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• 21. [Image] Implementation of the Endangered Species Act of 1973 (Report to the House Committee on Resources)

  	I. Executive Summary There is increasing recognition from most quarters that the Endangered Species Act (ESA) needs to be improved. Exactly what those improvements should be is less uniform. ...
  	Citation × Citation Citation Abstract Copy Title: Implementation of the Endangered Species Act of 1973 (Report to the House Committee on Resources) Author: United States. Congress. House. Committee on Resources Year: 2005, 2007 I. Executive Summary There is increasing recognition from most quarters that the Endangered Species Act (ESA) needs to be improved. Exactly what those improvements should be is less uniform. This report examines the implementation of selected aspects of the endangered species program relying predominately on information provided by the primary implementing agencies, the United States Fish and Wildlife Service (FWS) and National Marine Fisheries Service (NMFS) and offers some recommendations for possible improvements to the program. Debate over the ESA has traditionally been highly polarized. For example, compensating landowners for takings or reductions in property value has been opposed by some who argue updating the law to address this is not necessary. While consensus on other issues such as the need for increasing conservation incentives and the role states play in endangered species conservation has begun to emerge, one of the most debated aspects of ESA implementation continues to be whether the ESA is effectively conserving endangered and threatened species. While there have been significant strides in conserving individual species such as the whooping crane, red-cockaded woodpecker and gray wolf, few species have been delisted (removed from the endangered list) or downlisted (changed in status from endangered to threatened) because of successful ESA conservation efforts. Some argue that the number of recovered species is an unfair measure, asserting that the three decades the ESA has been in existence is an insufficient amount of time for the lengthy process of species recovery and point to listed species that have not gone extinct as evidence the ESA 'saves' species. From the opposing perspective, while recovery to the point of delisting may require a substantial amount of time for many species, after three decades more progress should be demonstrable through species that have recovered and been delisted. Even if a species has increased in numbers or distribution or the threats facing the species have been reduced, if it has not been delisted on the basis of recovery, the ESA's prohibitions and regulations remain applicable and the ESA should not be a 'one way street.' Of 40 total species removed from the list, 10 domestic species were delisted because of "recovery". Of 33 reclassified species, 10 domestic downlistings (a change from endangered to threatened status) reflected a reduced threat assessment which also allowed more flexibility in management. The FWS's most recent report to Congress (Fiscal years 2001-2002) shows that 77 percent of listed species fall in the 0 to 25 percent recovery achieved bracket and 2 percent fall in the 76 to 100 percent recovery achieved bracket. 39 percent of the FWS managed species are of uncertain status. Of those with an assessed trend, at one end of the spectrum are 3 percent possibly extinct, 1 percent occurring only in captivity and 21 percent declining and at the other end are 30 percent stable and 6 percent improving. These assessments however are subjective. Additionally, the assessment that a species is improving or stable may reflect, for example, a reduction in perceived threats or corrections to inaccurate threat assessments that stemmed from erroneous data rather than actual changes in species' trends that are demonstrated by improved numbers, distribution or other such measurements. Consequently, a meaningful assessment of conservation trends under the ESA using these data is not possible. The data used to list a number of species has been subsequently determined to be erroneous and species that likely do not merit classification as endangered or threatened remain listed. This can consume resources that could be directed to species that do merit listing. The assignment of recovery priorities appears highly skewed and the recovery priority for some species seems questionable. A meaningful distinction between endangered status and threatened status has been blurred as has been the framework for the mechanism of critical habitat. Expenditure reporting has improved but presents an incomplete picture of financial resources dedicated to endangered species. Workloads for litigation regarding activities such as consultation and listing under the ESA's complex structure compete for resources that could otherwise be directed at recovery efforts. The demands associated with ESA Section 4 determinations in combination with the pace of species listings and delistings, the number of possible future additions to the list and the economic impact of listings likely indicate that the current program is not sustainable. Title: Implementation of the Endangered Species Act of 1973 (Report to the House Committee on Resources) Author: United States. Congress. House. Committee on Resources Year: 2005, 2007 I. Executive Summary There is increasing recognition from most quarters that the Endangered Species Act (ESA) needs to be improved. Exactly what those improvements should be is less uniform. This report examines the implementation of selected aspects of the endangered species program relying predominately on information provided by the primary implementing agencies, the United States Fish and Wildlife Service (FWS) and National Marine Fisheries Service (NMFS) and offers some recommendations for possible improvements to the program. Debate over the ESA has traditionally been highly polarized. For example, compensating landowners for takings or reductions in property value has been opposed by some who argue updating the law to address this is not necessary. While consensus on other issues such as the need for increasing conservation incentives and the role states play in endangered species conservation has begun to emerge, one of the most debated aspects of ESA implementation continues to be whether the ESA is effectively conserving endangered and threatened species. While there have been significant strides in conserving individual species such as the whooping crane, red-cockaded woodpecker and gray wolf, few species have been delisted (removed from the endangered list) or downlisted (changed in status from endangered to threatened) because of successful ESA conservation efforts. Some argue that the number of recovered species is an unfair measure, asserting that the three decades the ESA has been in existence is an insufficient amount of time for the lengthy process of species recovery and point to listed species that have not gone extinct as evidence the ESA 'saves' species. From the opposing perspective, while recovery to the point of delisting may require a substantial amount of time for many species, after three decades more progress should be demonstrable through species that have recovered and been delisted. Even if a species has increased in numbers or distribution or the threats facing the species have been reduced, if it has not been delisted on the basis of recovery, the ESA's prohibitions and regulations remain applicable and the ESA should not be a 'one way street.' Of 40 total species removed from the list, 10 domestic species were delisted because of "recovery". Of 33 reclassified species, 10 domestic downlistings (a change from endangered to threatened status) reflected a reduced threat assessment which also allowed more flexibility in management. The FWS's most recent report to Congress (Fiscal years 2001-2002) shows that 77 percent of listed species fall in the 0 to 25 percent recovery achieved bracket and 2 percent fall in the 76 to 100 percent recovery achieved bracket. 39 percent of the FWS managed species are of uncertain status. Of those with an assessed trend, at one end of the spectrum are 3 percent possibly extinct, 1 percent occurring only in captivity and 21 percent declining and at the other end are 30 percent stable and 6 percent improving. These assessments however are subjective. Additionally, the assessment that a species is improving or stable may reflect, for example, a reduction in perceived threats or corrections to inaccurate threat assessments that stemmed from erroneous data rather than actual changes in species' trends that are demonstrated by improved numbers, distribution or other such measurements. Consequently, a meaningful assessment of conservation trends under the ESA using these data is not possible. The data used to list a number of species has been subsequently determined to be erroneous and species that likely do not merit classification as endangered or threatened remain listed. This can consume resources that could be directed to species that do merit listing. The assignment of recovery priorities appears highly skewed and the recovery priority for some species seems questionable. A meaningful distinction between endangered status and threatened status has been blurred as has been the framework for the mechanism of critical habitat. Expenditure reporting has improved but presents an incomplete picture of financial resources dedicated to endangered species. Workloads for litigation regarding activities such as consultation and listing under the ESA's complex structure compete for resources that could otherwise be directed at recovery efforts. The demands associated with ESA Section 4 determinations in combination with the pace of species listings and delistings, the number of possible future additions to the list and the economic impact of listings likely indicate that the current program is not sustainable. Close

