each method depending on the aims of the study, the focal species, and the type of outdoor recreation. Our review highlights the need for simultaneous measurements of both human activity and wildlife response. We also recommend that researchers consider how to capture both short- and long-term impacts on animal welfare. Our findings should guide applied wildlife conservation and management research in scenarios where human-wildlife interactions lead to conservation issues.


Upper-Division Courses

107. Ecology. W,S
Focuses on physiological, behavioral, and population ecology, and on linking ecological processes to evolution. It includes basic principles, experimental approaches, concepts of modeling, and applications to ecological problems. Prerequisite(s):satisfaction of the Entry Level Writing and Composition requirements BIOL 20A, BIOE 20B, and BIOE 20C. (W) B. Lyon, (S) J. Estes

108. Marine Ecology. W
Paradigms and designs in marine ecology. A review of the paradigms that have shaped our understanding of marine ecology analysis and discussion of experiments with these paradigms. Students cannot receive credit for this course and course 208. Prerequisite(s): satisfaction of the Entry Level Writing and Composition requirements BIOL 20A, BIOE 20B, and BIOE 20C BIOE 107 or 140 recommended. Enrollment restricted to juniors and seniors. M. Carr, P. Raimondi

109. Evolution. F,W
An examination of the history and mechanisms of evolutionary change. Topics include molecular evolution, natural and sexual selection, adaptation, speciation, biogeography, and macroevolution. Prerequisite(s): satisfaction of the Entry Level Writing and Composition requirements BIOL 20A, BIOE 20B, BIOE 20C, and BIOL 105. G. Pogson

112. Ornithology. F
Introduction to the evolution, ecology, behavior, and natural history of birds, using exemplary case histories to illustrate key concepts in evolution, ecology, and behavior. Prerequisite(s): BIOE 107, BIOE 109, or BIOE 140. Concurrent enrollment in BIOE 112L is required. B. Lyon

112L. Ornithology Field Studies (2 credits). F
Field trips introduce students to field identification skills and field investigation of census, foraging behavior, migration, social behavior, and communication. Examination of specimens in the laboratory will be used to highlight the diversity and taxonomy of birds. Students are billed a materials fee. Some field trips may require students to provide their own transportation. Prerequisite(s): BIOE 107, BIOE 109, or BIOE 140. Concurrent enrollment in BIOE 112 is required. Offered in alternate academic years. B. Lyon

114. Herpetology. S
Lectures introduce students to evolution, development, physiology, behavior, ecology, and life history of reptiles and amphibians. The materials integrate with conceptual and theoretical issues of ecology, evolution, physiology, and behavior. Prerequisite(s): BIOE 107, BIOE 109, BIOE 110, or BIOE 140. Concurrent enrollment in BIOE 114L required. Offered in alternate academic years. B. Sinervo

114L. Field Methods in Herpetological Research (2 credits). S
Field trips introduce students to natural history, censusing techniques, physiological ecology, and behavioral analysis of reptiles and amphibians. Laboratories introduce students to techniques for analyzing behavior and physiology. Field studies culminate with a group project in a natural setting. Some field trips may be held on weekends due to weather considerations. Some field trips may require students to provide their own transportation, some transportation will be provided by UCSC. Students are billed a materials fee. Prerequisite(s): BIOE 107, 109, 110, or 140. Concurrent enrollment in BIOE 114 is required. Offered in alternate academic years. B. Sinervo

117. Systematic Botany of Flowering Plants. S
An examination of the taxonomy and evolution of flowering plants. Special topics include phylogenetics and cladistics, plant species concepts, and modern methods of systematic research. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. Must be taken concurrently with BIOE 117L. K. Kay

117L. Systematic Botany of Flowering Plants Laboratory (2 credits). S
Weekly laboratory concerned primarily with California flora and plant families. Several field trips. Students are billed a materials fee. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. Must be taken concurrently with BIOE 117. K. Kay

120. Marine Botany. S
An introduction to the biology of marine algae, fungi, and angiosperms with regard to form and function. Major boreal, temperate, and tropical marine plant communities. Lecture format. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. Must be taken concurrently with BIOE 120L. The Staff

120L. Marine Botany Laboratory (2 credits). S
One laboratory weekly and several field trips. Focuses on marine algae, fungi, and angiosperms. Students are billed a materials fee. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. Must be taken concurrently with BIOE 120. The Staff

122. Invertebrate Zoology. W
An examination of invertebrates and their habitats. Lecture format. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. BIOE 122L must be taken concurrently. B. Marinovic

122L. Invertebrate Zoology Laboratory (2 credits). W
An examination of invertebrates and their habitats. Weekly laboratories or field trips. Students are billed a materials fee. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. BIOE 122 must be taken concurrently. B. Marinovic

124. Mammalogy. *
Introduces the biology of mammals, including their classification, evolution, behavior, reproductive strategies, and general ecology. Examines the diagnostic traits of mammals provides a survey of the living orders along with their diagnostic features, physiological and behavioral specializations, and adaptations. Prerequisite(s): BIOL 20A and BIOE 20B and 20C. Concurrent enrollment in course 124L is required. G. Dayton, D. Costa

124L. Mammalogy Laboratory (2 credits). W
Focuses on the identification of mammals and their specific traits. Exercises provide hands-on experience at identifying mammal orders, families, and species. Field trip provides students with field techniques in mammalogy. Prerequisite(s): BIOL 20A and BIOE 20B and 20C. Concurrent enrollment in course 124 is required. G. Dayton, D. Costa

127. Ichthyology. F
An introduction to the biology of jawless, cartilaginous, and bony fishes—their classification, evolution, form, physiology, and ecology. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. BIOE 127L must be taken concurrently. Offered in alternate academic years. G. Bernardi

127L. Ichthyology Laboratory (2 credits). F
One laboratory session a week and several field trips to study the biology of fish. Students are billed a materials fee. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. BIOE 127 must be taken concurrently. Offered in alternate academic years. G. Bernardi

128. Ecology and Physiology of Large Marine Vertebrates. W
Lectures and laboratory computer exercises familiarize students with research methods, study design, statistics, and research tools for large marine vertebrates (seals, birds, fish, and sharks). Research topics include: animal tracking diving physiology behavior foraging ecology and energetics. Prerequisite(s): BIOL 20A and BIOE 20B and 20C. The Staff

128L. Large Marine Vertebrates Field Course. S
Lectures combined on fieldwork with large marine vertebrates in the laboratory and lectures with large marine vertebrates in the field (Monterey Bay, Ano Nuevo). Fieldwork familiarizes students with research methods, study design, and statistical approaches for research on large marine vertebrates (seals, birds, fish, and sharks). Research includes: animal tracking physiology behavior foraging ecology and energetics. Students are billed a materials fee. Prerequisite(s): BIOL 20A and BIOE 20B, 20C, and 128. Enrollment limited to 24. P. Robinson