• 22. [Image] Water quality and nutrient loading in the Klamath River between Keno, Oregon and Seiad Valley, California from 1996-1998

  	ABSTRACT A water quality study was performed in the mainstem Klamath River from Keno, Oregon to Seiad Valley, California during 1996 through 1998. Four sites within the study area were continuously ...
  	Citation × Citation Citation Abstract Copy Title: Water quality and nutrient loading in the Klamath River between Keno, Oregon and Seiad Valley, California from 1996-1998 Author: Campbell, S. G Year: 2001, 2007, 2005 ABSTRACT A water quality study was performed in the mainstem Klamath River from Keno, Oregon to Seiad Valley, California during 1996 through 1998. Four sites within the study area were continuously monitored using multiparameter recorders. Water quality sampling was also performed at these four locations in 1996 and 1997. Additional water quality sampling sites were added in 1998 for a total of 8 locations between Keno and Seiad. Temperature ranged from near zero ?C to >25 ?C with cooler temperatures in early spring and fall, and maximum temperatures occurring in July and August of each year. Dissolved oxygen concentration ranged from near zero mg/L to >13 mg/L with highest DO occurring in early spring and fall and lowest DO occurring in mid-summer. Air temperature was generally highly correlated with water temperature with r values ranging from 0.8 to 0.9 during the study period from 1996-1998. Water temperature in the study area exceeded chronic (>16?C) and acute (>22?C) criteria for salmonids during the summer months. Although chronic DO (<7 mg/L) criteria were exceeded throughout most of the study area during the summer, in the free-flowing river below Iron Gate Dam the acute DO (<5.5 mg/L) criteria were not exceeded. Nonpoint source pollution in the form of agricultural return flows, industrial, or sewage effluent entering the stream may have resulted in higher ammonia and total organic nitrogen concentrations at the upstream locations in the Klamath River study area (Keno and J.C. Boyle Powerplant). Nitrification of ammonia and organic nitrogen seemed to result in higher concentrations of nitrate in the downstream Klamath River (Iron Gate Dam). Total phosphorus concentration stayed relatively stable through the reservoirs in the study area, but decreased in the downstream direction between Iron Gate Dam and Seiad. Ortho-phosphorus concentrations increased longitudinally through the reservoirs, then decreased in the downstream direction between Iron Gate Dam and Seiad. An increase in ortho-phosphorus concentration can indicate internal cycling occurring in the reservoirs as well as photosynthesis. On an annual basis total phosphorus loading increased longitudinally from up- to downstream between Keno and Seiad. The increase was statistically significant (p = .03) indicating that the reservoirs in series in the Klamath River study area do not function as a nutrient sink. However, during the summer there was no statistically significant difference in total P loading when Keno, Iron Gate and Seiad locations were compared, therefore, the reservoirs may act as a nutrient sink seasonally. The Klamath River study locations were generally nitrogen limited, although at Keno, a regular change from N limitation to P limitation occurred during the fall of all three years of the study. When the Klamath River annual nutrient loading values are compared to other rivers in the vicinity, the Carson, Truckee, and Long Tom Rivers also appear to be nutrient enriched. The Carson and South Yamhill Rivers seem to be N limited systems and the Wood, Long Tom, Snake and Truckee Rivers seem to be P limited systems. Implementing management strategies for reservoir operations to improve water quality and reduce nutrient concentration or loading in the Klamath River study area to benefit anadromous fisheries may be difficult and expensive. However, improving the thermal regime in spring to benefit YOY salmonids may be possible as is short-term relief in fate summer for over-summering species. Decreases in nutrient concentration or loading accomplished through best management practices in the water shed may allow general protection of water resources in the Klamath Basin for future needs. Title: Water quality and nutrient loading in the Klamath River between Keno, Oregon and Seiad Valley, California from 1996-1998 Author: Campbell, S. G Year: 2001, 2007, 2005 ABSTRACT A water quality study was performed in the mainstem Klamath River from Keno, Oregon to Seiad Valley, California during 1996 through 1998. Four sites within the study area were continuously monitored using multiparameter recorders. Water quality sampling was also performed at these four locations in 1996 and 1997. Additional water quality sampling sites were added in 1998 for a total of 8 locations between Keno and Seiad. Temperature ranged from near zero ?C to >25 ?C with cooler temperatures in early spring and fall, and maximum temperatures occurring in July and August of each year. Dissolved oxygen concentration ranged from near zero mg/L to >13 mg/L with highest DO occurring in early spring and fall and lowest DO occurring in mid-summer. Air temperature was generally highly correlated with water temperature with r values ranging from 0.8 to 0.9 during the study period from 1996-1998. Water temperature in the study area exceeded chronic (>16?C) and acute (>22?C) criteria for salmonids during the summer months. Although chronic DO (<7 mg/L) criteria were exceeded throughout most of the study area during the summer, in the free-flowing river below Iron Gate Dam the acute DO (<5.5 mg/L) criteria were not exceeded. Nonpoint source pollution in the form of agricultural return flows, industrial, or sewage effluent entering the stream may have resulted in higher ammonia and total organic nitrogen concentrations at the upstream locations in the Klamath River study area (Keno and J.C. Boyle Powerplant). Nitrification of ammonia and organic nitrogen seemed to result in higher concentrations of nitrate in the downstream Klamath River (Iron Gate Dam). Total phosphorus concentration stayed relatively stable through the reservoirs in the study area, but decreased in the downstream direction between Iron Gate Dam and Seiad. Ortho-phosphorus concentrations increased longitudinally through the reservoirs, then decreased in the downstream direction between Iron Gate Dam and Seiad. An increase in ortho-phosphorus concentration can indicate internal cycling occurring in the reservoirs as well as photosynthesis. On an annual basis total phosphorus loading increased longitudinally from up- to downstream between Keno and Seiad. The increase was statistically significant (p = .03) indicating that the reservoirs in series in the Klamath River study area do not function as a nutrient sink. However, during the summer there was no statistically significant difference in total P loading when Keno, Iron Gate and Seiad locations were compared, therefore, the reservoirs may act as a nutrient sink seasonally. The Klamath River study locations were generally nitrogen limited, although at Keno, a regular change from N limitation to P limitation occurred during the fall of all three years of the study. When the Klamath River annual nutrient loading values are compared to other rivers in the vicinity, the Carson, Truckee, and Long Tom Rivers also appear to be nutrient enriched. The Carson and South Yamhill Rivers seem to be N limited systems and the Wood, Long Tom, Snake and Truckee Rivers seem to be P limited systems. Implementing management strategies for reservoir operations to improve water quality and reduce nutrient concentration or loading in the Klamath River study area to benefit anadromous fisheries may be difficult and expensive. However, improving the thermal regime in spring to benefit YOY salmonids may be possible as is short-term relief in fate summer for over-summering species. Decreases in nutrient concentration or loading accomplished through best management practices in the water shed may allow general protection of water resources in the Klamath Basin for future needs. Close