129. Biology of Marine Mammals. S
A survey of cetaceans, pinnipeds, sirenians, and sea otters, including natural history, systematics, physiology, behavior, anatomy, and conservation. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C BIOL 110 is recommended. D. Costa

129L. Biology of Marine Mammals Laboratory (2 credits). S
Covers the basics of marine mammal taxonomy, anatomy, and field methods with an emphasis on local field identification and understanding of local species. Will include field trips to Long Marine Lab, Ano Nuevo, and Monterey Bay. Students are billed a materials fee. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. Must be taken concurrently with BIOE 129. D. Costa

131. Animal Physiology. W
Principles and concepts underlying the function of tissues and organ systems in animals with emphasis on vertebrate systems. Students cannot receive credit for this course and BIOL 130. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. T. Williams

131L. Animal Physiology Laboratory (2 credits). *
Experiments conducted with primary focus on quantitative physiological principles of organ systems and intact organisms. Students cannot receive credit for this course and course 130L. Students are billed a materials fee. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. Concurrent enrollment in BIOE 131 is required. T. Williams

133. Exercise Physiology. S
An advanced-level course concerning physiological and biochemical processes associated with human performance. Emphasis is on the integration of organ systems for exercise. Topics include metabolism and fuel utilization, cardiovascular and respiratory dynamics during activity, and the effects of training. Requires a good understanding of basic physiological function and anatomy. Prerequisite(s): BIOL 20A, BIOE 20B and 20C. BIOE 131 recommended. Concurrent enrollment in BIOE 133L required. Offered in alternate academic years. T. Williams

133L. Exercise Physiology Laboratory (2 credits). S
An introduction to basic measurement techniques used in assessing the physiological response of humans to exercise. Sessions cover oxygen consumption, respiratory rate, and heart rate monitoring during aerobic and anaerobic activity. Students are billed a materials fee. Prerequisite(s): BIOL 20A, and BIOE 20B and 20C. BIOE 131 recommended. Concurrent enrollment in BIOE 133 is required. Offered in alternate academic years. T. Williams

134. Comparative Vertebrate Anatomy. F
Course focuses on vertebrate form and function: an integration of physiology and biomechanics. Topics include: the physiology and biomechanics underlying vertebrate locomotion vertebrate feeding and the morphological changes associated with different locomotion and feeding strategies through evolutionary time. Prerequisite(s): BIOL 20A, BIOE 20B and BIOE 20C Physics 6A. Concurrent enrollment in BIOE 134L is required. R. Mehta

134L. Comparative Vertebrate Anatomy Laboratory (2 credits). F
Course focuses on the gross dissections all major clades of vertebrates: development, form, and diversity of organ systems and basic principles of evolution vertebrate classification and functional morphology, with emphasis on feeding and locomotion. Anatomical dissections integrated with the associated lecture material focusing on biomechanics, form, and function. Prerequisite(s): BIOL 20A, BIOE 20B and BIOE 20C Physics 6A. Concurrent enrollment in BIOE 134 is required. R. Mehta

135. Plant Physiology. W
Cellular and organismal functions important in the life of green plants. Prerequisite(s): BIOL 20A and BIOE 20B and 20C concurrent enrollment in course 135L is required. J. Pittermann

135L. Plant Physiology Laboratory (2 credits). W
Weekly laboratory concerning the cellular and organismal functions of green plants. Students are billed a materials fee. Prerequisite(s): BIOL 20A and BIOE 20B and BIOE 20C concurrent enrollment in course 135. J. Pittermann

140. Behavioral Ecology. F
An introduction to social and reproductive behavior. Emphasis on studies of vertebrates in their natural habitat. Ideas concerning the evolution of social behavior, mating systems, and individual reproductive strategies. Case histories of well-studied animals that illustrate key principles in courtship and mating, parental behavior, and food-getting behavior. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. The Staff

141L. Behavioral Ecology Field Course. *
A field-based course introducing students to concepts and methods for studying behavioral ecology in nature. Students will conduct observations and field experiments on various local model organisms including elephant seals, hummingbirds, sparrows, lizards, ants, bees, frogs, and salamanders. Students are billed a materials fee. Prerequisite(s): BIOE 107 or BIOE 140 or BIOE 110 satisfaction of the Entry Level Writing and Composition requirements. Enrollment limited to 25. Offered in alternate academic years. (General Education Code(s): W.) B. Sinervo, B. Lyon

145. Plant Ecology. F
An exploration of the ecology of plant form, function, distribution, abundance, and diversity. Topics include plant adaptations to environmental conditions, life history variation, competition, reproductive ecology, herbivory, and patterns of diversity. Lecture with discussions of original papers and independent field project. Students cannot receive credit for this course and course 245. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. BIOE 107 is recommended. I. Parker

145L. Field Methods in Plant Ecology. F
Hands-on exploration of the concepts and techniques of plant ecology. A combination of lab, greenhouse, and field-based exercises (irrespective of weather conditions). Statistical analysis and scientific writing. One required weekend field trip. Students cannot receive credit for this course and course 245L. Students are billed a materials fee. Prerequisite(s): satisfaction of the Entry Level Writing and Composition requirements BIOL 20A, BIOE 20B, and BIOE 20C. Concurrent enrollment in BIOE 145 is required. BIOE 107 is recommended. (General Education Code(s): W.) I. Parker

147. Community Ecology. S
Develops the major themes of community biology: structure, trophic dynamics, succession, complex interactions among species, herbivory, evolution and coevolution. Uses case histories of well-studied marine and terrestrial systems. Students cannot receive credit for this course and course 247. Prerequisite(s): BIOE 107, 108, 145, 155 or 159A or Environmental Studies 24 by permission of instructor. L. Fox

148. Quantitative Ecology. S
Quantitative treatment of the central concepts and applications of theoretical ecology. Emphasis on the mathematical modeling of single populations and species interactions, and the integration of models with data. Topics include stochastic and deterministic processes of extinction discrete- and continuous-time models of growth and population viability analysis relevant to small and harvested populations numeric and analytical investigations of dynamics and stability introduction to model-fitting in information theoretic framework using R and/or MATLAB. Prerequisite(s): BIOE 107. M. Tinker

149. Disease Ecology. W
Focuses on the ecological and evolutionary processes that drive the transmission of pathogens between hosts the impact of disease on host populations and what causes the emergence of an infectious disease. Includes theoretical framework, description of field techniques, and discussion of wildlife and human diseases including malaria, West Nile virus, Lyme disease, HIV, avian influenza (bird flu), Chikungunya, tuberculosis, chytridiomycosis, and Ebola. Prerequisite(s): BIOL 20A, and BIOE 20B and 20C and 107. A. Kilpatrick

150. Ecological Field Methods. *
Lectures and laboratory computer exercises designed to familiarize students with research methods, study design, statistical approaches, and analysis tools for ecological research. Students cannot receive credit for this course and Environmental Studies 104A. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C concurrent enrollment in BIOE 150L is required. BIOE 107, 108, 140, or 147 recommended. Enrollment limited to 25. D. Croll

150L. Ecological Field Methods Laboratory. *
Field-oriented course in the study of animal ecology and behavior. Combines overview of methodologies and approaches to field research with practical field studies. Students are billed a materials fee. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C concurrent enrollment in BIOE 150 is required. BIOE 107, 108, 140, or 147 recommended. Enrollment limited to 25. (General Education Code(s): W.) D. Croll

151A. Ecology and Conservation in Practice Supercourse: Ecological Field Methods. S
An intensive, on-site learning experience in terrestrial field ecology and conservation, using the University of California Natural Reserves. Students study advance concepts in ecology, conservation, and field methods for four weeks, then experience total immersion in field research at the UC Natural Reserves. Lectures, field experiments, and computer exercises familiarize students with research methods, study design, statistical approaches, and analytical tools for ecological research. Enrollment by application. Prerequisite(s): BIOL 20A, BIOE 20B, BIOE 20C or ENVS 23, 24, 100 and AMS 7 and 7L. Concurrent enrollment in BIOE 151B-C-D or ENVS 109B-C-D is required. Satisfies the senior exit requirement for biological sciences majors and satisfies the senior exit requirement for environmental studies majors by prior approval. Students cannot receive credit for this course and BIOE 150, 150L, ENVS 104A or 196A. (Also offered as Environmental Studies 109A. Students cannot receive credit for both courses.) D. Croll, E. Zavaleta

151B. Ecology and Conservation in Practice Supercourse: Ecological Field Methods Laboratory. S
Field-oriented course in ecological research. Combines overview of methodologies and approaches to field research with practical field studies. Students complete field projects in ecology and also learn the natural history of the flora and fauna of California. Students are billed a materials fee. Enrollment by application. Prerequisite(s): Entry Level Writing and Composition requirements BIOL 20A, BIOE 20B, BIOE 20C or ENVS 23, 24, 100 and AMS 7 and 7L. Concurrent enrollment in BIOE 151A-C-D or ENVS 109A-C-D is required. Satisfies the senior exit requirement for biological sciences majors and satisfies the senior exit requirement for environmental studies majors by prior approval. Students cannot receive credit for this course and BIOE 150, 150L, ENVS 104A or 196A. (Also offered as Environmental Studies 109B. Students cannot receive credit for both courses.) (General Education Code(s): W.) D. Croll, E. Zavaleta

151C. Ecology and Conservation in Practice Supercourse: Functions and Processes of Terrestrial Ecosystems. S
From lectures and discussion of terrestrial community and ecosystem ecology, students work individually or in small groups to present an idea for a project, review relevant literature, develop a research question/hypothesis, design and perform an experiment, collect and analyze data, and write a report. The instructor evaluates the feasibility of each student's project before it begins. Enrollment by application. Prerequisite(s): BIOL 20A, BIOE 20B, BIOE 20C or ENVS 23, 24, 100 and AMS 7 and 7L. Concurrent enrollment in BIOE 151A-B-D or ENVS 109A-B-D is required. Satisfies the senior exit requirement for biological sciences majors and satisfies the senior exit requirement for environmental studies majors by prior approval. Students cannot receive credit for this course and BIOE 150, 150L, ENVS 104A or 196A. (Also offered as Environmental Studies 109C. Students cannot receive credit for both courses.) D. Croll, E. Zavaleta

151D. Ecology and Conservation in Practice Supercourse: Conservation in Practice. S
Focuses on current issues in environmental and conservation biology and the emerging field methods used to address them. From field-oriented lectures about current issues in environmental and conservation biology, students pursue research project as individuals and small groups to develop hands-on experience with field skills in conservation research and resource management. Enrollment by application. Prerequisite(s): BIOL 20A, BIOE 20B, BIOE 20C or ENVS 23, 24, 100 and AMS 7 and 7L. Concurrent enrollment in BIOE 151A-B-C or ENVS 109A-B-C is required. Satisfies the senior exit requirement for biological sciences majors and satisfies the senior exit requirement for environmental studies majors by prior approval. Students cannot receive credit for this course and BIOE 150, 150L, ENVS 104A or 196A. (Also offered as Environmental Studies 109D. Students cannot receive credit for both courses.) D. Croll, E. Zavaleta

155. Freshwater Ecology. F
Provides an overview of the physical, chemical, and biological processes that characterize inland waters such as lakes, streams, rivers, and wetlands. Also addresses relationships between humans and freshwater, and discusses these challenges in conservation. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. E. Palkovacs

158L. Marine Ecology Laboratory. S
Supervised individual research projects in experimental marine biology. Students carry out a complete research project, including (1) the formation of hypotheses (2) the design and implementation of experiments (3) collection, analysis, and interpretation of data and (4) write-up of an oral presentation. Students are billed a materials fee. Prerequisite(s): BIOE 108 satisfaction of the Entry Level Writing and Composition requirements. Offered in alternate academic years. (General Education Code(s): W.) M. Carr, P. Raimondi

159A. Marine Ecology Field Quarter: Marine Ecology with Laboratory. *
Total immersion in marine ecology for very motivated students. Students develop a research project during first five weeks on campus and then spend five weeks of immersion in directed research without distraction in isolated locations off campus (past locations include the Gulf of California in Mexico and Moorea in French Polynesia). Not available through University Extension. No other courses may be taken during this quarter. Students must sign a contract agreeing to standards of behavior outlined in the UCSC Rule Book and by the instructors. Students are billed a materials, transportation (not airfare), and room and board fee. Paradigms and designs in marine ecology. A review of the paradigms that have shaped our understanding of marine ecology and analysis and discussion of experiments with these paradigms. Students carry out a complete research project, including the formation of hypotheses the design and implementation of experiments the collection, analysis, and interpretation of data and the write-up and oral presentation of results. Admission by interview during previous winter quarter. BIOE 159A, 159B, 159C, and 159D are equivalent to BIOE 127, 127L, 108, and 158L for major requirements. Prerequisite(s): satisfaction of the Entry Level Writing and Composition requirements BIOE 159A, 159B, 159C, and 159D must be taken concurrently. Enrollment limited to 26. Offered in alternate academic years. (General Education Code(s): W.) P. Raimondi

159B. Marine Ecology Field Quarter: Ichthyology with Laboratory. *
An introduction to the biology of jawless, cartilaginous, and bony fishes—their classification, evolution, form, physiology, and ecology. Admission by interview during previous winter quarter. BIOE 159A, 159B, 159C, and 159D are equivalent to BIOE 127, 127L, 108, and 158L for major requirements. BIOE 159A, 159B, 159C, and 159D must be taken concurrently. Enrollment limited to 26. Offered in alternate academic years. G. Bernardi