• 23. [Image] Lost River and shortnose sucker : proposed critical habitat : biological support document : draft

  	Proposed rule from Federal Register, vol. 59, no. 230, December 1, 1994, pages 61744-61759, inserted after p. 35; Includes biliographical references (p. 31-35)
  	Citation × Citation Citation Abstract Copy Title: Lost River and shortnose sucker : proposed critical habitat : biological support document : draft Author: U.S. Fish and Wildlife Service. Portland Field Office Year: 1994, 2004 Proposed rule from Federal Register, vol. 59, no. 230, December 1, 1994, pages 61744-61759, inserted after p. 35; Includes biliographical references (p. 31-35) Title: Lost River and shortnose sucker : proposed critical habitat : biological support document : draft Author: U.S. Fish and Wildlife Service. Portland Field Office Year: 1994, 2004 Proposed rule from Federal Register, vol. 59, no. 230, December 1, 1994, pages 61744-61759, inserted after p. 35; Includes biliographical references (p. 31-35) Close

• 24. [Image] An assessment of ecosystem components in the interior Columbia Basin and portions of the Klamath and Great Basins [volume 2]

  	Abstract Quigley, Thomas M.; Arbelbide, Sylvia J., tech. eds. 1997. An assessment of ecosystem components in the interior Columbia basin and portions of the Klamath and Great Basins: volume 2. Gen. Tech. ...
  	Citation × Citation Citation Abstract Copy Title: An assessment of ecosystem components in the interior Columbia Basin and portions of the Klamath and Great Basins [volume 2] Author: Quigley, Thomas Milton; Arbelbide, S. J. (Sylvia J.) Year: 1997, 2008, 2005 Abstract Quigley, Thomas M.; Arbelbide, Sylvia J., tech. eds. 1997. An assessment of ecosystem components in the interior Columbia basin and portions of the Klamath and Great Basins: volume 2. Gen. Tech. Rep. PNW-GTR-405. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 4 vol. (Quigley, Thomas M., tech. ed.; The Interior Columbia Basin Ecosystem Management Project: Scientific Assessment). The Assessment of Ecosystem Components in the Interior Columbia Basin and Portions of the Klamath and Great Basins provides detailed information about current conditions and trends for the biophysical and social systems within the Basin. This information can be used by land managers to develop broad land management goals and priorities and provides the context for decisions specific to smaller geographic areas. The Assessment area covers about 8 percent of the U.S. land area, 24 percent of the Nations National Forest System lands, 10 percent of the Nations BLM-administered lands, and contains about 1.2 percent of the Nations population. This results in a population density that is less than one-sixth of the U.S. average. The area has experienced recent, rapid population growth and generally has a robust, diverse economy. As compared to historic conditions, the terrestrial, aquatic, forest, and rangeland systems have undergone dramatic changes. Forested landscapes are more susceptible to fire, insect, and disease than under historic conditions. Rangelands are highly susceptible to noxious weed invasion. The disturbance regimes that operate on forest and rangeland have changed substantially, with lethal fires dominating many areas where non-lethal fires were the norm historically. Terrestrial habitats that have experienced the greatest decline include the native grassland, native shrubland, and old forest structures. There are areas within the Assessment area that have higher diversity than others. Aquatic systems are now more fragmented and isolated than historically and the introduction of non-native fish species has complicated current status of native fishes. Core habitat and population centers do remain as building blocks for restoration. Social and economic conditions within the Assessment area vary considerably, depending to a great extent on population, diversity of employment opportunities, and changing demographics. Those counties with the higher population densities and greater diversity of employment opportunities are generally more resilient to economic downturns. This Assessment provides a rich information base, including over 170 mapped themes with associated models and databases, from which future decisions can benefit. Keywords: Columbia basin, biophysical systems, social systems, ecosystem. Title: An assessment of ecosystem components in the interior Columbia Basin and portions of the Klamath and Great Basins [volume 2] Author: Quigley, Thomas Milton; Arbelbide, S. J. (Sylvia J.) Year: 1997, 2008, 2005 Abstract Quigley, Thomas M.; Arbelbide, Sylvia J., tech. eds. 1997. An assessment of ecosystem components in the interior Columbia basin and portions of the Klamath and Great Basins: volume 2. Gen. Tech. Rep. PNW-GTR-405. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 4 vol. (Quigley, Thomas M., tech. ed.; The Interior Columbia Basin Ecosystem Management Project: Scientific Assessment). The Assessment of Ecosystem Components in the Interior Columbia Basin and Portions of the Klamath and Great Basins provides detailed information about current conditions and trends for the biophysical and social systems within the Basin. This information can be used by land managers to develop broad land management goals and priorities and provides the context for decisions specific to smaller geographic areas. The Assessment area covers about 8 percent of the U.S. land area, 24 percent of the Nations National Forest System lands, 10 percent of the Nations BLM-administered lands, and contains about 1.2 percent of the Nations population. This results in a population density that is less than one-sixth of the U.S. average. The area has experienced recent, rapid population growth and generally has a robust, diverse economy. As compared to historic conditions, the terrestrial, aquatic, forest, and rangeland systems have undergone dramatic changes. Forested landscapes are more susceptible to fire, insect, and disease than under historic conditions. Rangelands are highly susceptible to noxious weed invasion. The disturbance regimes that operate on forest and rangeland have changed substantially, with lethal fires dominating many areas where non-lethal fires were the norm historically. Terrestrial habitats that have experienced the greatest decline include the native grassland, native shrubland, and old forest structures. There are areas within the Assessment area that have higher diversity than others. Aquatic systems are now more fragmented and isolated than historically and the introduction of non-native fish species has complicated current status of native fishes. Core habitat and population centers do remain as building blocks for restoration. Social and economic conditions within the Assessment area vary considerably, depending to a great extent on population, diversity of employment opportunities, and changing demographics. Those counties with the higher population densities and greater diversity of employment opportunities are generally more resilient to economic downturns. This Assessment provides a rich information base, including over 170 mapped themes with associated models and databases, from which future decisions can benefit. Keywords: Columbia basin, biophysical systems, social systems, ecosystem. Close