159C. Marine Ecology Field Quarter: Methods in Field Ecology. *
Students learn quantitative methods for field experiments and surveys. Emphasis will be on marine environments, but there will also be exposure to terrestrial systems. This is the lecture component to course 159D. No text is required for this course instead, readings from the current literature will be assigned. Students are evaluated on written independent field project proposals and class participation. Admission by interview during previous winter quarter. BIOE 159A, 159B, 159C, and 159D are equivalent to BIOE 127, 127L, 108, and 158L for major requirements. BIOE 159A, 159B, 159C, and 159D must be taken concurrently. Enrollment limited to 26. Offered in alternate academic years. P. Raimondi

159D. Marine Ecology Field Quarter: Methods in Field Ecology Laboratory. *
This is laboratory portion of course 159C. Students carry out independent field projects under the supervision of course instructors. All work is done during the 5𔃄 week off-campus portion of course 159. Students are evaluated on field techniques, the final write-up of their independent field projects, and class participation. Admission by interview during previous winter quarter. BIOE 159A, 159B, 159C, and 159D are equivalent to BIOE 127, 127L, 108, and 158L for major requirements. BIOE 159A, 159B, 159C, and 159D must be taken concurrently. Enrollment limited to 26. Offered in alternate academic years. G. Bernardi

161. Kelp Forest Ecology. F
Study of organization of kelp forests as models for examining biological communities. The physical and biotic factors responsible for community organization of kelp forests are explored using original literature and data collected in BIOE 161L. Class meets one full morning each week. Prerequisite(s): by interview only BIOL 20A, BIOE 20B, and BIOE 20C are required. Students must pass the University Research Diving Certification (contact the diving safety officer, Institute of Marine Sciences, for further information). Enrollment restricted to seniors. BIOE 161L must be taken concurrently BIOE 107, 120/L, 122/L are recommended. Enrollment limited to 24. Offered in alternate academic years. M. Carr, P. Raimondi

161L. Kelp Forest Ecology Laboratory. F
Fieldwork using SCUBA to quantitatively and qualitatively examine the abundance and distribution of organisms in kelp forests, with additional laboratory work. Culminates with a directed individual research project. Class meets one full morning each week. Students are billed a materials fee. Admission by interview. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C satisfaction of the Entry Level Writing and Composition requirements BIOE 161 must be taken concurrently BIOE 107, 120/L, 122/L are recommended. Students must pass the University Research Diving Certification (contact the Diving Safety Officer, Institute of Marine Sciences, for further information). Enrollment limited to 24. Offered in alternate academic years. (General Education Code(s): W.) M. Carr, P. Raimondi

163. Ecology of Reefs, Mangroves, and Seagrasses. W
Integrated treatment of coral reefs, sea grasses, and mangroves emphasizing interactions and processes through time. Major topics: biological and geological history, biogeography, evolution and ecology of dominant organisms, biodiversity, community and ecosystem ecology, geology, biogeochemistry, global change, human impacts. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. Concurrent enrollment in BIOE 163L is required. D. Potts

163L. Ecology of Reefs, Mangroves, and Seagrasses Laboratory (2 credits). W
An interdisciplinary laboratory exploration of the anatomy, morphology, adaptations, diversity, evolution, and ecology of corals, mangroves, and seagrasses and of their physical, chemical, and geological environments. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C. Concurrent enrollment in BIOE 163 is required. D. Potts

165. Marine Conservation Biology. F
Initially undertakes an in-depth comparison of the biology and conservation of marine versus terrestrial ecosystems. With this foundation, course examines marine biodiversity loss resulting from overexploitation, habitat loss, species introduction, and pollution, with particular emphasis on the resulting trophic cascades, biodiversity losses, and climate change. Students cannot receive credit for this course and Environmental Studies 120. Prerequisite(s): BIOL 20A, BIOE 20B, and BIOE 20C OCEA 101 recommended. D. Croll

172. Population Genetics. *
Basic population genetics and selected topics will be covered, including genetics of speciation, tempo and mode of evolution, genetics of social behavior, natural selection in human populations, and the impact of molecular studies on evolutionary theory. Students cannot receive credit for this course and BIOE 272. Prerequisite(s): BIOL 20A, BIOE 20B, BIOE 20C, and BIOL 105. Concurrent enrollment in BIOE 172L is required. Offered in alternate academic years. G. Pogson

172L. Population Genetics Laboratory (2 credits). *
A companion course to 172, Population Genetics, that applies the theory developed in that course to related disciplines including conservation biology, ecology, agriculture, and population biology. Original scientific literature relating to the theory developed in BIOE 172 is read, and applied problem sets are solved by the students. Students cannot receive credit for this course and BIOE 272L. Prerequisite(s): BIOL 20A, BIOE 20B, BIOE 20C, and BIOL 105. Concurrent enrollment in BIOE 172 is required. Offered in alternate academic years. G. Pogson

182F. Exploring Research in EEB (2 credits). *
Provides undergraduate students with exposure to research in the laboratory of an Ecology and Evolutionary Biology (EEB) faculty member, affiliate, or adjunct. Students are not expected to do independent research but rather to assist in laboratory or field research projects under the supervision of the faculty mentor or appointed researcher. Prerequisite(s): Undergraduate research contract on file with the department. M. Carr

183L. Undergraduate Research in EEB (3 credits). *
Designed to ensure that students are intellectually engaged in the planning or implementation of a supervised or independent research project, achieve a fundamental understanding of implementing the scientific method, and develop their scientific writing and and presentation skills. Prerequisite(s): concurrent enrollment in course 183W and an Undergraduate Research Contract on file with the department. (General Education Code(s): W satisfied by taking this course and course 183W.) The Staff

183W. Undergraduate Research in EEB--Writing (2 credits). F,W,S
Ensures that students are intellectually engaged in the planning or implementation of a supervised or independent research project, achieve a fundamental understanding of implementing the scientific method, and develop their scientific writing and presentation skills. (General Education Code(s): W satisfied by taking this course and course 183L.) Prerequisite(s): satisfaction of the Entry Level Writing and Composition requirements and course 107, 108, or 109 and an undergraduate research contract on file with the department. Concurrent enrollment in course 183L required. D. Potts, A. Kilpatrick, M. Carr

188. Introduction to Science Writing. S
A rigorous examination and practice of the skills involved in writing articles about science, health, technology, and the environment for the general public. Covers the essential elements of news writing and explanatory journalism, including developing a story idea, interviewing scientists, fact checking, composition, and editing of multiple drafts about scientific research. (Also offered as Science Communication 160. Students cannot receive credit for both courses.) Prerequisite(s): satisfaction of the Entry Level Writing and C1, C2 requirements. Enrollment restricted to junior and senior biological sciences majors. Enrollment limited to 18. (General Education Code(s): W.) R. Irion

190. Senior Seminar (2 credits). S
Satisfies the senior exit requirement for all biological sciences majors. (Also offered as Biology: Molecular Cell & Dev 190. Students cannot receive credit for both courses.) J. Lee

193. Independent Research in EEB. F,W,S
Supervised undergraduate research on a project with an Ecology and Evolutionary Biology (EEB) faculty member, adjunct, or affiliate mentor. Prerequisites: course 183W and an undergraduate research contract on file with the department. M. Carr

193F. Independent Research in EEB (2 credits). *
Supervised undergraduate research on a project with an Ecology and Evolutionary Biology (EEB) faculty member, adjunct, or affiliate mentor. Prerequisites: course 183W and an undergraduate research contract on file with the department. M. Carr

195. Senior Thesis. F,W,S
An individually supervised course, with emphasis on independent research. Students required to submit a senior thesis. Enrollment restricted to majors in biology, ecology and evolution, marine biology, plant sciences, and the combined major with environmental studies. Students submit petition to sponsoring agency. The Staff

198. Independent Field Study. F,W,S
Provides for individual programs of study (a) by means other than the usual supervision in person, or (b) when the student is doing all or most of the course work off campus. With permission of the department, may be repeated for credit, or two or three courses taken concurrently. Students submit petition to sponsoring agency. May be repeated for credit. The Staff

198F. Independent Field Study (2 credits). F,W,S
Provides for two units of independent field study (a) by means other than the usual supervision in person, or (b) when the student is doing all or most of the course work off campus. Students submit petition to sponsoring agency. May be repeated for credit. The Staff

199. Tutorial. F,W,S
Reading, discussion, written reports, and laboratory research on selected biological topics, using facilities normally available on campus. Students submit petition to sponsoring agency. May be repeated for credit. The Staff

199F. Tutorial (2 credits). F,W,S
Two-unit Tutorial. Reading, discussion, written reports, and laboratory research on selected biological topics, using facilities normally available on campus. Students submit petition to sponsoring agency. May be repeated for credit. The Staff


Contents

1: Luigi Boitani and Roger A. Powell: Introduction: research and conservation of carnivores
2: Luigi Boitani, Paolo Ciucci, and Alessio Mortelliti: Designing carnivore surveys
3: Carlo Rondinini and Luigi Boitani: Mind the map: trips and pitfalls in making and reading maps of carnivore distribution
4: Marcella J. Kelly, Julie Betsch, Claudia Wultsch, Bernardo Mesa, and L. Scott Mills: Non-invasive sampling for carnivores
5: Gilbert Proulx, Marc R. L. Cattet, and Roger A. Powell: Humane and efficient capture and handling methods for carnivores
6: Kerry R. Foresman: Carnivores in hand
7: Mark R. Fuller and Todd K. Fuller: Radio telemetry equipment and applications for carnivores
8: Ken H. Pollock, James D. Nichols, and K. Ullas Karanth: Estimating demographic parameters
9: Roger A. Powell: Movements, home ranges, activity, and dispersal
10: Michael S. Mitchell and Mark Hebblewhite: Carnivore habitat ecology: integrating theory and application
11: Erlend B. Nilsen, David Christianson, Jean-Michel Gaillard, Duncan Halley, John D.C. Linnell, Morten Odden, Manuela Panzacchi, Carole Toigo, and Barbara Zimmermann: Describing food habits and predation: field methods and statistical considerations
12: Cheryl S. Asa: Reproductive biology and endocrine studies
13: Greta M. Wengert, Mourad W. Gabriel, and Deana L. Clifford: Investigating cause-specific mortality and diseases in carnivores: tools and techniques
14: John D. C. Linnell, John Odden, and Annette Mertens: Mitigation methods for conflicts associated with carnivore depredation on livestock
15: Michael K. Stoskopf: Carnivore restoration
16: Eric M. Gese, Hilary S. Cooley, and Frederick F. Knowlton: Designing a monitoring plan
17: Urs Breitenmoser, Christine Breitenmoser-Würsten, and Luigi Boitani: Assessing conservation status and units for conservation


We have to make ecology count and contemporary approaches should have real-life impact, including influencing policy and effectively engaging stakeholders and end-users. To this end, we have recently seen the acceptance of eDNA qPCR results to be taken as evidence of the presence of protected species in the UK (Biggs et al. 2015 ), complemented by a number of programs around the world using eDNA for the detection of alien invasive species. Metabarcoding will likely follow for high profile, costly and labour-intensive biomonitoring programs (Baird & Hajibabaei 2012 ), with the hope of freeing up resources to more robustly and frequently assess ecosystem health in relation to environmental stressors (Lallias et al. 2015 ). Importantly, sequencing-based approaches are not constrained to focus on particular a priori defined biomonitoring candidate species and may therefore yield additional insights into the interplay between environmental stressors and biodiversity of all life (Baird & Hajibabaei 2012 ).

Over the past 10 years, advances in sequencing technology and accompanying methodological breakthroughs have revolutionized our ability to quantify community biodiversity, but where do we go from here? From an empirical perspective, there is a clear need to link genotype to phenotype and associated ecological function (Fig. 3). There are now opportunities to map prokaryotic taxonomy marker genes to sequenced bacterial genomes of known function (Langille et al. 2013 ), complemented by metagenomics and metatranscriptomics. However, the vast task of characterizing all prokaryotic gene content will probably never be complete and the relationships between expressed mRNA transcripts and proteins/function are not always intuitive (Moran et al. 2013 ). Perhaps the biggest gains in these fields will lie in targeted assessment of specific gene pathways in relation to well-characterized systems (Toseland et al. 2013 ). From the macro-eukaryotic perspective, combinations of standardized marker gene libraries, complemented with taxonomy and metadata, do already provide a phenotype/genotype link (Ratnasingham & Hebert 2007 ) to functional ecology, at least as far as likely broad ecological classification, or trophic level is concerned (e.g. producer, grazer, predator, omnivore, detritivore). Therefore, these should be supported, irrespective of the gene, or genomic approach of community biodiversity classification. As with so many studies, robust reference data bases are essential links between genes and function, including studies investigating trophic relationships/food webs (Clare 2014 ).

In conclusion, the standardized format and open source nature of sequencing data, accompanied by radical shifts in sequencing technology, mean that we can catalogue the spatial and temporal distribution of species from all domains of life and from all habitats. Having this global view should therefore facilitate hypothesis-driven scientific questions regarding biodiversity ecosystem–function relationships (Purdy et al. 2010 Hagen et al. 2012 ) in relation to external forcing, whether the drivers are anthropogenic or natural. Combined with carefully controlled experimental systems, classification of species’ ecological tolerances, plasticity, distribution, rate of evolution and trophic interactions should mean that we are a step closer to making systems ecology predictions (Evans et al. 2013 ) associated with a changing environment. Without a doubt, it will certainly be challenging, but makes for exciting collaborations between the traditional fields of ecology and molecular ecologists in what is emerging to be a paradigm-shifting age of biodiversity discovery.