• 25. [Image] An assessment of ecosystem components in the interior Columbia Basin and portions of the Klamath and Great Basins [volume 1]

  	Quigley, Thomas M.; Arbelbide, Sylvia J., tech. eds. 1997. An assessment of ecosystem components in the interior Columbia basin and portions of the Klamath and Great Basins: volume 1. Gen. Tech. Rep. PNW-GTR-405. ...
  	Citation × Citation Citation Abstract Copy Title: An assessment of ecosystem components in the interior Columbia Basin and portions of the Klamath and Great Basins [volume 1] Author: Quigley, Thomas Milton; Arbelbide, S. J. (Sylvia J.) Year: 1997, 2008, 2005 Quigley, Thomas M.; Arbelbide, Sylvia J., tech. eds. 1997. An assessment of ecosystem components in the interior Columbia basin and portions of the Klamath and Great Basins: volume 1. Gen. Tech. Rep. PNW-GTR-405. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 4 vol. (Quigley, Thomas M., tech. ed.; The Interior Columbia Basin Ecosystem Management Project: Scientific Assessment). The Assessment of Ecosystem Components in the Interior Columbia Basin and Portions of the Klamath and Great Basins provides detailed information about current conditions and trends for the biophysical and social systems within the Basin. This information can be used by land managers to develop broad land management goals and priorities and provides the context for decisions specific to smaller geographic areas. The Assessment area covers about 8 percent of the U.S. land area, 24 percent of the Nation's National Forest System lands, 10 percent of the Nation's BLM-administered lands, and contains about 1.2 percent of the Nation's population. This results in a population density that is less than one-sixth of the U.S. average. The area has experienced recent, rapid population growth and generally has a robust, diverse economy. As compared to historic conditions, the terrestrial, aquatic, forest, and rangeland systems have undergone dramatic changes. Forested landscapes are more susceptible to fire, insect, and disease than under historic conditions. Rangelands are highly susceptible to noxious weed invasion. The disturbance regimes that operate on forest and rangeland have changed substantially, with lethal fires dominating many areas where non-lethal fires were the norm historically. Terrestrial habitats that have experienced the greatest decline include the native grassland, native shrubland, and old forest structures. There are areas within the Assessment area that have higher diversity than others. Aquatic systems are now more fragmented and isolated than historically and the introduction of non-native fish species has complicated current status of native fishes. Core habitat and population centers do remain as building blocks for restoration. Social and economic conditions within the Assessment area vary considerably, depending to a great extent on population, diversity of employment opportunities, and changing demographics. Those counties with the higher population densities and greater diversity of employment opportunities are generally more resilient to economic downturns. This Assessment provides a rich information base, including over 170 mapped themes with associated models and databases, from which future decisions can benefit. Keywords: Columbia basin, biophysical systems, social systems, ecosystem. Title: An assessment of ecosystem components in the interior Columbia Basin and portions of the Klamath and Great Basins [volume 1] Author: Quigley, Thomas Milton; Arbelbide, S. J. (Sylvia J.) Year: 1997, 2008, 2005 Quigley, Thomas M.; Arbelbide, Sylvia J., tech. eds. 1997. An assessment of ecosystem components in the interior Columbia basin and portions of the Klamath and Great Basins: volume 1. Gen. Tech. Rep. PNW-GTR-405. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 4 vol. (Quigley, Thomas M., tech. ed.; The Interior Columbia Basin Ecosystem Management Project: Scientific Assessment). The Assessment of Ecosystem Components in the Interior Columbia Basin and Portions of the Klamath and Great Basins provides detailed information about current conditions and trends for the biophysical and social systems within the Basin. This information can be used by land managers to develop broad land management goals and priorities and provides the context for decisions specific to smaller geographic areas. The Assessment area covers about 8 percent of the U.S. land area, 24 percent of the Nation's National Forest System lands, 10 percent of the Nation's BLM-administered lands, and contains about 1.2 percent of the Nation's population. This results in a population density that is less than one-sixth of the U.S. average. The area has experienced recent, rapid population growth and generally has a robust, diverse economy. As compared to historic conditions, the terrestrial, aquatic, forest, and rangeland systems have undergone dramatic changes. Forested landscapes are more susceptible to fire, insect, and disease than under historic conditions. Rangelands are highly susceptible to noxious weed invasion. The disturbance regimes that operate on forest and rangeland have changed substantially, with lethal fires dominating many areas where non-lethal fires were the norm historically. Terrestrial habitats that have experienced the greatest decline include the native grassland, native shrubland, and old forest structures. There are areas within the Assessment area that have higher diversity than others. Aquatic systems are now more fragmented and isolated than historically and the introduction of non-native fish species has complicated current status of native fishes. Core habitat and population centers do remain as building blocks for restoration. Social and economic conditions within the Assessment area vary considerably, depending to a great extent on population, diversity of employment opportunities, and changing demographics. Those counties with the higher population densities and greater diversity of employment opportunities are generally more resilient to economic downturns. This Assessment provides a rich information base, including over 170 mapped themes with associated models and databases, from which future decisions can benefit. Keywords: Columbia basin, biophysical systems, social systems, ecosystem. Close