Minor in Biology

The Biology minor introduces students to foundational and advanced courses across the major subdisciplines of modern biology. Lecture and lab experiences are grounded on fundamental principles. In addition to the General Biology courses, a diversity of life science topics are available in upper division courses at the cellular and molecular, organismal, and ecological and evolutionary biology levels. Students can design a study plan which allows an in-depth exploration of one area or a broader survey of several subdisciplinary areas of biology.

Biology Minor requirements

Courses in departments other than Biology may not be applied towards this minor. Additionally, BIO 311 Biostatistics , BIO 425 Development of Biological Thought , BIO 297 Directed Research , BIO 397 Directed Independent Research (Extramural) , BIO 490 Seminar In Undergraduate Biology Instruction , BIO 492 Seminar in Undergraduate Classroom Instruction , BIO 493 Directed Independent Readings , BIO 495 Directed Independent Study , and BIO 497 Directed Independent Research do not apply towards this minor


Contents

All cellular respiration releases energy, water and CO2 from organic compounds. Any respiration that occurs below-ground is considered soil respiration. Respiration by plant roots, bacteria, fungi and soil animals all release CO2 in soils, as described below.

Tricarboxylic acid (TCA) cycle Edit

The tricarboxylic acid (TCA) cycle – or citric acid cycle – is an important step in cellular respiration. In the TCA cycle, a six carbon sugar is oxidized. [1] This oxidation produces the CO2 and H2O from the sugar. Plants, fungi, animals and bacteria all use this cycle to convert organic compounds to energy. This is how the majority of soil respiration occurs at its most basic level. Since the process relies on oxygen to occur, this is referred to as aerobic respiration.

Fermentation Edit

Fermentation is another process in which cells gain energy from organic compounds. In this metabolic pathway, energy is derived from the carbon compound without the use of oxygen. The products of this reaction are carbon dioxide and usually either ethyl alcohol or lactic acid. [2] Due to the lack of oxygen, this pathway is described as anaerobic respiration. This is an important source of CO2 in soil respiration in waterlogged ecosystems where oxygen is scarce, as in peat bogs and wetlands. However, most CO2 released from the soil occurs via respiration and one of the most important aspects of below-ground respiration occurs in the plant roots.

Root respiration Edit

Plants respire some of the carbon compounds which were generated by photosynthesis. When this respiration occurs in roots, it adds to soil respiration. Root respiration accounts for approximately half of all soil respiration. However, these values can range from 10–90% depending on the dominate plant types in an ecosystem and conditions under which the plants are subjected. Thus, the amount of CO2 produced through root respiration is determined by the root biomass and specific root respiration rates. [3] Directly next to the root is the area known as the rhizosphere, which also plays an important role in soil respiration.

Rhizosphere respiration Edit

The rhizosphere is a zone immediately next to the root surface with its neighboring soil. In this zone there is a close interaction between the plant and microorganisms. Roots continuously release substances, or exudates, into the soil. These exudates include sugars, amino acids, vitamins, long chain carbohydrates, enzymes and lysates which are released when roots cells break. The amount of carbon lost as exudates varies considerably between plant species. It has been demonstrated that up to 20% of carbon acquired by photosynthesis is released into the soil as root exudates. [4] These exudates are decomposed primarily by bacteria. These bacteria will respire the carbon compounds through the TCA cycle however, fermentation is also present. This is due to the lack of oxygen due to greater oxygen consumption by the root as compared to the bulk soil, soil at a greater distance from the root. [5] Another important organism in the rhizosphere are root-infecting fungi or mycorrhizae. These fungi increase the surface area of the plant root and allow the root to encounter and acquire a greater amount of soil nutrients necessary for plant growth. In return for this benefit, the plant will transfer sugars to the fungi. The fungi will respire these sugars for energy thereby increasing soil respiration. [6] Fungi, along with bacteria and soil animals, also play a large role in the decomposition of litter and soil organic matter.

Soil animals Edit

Soil animals graze on populations of bacteria and fungi as well as ingest and break up litter to increase soil respiration. Microfauna are made up of the smallest soil animals. These include nematodes and mites. This group specializes on soil bacteria and fungi. By ingesting these organisms, carbon that was initially in plant organic compounds and was incorporated into bacterial and fungal structures will now be respired by the soil animal. Mesofauna are soil animals from 0.1 to 2 millimeters (0.0039 to 0.0787 in) in length and will ingest soil litter. The fecal material will hold a greater amount of moisture and have a greater surface area. This will allow for new attack by microorganisms and a greater amount of soil respiration. Macrofauna are organisms from 2 to 20 millimeters (0.079 to 0.787 in), such as earthworms and termites. Most macrofauna fragment litter, thereby exposing a greater amount of area to microbial attack. Other macrofauna burrow or ingest litter, reducing soil bulk density, breaking up soil aggregates and increasing soil aeration and the infiltration of water. [7]

Regulation of CO2 production in soil is due to various abiotic, or non-living, factors. Temperature, soil moisture and nitrogen all contribute to the rate of respiration in soil.

Temperature Edit

Temperature affects almost all aspects of respiration processes. Temperature will increase respiration exponentially to a maximum, at which point respiration will decrease to zero when enzymatic activity is interrupted. Root respiration increases exponentially with temperature in its low range when the respiration rate is limited mostly by the TCA cycle. At higher temperatures the transport of sugars and the products of metabolism become the limiting factor. At temperatures over 35 °C (95 °F), root respiration begins to shut down completely. [8] Microorganisms are divided into three temperature groups cryophiles, mesophiles and thermophiles. Cryophiles function optimally at temperatures below 20 °C (68 °F), mesophiles function best at temperatures between 20 and 40 °C (104 °F) and thermophiles function optimally at over 40 °C (104 °F). In natural soils many different cohorts, or groups of microorganisms exist. These cohorts will all function best at different conditions, so respiration may occur over a very broad range. [9] Temperature increases lead to greater rates of soil respiration until high values retard microbial function, this is the same pattern that is seen with soil moisture levels.

Soil moisture Edit

Soil moisture is another important factor influencing soil respiration. Soil respiration is low in dry conditions and increases to a maximum at intermediate moisture levels until it begins to decrease when moisture content excludes oxygen. This allows anaerobic conditions to prevail and depress aerobic microbial activity. Studies have shown that soil moisture only limits respiration at the lowest and highest conditions with a large plateau existing at intermediate soil moisture levels for most ecosystems. [10] Many microorganisms possess strategies for growth and survival under low soil moisture conditions. Under high soil moisture conditions, many bacteria take in too much water causing their cell membrane to lyse, or break. This can decrease the rate of soil respiration temporarily, but the lysis of bacteria causes for a spike in resources for many other bacteria. This rapid increase in available labile substrates causes short-term enhanced soil respiration. Root respiration will increase with increasing soil moisture, especially in dry ecosystems however, individual species' root respiration response to soil moisture will vary widely from species to species depending on life history traits. Upper levels of soil moisture will depress root respiration by restricting access to atmospheric oxygen. With the exception of wetland plants, which have developed specific mechanisms for root aeration, most plants are not adapted to wetland soil environments with low oxygen. [11] The respiration dampening effect of elevated soil moisture is amplified when soil respiration also lowers soil redox through bioelectrogenesis. [12] Soil-based microbial fuel cells are becoming popular educational tools for science classrooms.