• 26. [Image] Annual program summary 2004

  	Annual Program Summary and Monitoring Report - FY2004 Table of Contents ANNUAL PROGRAM SUMMARY 1.0 Introduction 3 2.0 Summary of Accomplishments 3 3.0 Budget and Employment 6 4.0 Land ...
  	Citation × Citation Citation Abstract Copy Title: Annual program summary 2004 Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office District Year: 2005 Annual Program Summary and Monitoring Report - FY2004 Table of Contents ANNUAL PROGRAM SUMMARY 1.0 Introduction 3 2.0 Summary of Accomplishments 3 3.0 Budget and Employment 6 4.0 Land Use Allocations within the Klamath Falls Resource Area 6 Late-Successional Reserves and Assessments 8 Matrix 8 5.0 Aquatic Conservation Strategy 9 Riparian Reserves 9 Watershed Analysis and Key Watersheds 9 Watershed Restoration 10 Roads 10 Riparian Habitat Enhancement 10 Stream Restoration 11 6.0 Air Quality 11 7.0 Water and Soils 11 Water - Project Implementation 11 Soils - Project Implementation 12 Water - Inventory and Monitoring 12 Soils -Inventory and Monitoring 13 State-listed Clean Water Act 303d Streams 13 RMP Best Management Practices 13 8.0 Terrestrial Species and Habitat Management 14 Survey and Manage Species 14 Threatened/Endangered Species 14 Northern Spotted Owl 14 Bald Eagle 14 Special Status Species-Animals 15 Peregrine Falcon 15 Yellow Rails 15 Bats 15 Northern Goshawk 15 Oregon Spotted Frog 15 Sage Grouse 16 vii Klamath Falls Resource Area Mollusks 16 Great Gray Owl 16 Special Status Species - Plants 16 Other Species of Concern 17 Neotropical Migratory Landbirds 17 Terrestrial Habitat Management 17 Nest Sites, Activity Centers, and Rookeries 17 Big Game Habitat 19 9.0 Aquatic Species and Habitat Management 19 Threatened/Endangered Species 19 Lost River and Shortnose Suckers 19 Bull Trout 20 Endangered Species Act Consultation 20 Aquatic Habitat Restoration 20 Klamath River Hydroelectric Facility Relicensing 21 10.0 Pathogen, Disease, and Pest Management 21 11.0 Weed Management 22 Inventories 22 Control 22 12.0 Special Areas/Management 23 Wild and Scenic Rivers 23 Wilderness 23 Areas of Critical Environmental Concern 23 Tunnel Creek Special Botanical Area 24 Klamath Canyon ACEC 24 Old Baldy Research Natural Area 24 Wood River Wetland ACEC 24 Environmental Education Areas 25 13.0 Cultural Resources 26 14.0 Visual Resources 26 15.0 Rural Interface Areas 26 16.0 Socioeconomic Conditions 27 Jobs-in-the-Woods 28 17.0 Environmental Justice 30 18.0 Recreation 30 Recreation Pipeline Restoration Funds 30 Recreation Projects 31 viii Annual Program Summary and Monitoring Report - FY2004 Recreation Fee Demonstration Project 31 Status of Recreation Plans 32 Volunteer Activities 32 Tourism 33 19.0 Forest Management and Timber Resources 33 Silvicultural Prescriptions 33 Timber Sale Planning 34 FY 2004 Timber Sale Accomplishments 34 Status of Sold & Awarded Klamath Falls RMP Timber Sales 35 Forest Development Activities 39 Stewardship Contracting 42 20.0 Special Forest Products 42 21.0 Energy and Minerals 43 22.0 Land Tenure Adjustments 44 23.0 Access and Rights-of-Way 45 24.0 Transportation and Roads 45 25.0 Hazardous Materials 46 26.0 Wildfire/Fuels Management 46 27.0 Law Enforcement 47 28.0 Rangeland Resources / Grazing Management 48 Fiscal Year 2004 Summary 49 Fiscal Years 1996-2004 Summary 50 Wild Horse Management 51 29.0 Cadastral Survey 52 30.0 Education and Outreach 52 31.0 Research 56 32.0 Coordination and Consultation 58 Federal Agencies 58 State of Oregon 58 Counties 59 Cities 59 Tribes 59 IX Klamath Falls Resource Area Watershed Councils 59 Chartered Advisory Groups 60 Other Local Coordination and Cooperation 61 33.0 National Environmental Policy Act Analysis and Documentation 63 NEPA documentation 63 Klamath Falls Resource Area Environmental Documentation 63 Protests and Appeals 63 34.0 Plan Evaluations 64 Third Year Evaluation 64 Eighth Year Evaluation 64 35.0 Plan Maintenance 65 36.0 Plan Amendments 72 Plan Revision 76 MONITORING REPORT Introduction 79 All Land Use Allocations 83 Late-Successional Reserves 86 Matrix 88 Riparian Reserves 92 Air Quality 95 Water and Soils 96 Terrestrial Species Habitat 101 Special Status and SEIS Special Attention Species Habitat 106 Aquatic Species Habitat 110 Noxious Weeds 112 Special Areas 113 Wild and Scenic Rivers 115 Cultural Resources Including American Indian Values 116 Visual Resources 118 Rural Interface Areas 119 Socioeconomic Conditions 120 Recreation 121 Forest Management and Timber Resources 121 Special Forest/Natural Products 122 Wildfire / Fuels Management 124 Rangeland Resources / Grazing Management 124 GLOSSARY/ACRONYMS 129 Annual Program Summary and Monitoring Report - FY2004 List of Tables Table 2.1 - Summary of Resource Management Actions, Directions, and Accomplishments 4 Table 2.1 - Summary of Resource Management Actions, Directions, and Accomplishments (Cont.).5 Table 3.1 - Resource Area Budget Fiscal Year 2004 6 Table 4.1 - Land Use Allocation 8 Table 5.1 - Watershed Analysis Schedule 10 Table 5.2-Watershed Analysis Status Fiscal Year 2004 10 Table 6.1 -Air Quality Management Fiscal Year 2004 11 Table 7.1 - Watershed Activity Fiscal Year 2004 12 Table 7.2 - KFRA Clean Water Act 303(d) Water Bodies 13 Table 8.1a - BLM /KFRA Special Status Species Designations Summary -Animals 18 Table 8.1b - BLM (KFRA) Special Status Species Designations Summary - Plants 18 Table 8.2 - Terrestrial Habitat Monitoring Fiscal Year 2004 18 Table 8.3 - Monitoring for Nest Sites, Activity Centers, Rookeries, Special Habitats 18 Table 9.1 -Aquatic Habitat/ Fish Passage Management Fiscal Year 2004 19 Table 11.1 - Managed Weed Species 20 Table 12.1 - Special Management Areas 25 Table 13.1 - Cultural Resources Management Fiscal Year 2004 26 Table 16.1 - Total Payments in Lieu of Taxes and Acres by County for FY 2004 28 Table 16.2 - O&C Payments To Counties FY 2004 29 Table 16.3 - Jobs in the Woods Program Fiscal Year 2004 29 Table 18.1 - Recreation Statistics Fiscal Year 2004 30 Table 18.2 - Recreation Fee Demonstration Project Fiscal Year 2004 32 Table 19.1 - Klamath Falls Timber Sale Volume (MBF) and Acres FY 2004 35 Table 19.2-Timber Volume Sold in FY 2004 36 Table 19.3 - Harvest Activity for FY 2004 36 Table 19.4 - Planned Timber Sales (FY 2005 & 2006) 36 Table 19.5 - Status of Sold and Awarded Timber Sales 37 Table 19.6 - Summary of Volume Sold 38 Table 19.7 -Volume and Acres Sold by Allocations 38 Table 19.8 - Timber Sales Sold by Harvest Types 38 Table 19.9 - Timber Sale Acres Sold by Age Class 39 Table 19.10 - Forest Development Activities 41 Table 20.1 - Special Forest Products Fiscal Year 2004 43 Table 21.1 - Energy and Minerals Management Fiscal Year 2004 44 Table 22.1 - Land Use Tenure Adjustments Fiscal Year 2004 45 Table 24.1 - Roads and Transportation Management Fiscal Year 2004 45 Table 25.1 - Hazardous Materials Management Fiscal Year 2004 46 Table 26.1 - Fire and Fuels Management Fiscal Year 2004 46 Table 27.1 - Law Enforcement Fiscal Year 2004 47 Table 28.1 - Range Resources Management Fiscal Year 2004 48 Table 29.1 -Cadastral Survey Summary Fiscal Year 2004 52 Table 30.1 - Environmental Education/Outreach Program Summary FY2004 54 Table 30.2 - Environmental Education/Outreach Special Events FY2004 55 Table 30.3 - Environmental Education/Outreach Programs & Tours FY 2004 56 Table 32.1 - Challenge Cost Share Fiscal Year 2004 62 XI Klamath Falls Resource Area Table 33.1 - NEPA Analyses and Documentation Fiscal Year 2004 64 Table 36.1 - Redefined Survey and Manage Categories 74 Table M.I - Projects Monitored FY 2004 80 Table M-2 - FY 2004 Implementation Monitoring Selection Categories 81 Table M-3 - Comparison of Projected vs. Actual Harvest Volume (MMBF)/Acres to Date 82 Table M-4 - Timber Sale Volume and Acres Offered (Entire Resource Area) 83 Table M-5 - Timber Sale Monitoring Summary 89 Table M-6 - Post Treatment Stand Characteristics for West Grenada Timber Sale - FY 2004 