Nitrogen Edit

Nitrogen directly affects soil respiration in several ways. Nitrogen must be taken in by roots in order to promote plant growth and life. Most available nitrogen is in the form of NO3 − , which costs 0.4 units of CO2 to enter the root because energy must be used to move it up a concentration gradient. Once inside the root the NO3 − must be reduced to NH3. This step requires more energy, which equals 2 units of CO2 per molecule reduced. In plants with bacterial symbionts, which fix atmospheric nitrogen, the energetic cost to the plant to acquire one molecule of NH3 from atmospheric N2 is 2.36 CO2. [13] It is essential that plants uptake nitrogen from the soil or rely on symbionts to fix it from the atmosphere in order to assure growth, reproduction and long-term survival.

Another way nitrogen affects soil respiration is through litter decomposition. High nitrogen litter is considered high quality and is more readily decomposed by microorganisms than low quality litter. Degradation of cellulose, a tough plant structural compound, is also a nitrogen limited process and will increase with the addition of nitrogen to litter. [14]

Different methods exist for the measurement of soil respiration rate and the determination of sources. The most common methods include the use of long-term stand alone soil flux systems for measurement at one location at different times survey soil respiration systems for measurement of different locations and at different times and the use of stable isotope ratios.

Long-term stand-alone soil flux systems for measurement at one location over time Edit

These systems measure at one location over long periods of time. Since they only measure at one location, it is common to use multiple stations to reduce measuring error caused by soil variability over small distances. Soil variability may be tested with survey soil respiration instruments.

The long-term instruments are designed to expose the measuring site to ambient conditions as much as is possible between measurements.

Types of long-term stand-alone instruments Edit

Closed, non-steady state systems Edit

Closed systems take short-term measurements (typically over few minutes only) in a chamber sealed over the soil. [15] The rate of soil CO2 efflux is calculated on the basis of CO2 increased inside the chamber. As it is within the nature of closed chambers that CO2 continues to accumulate, measurement periods are reduced to a minimum to achieve a detectable, linear concentration increase, avoiding an excessive build-up of CO2 inside the chamber over time.

Both individual assay information and diurnal CO2 respiration measuring information is accessible. It is also common for such systems to also measure soil temperature, soil moisture and PAR (photosynthetically active radiation). These variables are normally recorded in the measuring file along with CO2 values.

For determination of soil respiration and the slope of CO2 increase, researchers have used linear regression analysis, the Pedersen (2001) algorithm, and exponential regression. There are more published references for linear regression analysis however, the Pedersen algorithm and exponential regression analysis methods also have their following. Some systems offer a choice of mathematical methods. [16]

When using linear regression, multiple data points are graphed and the points can be fitted with a linear regression equation, which will provide a slope. This slope can provide the rate of soil respiration with the equation F = b V / A , where F is the rate of soil respiration, b is the slope, V is the volume of the chamber and A is the surface area of the soil covered by the chamber. [17] It is important that the measurement is not allowed to run over a longer period of time as the increase in CO2 concentration in the chamber will also increase the concentration of CO2 in the porous top layer of the soil profile. This increase in concentration will cause an underestimation of soil respiration rate due to the additional CO2 being stored within the soil. [18]

Open, steady-state systems Edit

Open mode systems are designed to find soil flux rates when measuring chamber equilibrium has been reached. Air flows through the chamber before the chamber is closed and sealed. This purges any non-ambient CO2 levels from the chamber before measurement. After the chamber is closed, fresh air is pumped into the chamber at a controlled and programmable flow rate. This mixes with the CO2 from the soil, and after a time, equilibrium is reached. The researcher specifies the equilibrium point as the difference in CO2 measurements between successive readings, in an elapsed time. During the assay, the rate of change slowly reduces until it meets the customer's rate of change criteria, or the maximum selected time for the assay. Soil flux or rate of change is then determined once equilibrium conditions are reached within the chamber. Chamber flow rates and times are programmable, accurately measured, and used in calculations. These systems have vents that are designed to prevent a possible unacceptable buildup of partial CO2 pressure discussed under closed mode systems. Since the air movement inside the chamber might cause increased chamber pressure, or external winds may produce reduced chamber pressure, a vent is provided that is designed to be as wind proof as possible.

Open systems are also not as sensitive to soil structure variation, or to boundary layer resistance issues at the soil surface. Air flow in the chamber at the soil surface is designed to minimize boundary layer resistance phenomena.

Hybrid Mode Systems Edit

A hybrid system also exists. It has a vent that is designed to be as wind proof as possible, and prevent possible unacceptable partial CO2 pressure buildup, but is designed to operate like a closed mode design system in other regards.

Survey soil respiration systems – for testing the variation of CO2 respiration at different locations and at different times Edit

These are either open or closed mode instruments that are portable or semi-portable. They measure CO2 soil respiration variability at different locations and at different times. With this type of instrument, soil collars that can be connected to the survey measuring instrument are inserted into the ground and the soil is allowed to stabilize for a period of time. The insertion of the soil collar temporarily disturbs the soil, creating measuring artifacts. For this reason, it is common to have several soil collars inserted at different locations. Soil collars are inserted far enough to limit lateral diffusion of CO2. After soil stabilization, the researcher then moves from one collar to another according to experimental design to measure soil respiration.

Survey soil respiration systems can also be used to determine the number of long-term stand-alone temporal instruments that are required to achieve an acceptable level of error. Different locations may require different numbers of long-term stand-alone units due to greater or lesser soil respiration variability.

Isotope methods Edit

Plants acquire CO2 and produce organic compounds with the use of one of three photosynthetic pathways. The two most prevalent pathways are the C3 and C4 processes. C3 plants are best adapted to cool and wet conditions while C4 plants do well in hot and dry ecosystems. Due to the different photosynthetic enzymes between the two pathways, different carbon isotopes are acquired preferentially. Isotopes are the same element that differ in the number of neutrons, thereby making one isotope heavier than the other. The two stable carbon isotopes are 12 C and 13 C. The C3 pathway will discriminate against the heavier isotope more than the C4 pathway. This will make the plant structures produced from C4 plants more enriched in the heavier isotope and therefore root exudates and litter from these plants will also be more enriched. When the carbon in these structures is respired, the CO2 will show a similar ratio of the two isotopes. Researchers will grow a C4 plant on soil that was previously occupied by a C3 plant or vice versa. By taking soil respiration measurements and analyzing the isotopic ratios of the CO2 it can be determined whether the soil respiration is mostly old versus recently formed carbon. For example, maize, a C4 plant, was grown on soil where spring wheat, a C3 plant, was previously grown. The results showed respiration of C3 SOM in the first 40 days, with a gradual linear increase in heavy isotope enrichment until day 70. The days after 70 showed a slowing enrichment to a peak at day 100. [19] By analyzing stable carbon isotope data it is possible to determine the source components of respired SOM that was produced by different photosynthetic pathways.

Throughout the past 160 years, humans have changed land use and industrial practices, which have altered the climate and global biogeochemical cycles. These changes have affected the rate of soil respiration around the planet.

Elevated carbon dioxide Edit

Since the Industrial Revolution, humans have emitted vast amounts of CO2 into the atmosphere. These emissions have increased greatly over time and have increased global atmospheric CO2 levels to their highest in over 750,000 years. Soil respiration increases when ecosystems are exposed to elevated levels of CO2. Numerous free air CO2 enrichment (FACE) studies have been conducted to test soil respiration under predicted future elevated CO2 conditions. Recent FACE studies have shown large increases in soil respiration due to increased root biomass and microbial activity. [20] Soil respiration has been found to increase up to 40.6% in a sweetgum forest in Tennessee and poplar forests in Wisconsin under elevated CO2 conditions. [21] It is extremely likely that CO2 levels will exceed those used in these FACE experiments by the middle of this century due to increased human use of fossil fuels and land use practices.

Climate warming Edit

Due to the increase in temperature of the soil, CO2 levels in our atmosphere increase, and as such the mean average temperature of the Earth is rising. This is due to human activities such as forest clearing, soil denuding, and developments that destroy autotrophic processes. With the loss of photosynthetic plants covering and cooling the surface of the soil, the infrared energy penetrates the soil heating it up and causing a rise in heterotrophic bacteria. Heterotrophs in the soil quickly degrade the organic matter and soil structure crumbles, thus it dissolves into streams and rivers into the sea. Much of the organic matter swept away in floods caused by forest clearing goes into estuaries, wetlands and eventually into the open ocean. Increased turbidity of surface waters causes biological oxygen demand and more autotrophic organisms die. Carbon dioxide levels rise with increased respiration of soil bacteria after temperatures rise due to loss of soil cover.

As mentioned earlier, temperature greatly affects the rate of soil respiration. This may have the most drastic influence in the Arctic. Large stores of carbon are locked in the frozen permafrost. With an increase in temperature, this permafrost is melting and aerobic conditions are beginning to prevail, thereby greatly increasing the rate of respiration in that ecosystem. [22]

Changes in precipitation Edit

Due to the shifting patterns of temperature and changing oceanic conditions, precipitation patterns are expected to change in location, frequency and intensity. Larger and more frequent storms are expected when oceans can transfer more energy to the forming storm systems. This may have the greatest impact on xeric, or arid, ecosystems. It has been shown that soil respiration in arid ecosystems shows dynamic changes within a raining cycle. The rate of respiration in dry soil usually bursts to a very high level after rainfall and then gradually decreases as the soil dries. [10] With an increase in rainfall frequency and intensity over area without previous extensive rainfall, a dramatic increase in soil respiration can be inferred.

Nitrogen fertilization Edit

Since the onset of the Green Revolution in the middle of the last century, vast amounts of nitrogen fertilizers have been produced and introduced to almost all agricultural systems. This has led to increases in plant available nitrogen in ecosystems around the world due to agricultural runoff and wind-driven fertilization. As discussed earlier, nitrogen can have a significant positive effect on the level and rate of soil respiration. Increases in soil nitrogen have been found to increase plant dark respiration, stimulate specific rates of root respiration and increase total root biomass. [23] This is because high nitrogen rates are associated with high plant growth rates. High plant growth rates will lead to the increased respiration and biomass found in the study. With this increase in productivity, an increase in soil activities and therefore respiration can be assured.

Soil respiration plays a significant role in the global carbon and nutrient cycles as well as being a driver for changes in climate. These roles are important to our understanding of the natural world and human preservation.

Global carbon cycling Edit

Soil respiration plays a critical role in the regulation of carbon cycling at the ecosystem level and at global scales. Each year approximately 120 petagrams (Pg) of carbon are taken up by land plants and a similar amount is released to the atmosphere through ecosystem respiration. The global soils contain up to 3150 Pg of carbon, of which 450 Pg exist in wetlands and 400 Pg in permanently frozen soils. The soils contain more than four times the carbon as the atmosphere. [24] Researchers have estimated that soil respiration accounts for 77 Pg of carbon released to the atmosphere each year. [25] This level of release is one order of magnitude greater than the carbon release due to anthropogenic sources (6 Pg per year) such as fossil fuel burning. Thus, a small change in soil respiration can seriously alter the balance of atmosphere CO2 concentration versus soil carbon stores. Much like soil respiration can play a significant role in the global carbon cycle, it can also regulate global nutrient cycling.

Nutrient cycling Edit

A major component of soil respiration is from the decomposition of litter which releases CO2 to the environment while simultaneously immobilizing or mineralizing nutrients. During decomposition, nutrients such as nitrogen are immobilized by microbes for their own growth. As these microbes are ingested or die, nitrogen is added to the soil. Nitrogen is also mineralized from the degradation of proteins and nucleic acids in litter. This mineralized nitrogen is also added to the soil. Due to these processes, the rate of nitrogen added to the soil is coupled with rates of microbial respiration. Studies have shown that rates of soil respiration were associated with rates of microbial turnover and nitrogen mineralization. [5] Alterations of the global cycles can further act to change the climate of the planet.

Climate change Edit

As stated earlier, the CO2 released by soil respiration is a greenhouse gas that will continue to trap energy and increase the global mean temperature if concentrations continue to rise. As global temperature rises, so will the rate of soil respiration across the globe thereby leading to a higher concentration of CO2 in the atmosphere, again leading to higher global temperatures. This is an example of a positive feedback loop. It is estimated that a rise in temperature by 2° Celsius will lead to an additional release of 10 Pg carbon per year to the atmosphere from soil respiration. [26] This is a larger amount than current anthropogenic carbon emissions. There also exists a possibility that this increase in temperature will release carbon stored in permanently frozen soils, which are now melting. Climate models have suggested that this positive feedback between soil respiration and temperature will lead to a decrease in soil stored carbon by the middle of the 21st century. [27]

Soil respiration is a key ecosystem process that releases carbon from the soil in the form of carbon dioxide. Carbon is stored in the soil as organic matter and is respired by plants, bacteria, fungi and animals. When this respiration occurs below ground, it is considered soil respiration. Temperature, soil moisture and nitrogen all regulate the rate of this conversion from carbon in soil organic compounds to CO2. Many methods are used to measure soil respiration however, the closed dynamic chamber and utilization of stable isotope ratios are two of the most prevalent techniques. Humans have altered atmospheric CO2 levels, precipitation patterns and fertilization rates, all of which have had a significant role on soil respiration rates. The changes in these rates can alter the global carbon and nutrient cycles as well as play a significant role in climate change.


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