90 Table M-7 - Status of Watershed Analysis 98 List of Figures Figure 1 - General Location Map 2 Figure 2 - KFRA Land Allocations 7 Xll Title: Annual program summary 2004 Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office District Year: 2005 Annual Program Summary and Monitoring Report - FY2004 Table of Contents ANNUAL PROGRAM SUMMARY 1.0 Introduction 3 2.0 Summary of Accomplishments 3 3.0 Budget and Employment 6 4.0 Land Use Allocations within the Klamath Falls Resource Area 6 Late-Successional Reserves and Assessments 8 Matrix 8 5.0 Aquatic Conservation Strategy 9 Riparian Reserves 9 Watershed Analysis and Key Watersheds 9 Watershed Restoration 10 Roads 10 Riparian Habitat Enhancement 10 Stream Restoration 11 6.0 Air Quality 11 7.0 Water and Soils 11 Water - Project Implementation 11 Soils - Project Implementation 12 Water - Inventory and Monitoring 12 Soils -Inventory and Monitoring 13 State-listed Clean Water Act 303d Streams 13 RMP Best Management Practices 13 8.0 Terrestrial Species and Habitat Management 14 Survey and Manage Species 14 Threatened/Endangered Species 14 Northern Spotted Owl 14 Bald Eagle 14 Special Status Species-Animals 15 Peregrine Falcon 15 Yellow Rails 15 Bats 15 Northern Goshawk 15 Oregon Spotted Frog 15 Sage Grouse 16 vii Klamath Falls Resource Area Mollusks 16 Great Gray Owl 16 Special Status Species - Plants 16 Other Species of Concern 17 Neotropical Migratory Landbirds 17 Terrestrial Habitat Management 17 Nest Sites, Activity Centers, and Rookeries 17 Big Game Habitat 19 9.0 Aquatic Species and Habitat Management 19 Threatened/Endangered Species 19 Lost River and Shortnose Suckers 19 Bull Trout 20 Endangered Species Act Consultation 20 Aquatic Habitat Restoration 20 Klamath River Hydroelectric Facility Relicensing 21 10.0 Pathogen, Disease, and Pest Management 21 11.0 Weed Management 22 Inventories 22 Control 22 12.0 Special Areas/Management 23 Wild and Scenic Rivers 23 Wilderness 23 Areas of Critical Environmental Concern 23 Tunnel Creek Special Botanical Area 24 Klamath Canyon ACEC 24 Old Baldy Research Natural Area 24 Wood River Wetland ACEC 24 Environmental Education Areas 25 13.0 Cultural Resources 26 14.0 Visual Resources 26 15.0 Rural Interface Areas 26 16.0 Socioeconomic Conditions 27 Jobs-in-the-Woods 28 17.0 Environmental Justice 30 18.0 Recreation 30 Recreation Pipeline Restoration Funds 30 Recreation Projects 31 viii Annual Program Summary and Monitoring Report - FY2004 Recreation Fee Demonstration Project 31 Status of Recreation Plans 32 Volunteer Activities 32 Tourism 33 19.0 Forest Management and Timber Resources 33 Silvicultural Prescriptions 33 Timber Sale Planning 34 FY 2004 Timber Sale Accomplishments 34 Status of Sold & Awarded Klamath Falls RMP Timber Sales 35 Forest Development Activities 39 Stewardship Contracting 42 20.0 Special Forest Products 42 21.0 Energy and Minerals 43 22.0 Land Tenure Adjustments 44 23.0 Access and Rights-of-Way 45 24.0 Transportation and Roads 45 25.0 Hazardous Materials 46 26.0 Wildfire/Fuels Management 46 27.0 Law Enforcement 47 28.0 Rangeland Resources / Grazing Management 48 Fiscal Year 2004 Summary 49 Fiscal Years 1996-2004 Summary 50 Wild Horse Management 51 29.0 Cadastral Survey 52 30.0 Education and Outreach 52 31.0 Research 56 32.0 Coordination and Consultation 58 Federal Agencies 58 State of Oregon 58 Counties 59 Cities 59 Tribes 59 IX Klamath Falls Resource Area Watershed Councils 59 Chartered Advisory Groups 60 Other Local Coordination and Cooperation 61 33.0 National Environmental Policy Act Analysis and Documentation 63 NEPA documentation 63 Klamath Falls Resource Area Environmental Documentation 63 Protests and Appeals 63 34.0 Plan Evaluations 64 Third Year Evaluation 64 Eighth Year Evaluation 64 35.0 Plan Maintenance 65 36.0 Plan Amendments 72 Plan Revision 76 MONITORING REPORT Introduction 79 All Land Use Allocations 83 Late-Successional Reserves 86 Matrix 88 Riparian Reserves 92 Air Quality 95 Water and Soils 96 Terrestrial Species Habitat 101 Special Status and SEIS Special Attention Species Habitat 106 Aquatic Species Habitat 110 Noxious Weeds 112 Special Areas 113 Wild and Scenic Rivers 115 Cultural Resources Including American Indian Values 116 Visual Resources 118 Rural Interface Areas 119 Socioeconomic Conditions 120 Recreation 121 Forest Management and Timber Resources 121 Special Forest/Natural Products 122 Wildfire / Fuels Management 124 Rangeland Resources / Grazing Management 124 GLOSSARY/ACRONYMS 129 Annual Program Summary and Monitoring Report - FY2004 List of Tables Table 2.1 - Summary of Resource Management Actions, Directions, and Accomplishments 4 Table 2.1 - Summary of Resource Management Actions, Directions, and Accomplishments (Cont.).5 Table 3.1 - Resource Area Budget Fiscal Year 2004 6 Table 4.1 - Land Use Allocation 8 Table 5.1 - Watershed Analysis Schedule 10 Table 5.2-Watershed Analysis Status Fiscal Year 2004 10 Table 6.1 -Air Quality Management Fiscal Year 2004 11 Table 7.1 - Watershed Activity Fiscal Year 2004 12 Table 7.2 - KFRA Clean Water Act 303(d) Water Bodies 13 Table 8.1a - BLM /KFRA Special Status Species Designations Summary -Animals 18 Table 8.1b - BLM (KFRA) Special Status Species Designations Summary - Plants 18 Table 8.2 - Terrestrial Habitat Monitoring Fiscal Year 2004 18 Table 8.3 - Monitoring for Nest Sites, Activity Centers, Rookeries, Special Habitats 18 Table 9.1 -Aquatic Habitat/ Fish Passage Management Fiscal Year 2004 19 Table 11.1 - Managed Weed Species 20 Table 12.1 - Special Management Areas 25 Table 13.1 - Cultural Resources Management Fiscal Year 2004 26 Table 16.1 - Total Payments in Lieu of Taxes and Acres by County for FY 2004 28 Table 16.2 - O&C Payments To Counties FY 2004 29 Table 16.3 - Jobs in the Woods Program Fiscal Year 2004 29 Table 18.1 - Recreation Statistics Fiscal Year 2004 30 Table 18.2 - Recreation Fee Demonstration Project Fiscal Year 2004 32 Table 19.1 - Klamath Falls Timber Sale Volume (MBF) and Acres FY 2004 35 Table 19.2-Timber Volume Sold in FY 2004 36 Table 19.3 - Harvest Activity for FY 2004 36 Table 19.4 - Planned Timber Sales (FY 2005 & 2006) 36 Table 19.5 - Status of Sold and Awarded Timber Sales 37 Table 19.6 - Summary of Volume Sold 38 Table 19.7 -Volume and Acres Sold by Allocations 38 Table 19.8 - Timber Sales Sold by Harvest Types 38 Table 19.9 - Timber Sale Acres Sold by Age Class 39 Table 19.10 - Forest Development Activities 41 Table 20.1 - Special Forest Products Fiscal Year 2004 43 Table 21.1 - Energy and Minerals Management Fiscal Year 2004 44 Table 22.1 - Land Use Tenure Adjustments Fiscal Year 2004 45 Table 24.1 - Roads and Transportation Management Fiscal Year 2004 45 Table 25.1 - Hazardous Materials Management Fiscal Year 2004 46 Table 26.1 - Fire and Fuels Management Fiscal Year 2004 46 Table 27.1 - Law Enforcement Fiscal Year 2004 47 Table 28.1 - Range Resources Management Fiscal Year 2004 48 Table 29.1 -Cadastral Survey Summary Fiscal Year 2004 52 Table 30.1 - Environmental Education/Outreach Program Summary FY2004 54 Table 30.2 - Environmental Education/Outreach Special Events FY2004 55 Table 30.3 - Environmental Education/Outreach Programs & Tours FY 2004 56 Table 32.1 - Challenge Cost Share Fiscal Year 2004 62 XI Klamath Falls Resource Area Table 33.1 - NEPA Analyses and Documentation Fiscal Year 2004 64 Table 36.1 - Redefined Survey and Manage Categories 74 Table M.I - Projects Monitored FY 2004 80 Table M-2 - FY 2004 Implementation Monitoring Selection Categories 81 Table M-3 - Comparison of Projected vs. Actual Harvest Volume (MMBF)/Acres to Date 82 Table M-4 - Timber Sale Volume and Acres Offered (Entire Resource Area) 83 Table M-5 - Timber Sale Monitoring Summary 89 Table M-6 - Post Treatment Stand Characteristics for West Grenada Timber Sale - FY 2004 90 Table M-7 - Status of Watershed Analysis 98 List of Figures Figure 1 - General Location Map 2 Figure 2 - KFRA Land Allocations 7 Xll Close

• 27. [Image] The Oregon conservation strategy

  	v, 419 p.; col.ill.; col.maps; "February 2006"; Foreword by Marla Rae, Chair, Oregon Fish and Wildlife Commission
  	Citation × Citation Citation Abstract Copy Title: The Oregon conservation strategy Year: 2006 v, 419 p.; col.ill.; col.maps; "February 2006"; Foreword by Marla Rae, Chair, Oregon Fish and Wildlife Commission Title: The Oregon conservation strategy Year: 2006 v, 419 p.; col.ill.; col.maps; "February 2006"; Foreword by Marla Rae, Chair, Oregon Fish and Wildlife Commission Close

• 28. [Image] Range maps of terrestrial species in the interior Columbia River basin and Northern portions of the Klamath and Great Basins

  	Abstract Marcot, Bruce G.; Wales, Barbara C; Demmer, Rick. 2003. Range maps of terrestrial species in the interior Columbia River basin and northern portions of the Klamath and Great Basins. Gen. Tech. ...
  	Citation × Citation Citation Abstract Copy Title: Range maps of terrestrial species in the interior Columbia River basin and Northern portions of the Klamath and Great Basins Author: Marcot, Bruce G. Year: 2003, 2005, 2004 Abstract Marcot, Bruce G.; Wales, Barbara C; Demmer, Rick. 2003. Range maps of terrestrial species in the interior Columbia River basin and northern portions of the Klamath and Great Basins. Gen. Tech. Rep. PNW-GTR-583. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 304 p. Current range distribution maps are presented for 14 invertebrate, 26 amphibian, 26 reptile, 339 bird, and 125 mammal species and selected subspecies (530 total taxa) of the interior Columbia River basin and northern portions of the Klamath and Great Basins in the United States. Also presented are maps of historical ranges of 3 bird and 10 mammal species, and 6 maps of natural areas designated by federal agencies and other organizations. The species range maps were derived from a variety of publications and from expert review and unpublished data, and thus differ in degree of accuracy and resolution. The species maps are available in computer versions and are indexed herein by common and scientific names. Keywords: Maps, species range, species distribution, wildlife, invertebrates, arthropods, amphibians, reptiles, birds, mammals, bats, biodiversity, endemism, natural areas, interior Columbia River basin, Klamath Basin, Great Basin. Title: Range maps of terrestrial species in the interior Columbia River basin and Northern portions of the Klamath and Great Basins Author: Marcot, Bruce G. Year: 2003, 2005, 2004 Abstract Marcot, Bruce G.; Wales, Barbara C; Demmer, Rick. 2003. Range maps of terrestrial species in the interior Columbia River basin and northern portions of the Klamath and Great Basins. Gen. Tech. Rep. PNW-GTR-583. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 304 p. Current range distribution maps are presented for 14 invertebrate, 26 amphibian, 26 reptile, 339 bird, and 125 mammal species and selected subspecies (530 total taxa) of the interior Columbia River basin and northern portions of the Klamath and Great Basins in the United States. Also presented are maps of historical ranges of 3 bird and 10 mammal species, and 6 maps of natural areas designated by federal agencies and other organizations. The species range maps were derived from a variety of publications and from expert review and unpublished data, and thus differ in degree of accuracy and resolution. The species maps are available in computer versions and are indexed herein by common and scientific names. Keywords: Maps, species range, species distribution, wildlife, invertebrates, arthropods, amphibians, reptiles, birds, mammals, bats, biodiversity, endemism, natural areas, interior Columbia River basin, Klamath Basin, Great Basin. Close

• 29. [Article] Effects of Arbuscular Mycorrhizal Fungal Infection and Common Mycelial Network Formation on Invasive Plant Competition

  Understanding the biotic factors influencing invasive plant performance is essential for managing invaded land and preventing further exotic establishment and spread. I studied how competition between ...

  Citation × Citation Citation Abstract Copy Title: Effects of Arbuscular Mycorrhizal Fungal Infection and Common Mycelial Network Formation on Invasive Plant Competition Author: Workman, Rachael Elizabeth Year: 2014 Understanding the biotic factors influencing invasive plant performance is essential for managing invaded land and preventing further exotic establishment and spread. I studied how competition between both conspecifics and native co-habitants and arbuscular mycorrhizal fungal (AMF) impacted the success of the invasive bunchgrass Brachypodium sylvaticumin early growth stages. I examined whether invasive plants performed and competed differently when grown in soil containing AMF from adjacent invaded and noninvaded ranges in order to determine the contribution of AMF to both monoculture stability and spread of the invasive to noninvaded territory. I also directly manipulated common mycelial network (CMN) formation by AMF to determine hyphal network contribution to competitive interactions. I found that invasive plants performed most poorly (as indicated by decreased chlorophyll content, size and shoot dry mass) in invaded range soil against conspecifics. This could be two-pronged evidence for existing biotic pressure on the invasives to expand into adjacent noninvaded ranges. I also found a negative effect of AMF colonization and invasive plant performance, potentially indicating deleterious plant-soil feedbacks which could help maintain plant biodiversity at a community level. CMN effects were found to be interactive with root competition and directly affected the performance and nutrient status of B. sylvaticum. Although no direct correlations between AMF colonization levels and competition were found, CMN presence contributed significantly to plant growth and nutrient status. Therefore AMF, through infection and CMN formation, may be able to influence invasive plant growth and spread in the field. Title: Effects of Arbuscular Mycorrhizal Fungal Infection and Common Mycelial Network Formation on Invasive Plant Competition Author: Workman, Rachael Elizabeth Year: 2014 Understanding the biotic factors influencing invasive plant performance is essential for managing invaded land and preventing further exotic establishment and spread. I studied how competition between both conspecifics and native co-habitants and arbuscular mycorrhizal fungal (AMF) impacted the success of the invasive bunchgrass Brachypodium sylvaticumin early growth stages. I examined whether invasive plants performed and competed differently when grown in soil containing AMF from adjacent invaded and noninvaded ranges in order to determine the contribution of AMF to both monoculture stability and spread of the invasive to noninvaded territory. I also directly manipulated common mycelial network (CMN) formation by AMF to determine hyphal network contribution to competitive interactions. I found that invasive plants performed most poorly (as indicated by decreased chlorophyll content, size and shoot dry mass) in invaded range soil against conspecifics. This could be two-pronged evidence for existing biotic pressure on the invasives to expand into adjacent noninvaded ranges. I also found a negative effect of AMF colonization and invasive plant performance, potentially indicating deleterious plant-soil feedbacks which could help maintain plant biodiversity at a community level. CMN effects were found to be interactive with root competition and directly affected the performance and nutrient status of B. sylvaticum. Although no direct correlations between AMF colonization levels and competition were found, CMN presence contributed significantly to plant growth and nutrient status. Therefore AMF, through infection and CMN formation, may be able to influence invasive plant growth and spread in the field. Close

• 30. [Article] The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem

  Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of ...

  Citation × Citation Citation Abstract Copy Title: The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem Author: Diemer, Geoffrey Scott Year: 2014 Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid- and thermo-tolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution.Metagenomic surveys of natural virus assemblages, including the survey of BSL, have revealed that the diversity within the virosphere far exceeds what has currently been determined through the detailed study of viruses that are relevant to human health and agriculture. The number of as-yet-uncharacterized virus protein families present in the BSL assemblage was estimated by clustering analysis. Genomic context analysis of the predicted viral protein sequences in the BSL dataset indicates that most of the putative uncharacterized proteins are endemic or unique to BSL, and are largely harbored by known virus types. A comparative metagenomic analysis approach identified a set of conserved, yet uncharacterized BSL protein sequences that are commonly found in other similar and dissimilar environments.New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA and DNA virus types, was detected in the BSL metagenome. Similar genomes were subsequently detected in other ecosystems around the globe. The discovery of this new virus genome dramatically underscores the scope and importance of genetic mobility and genomic mosaicism as major forces driving the evolution of viruses.The analyses conducted herein demonstrate the many ways in which viral metagenomic sequence data may be utilized to not only evaluate the composition of a natural virus assemblage, but to discover new viral genes, and to better understand the dynamics of both genomic and structural evolution within the virosphere. Title: The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem Author: Diemer, Geoffrey Scott Year: 2014 Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid- and thermo-tolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution.Metagenomic surveys of natural virus assemblages, including the survey of BSL, have revealed that the diversity within the virosphere far exceeds what has currently been determined through the detailed study of viruses that are relevant to human health and agriculture. The number of as-yet-uncharacterized virus protein families present in the BSL assemblage was estimated by clustering analysis. Genomic context analysis of the predicted viral protein sequences in the BSL dataset indicates that most of the putative uncharacterized proteins are endemic or unique to BSL, and are largely harbored by known virus types. A comparative metagenomic analysis approach identified a set of conserved, yet uncharacterized BSL protein sequences that are commonly found in other similar and dissimilar environments.New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA and DNA virus types, was detected in the BSL metagenome. Similar genomes were subsequently detected in other ecosystems around the globe. The discovery of this new virus genome dramatically underscores the scope and importance of genetic mobility and genomic mosaicism as major forces driving the evolution of viruses.The analyses conducted herein demonstrate the many ways in which viral metagenomic sequence data may be utilized to not only evaluate the composition of a natural virus assemblage, but to discover new viral genes, and to better understand the dynamics of both genomic and structural evolution within the virosphere. Close