We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).

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Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.

Publisher Summary This chapter reviews the rates at which Coarse Woody Debris (CWD) is added and removed from ecosystems, the biomass found in streams and forests, and many functions that CWD serves. CWD is an important component of temperate stream and forest ecosystems and is added to the ecosystem by numerous mechanisms, including wind, fire, insect attack, pathogens, competition, and geomorphic processes. Many factors control the rate at which CWD decomposes, including temperature, moisture, the internal gas composition of CWD, substrate quality, the size of the CWD, and the types of organisms involved. The mass of CWD in an ecosystem ideally represents the balance between addition and loss. In reality, slow decomposition rates and erratic variations in input of CWD cause the CWD mass to deviate markedly from steady-state projections. Many differences correspond to forest type, with deciduous-dominated systems having generally lower biomass than conifer-dominated systems. Stream size also influences CWD mass in lotic ecosystems, while successional stage dramatically influences CWD mass in boat aquatic and terrestrial settings. This chapter reviews many of these functions and concludes that CWD is an important functional component of stream and forest ecosystems. Better scientific understanding of these functions and the natural factors influencing CWD dynamics should lead to more enlightened management practices.

Ecology of Coarse Woody Debris in Temperate Ecosystems

▪ Abstract Local habitat and biological diversity of streams and rivers are strongly influenced by landform and land use within the surrounding valley at multiple scales. However, empirical associations between land use and stream response only varyingly succeed in implicating pathways of influence. This is the case for a number of reasons, including (a) covariation of anthropogenic and natural gradients in the landscape; (b) the existence of multiple, scale-dependent mechanisms; (c) nonlinear responses; and (d) the difficulties of separating present-day from historical influences. Further research is needed that examines responses to land use under different management strategies and that employs response variables that have greater diagnostic value than many of the aggregated measures in current use. In every respect, the valley rules the stream.      H.B.N. Hynes (1975)

http://deq.idaho.gov/media/525804-Landscapes_Riverscapes_Influence_landuse_stream_ecosystems_Allan_2004.pdf

Landscapes and Riverscapes: The Influence of Land Use on Stream Ecosystems

I. CONTEXT * The Ecosystem Concept * Earth's Climate System * Geology and Soils * II. MECHANISMS * Terrestrial Water and Energy Balance * Carbon Input to Terrestrial Ecosystems * Terrestrial Production Processes * Terrestrial Decomposition * Terrestrial Plant Nutrient Use * Terrestrial Nutrient Cycling * Aquatic Carbon and Nutrient Cycling * Trophic Dynamics * Community Effects on Ecosystem Processes * III. PATTERNS * Temporal Dynamics * Landscape Heterogeneity and Ecosystem Dynamics * IV. INTEGRATION * Global Biogeochemical Cycles * Managing and Sustaining Ecosystem * Abbreviations * Glossary * References

Principles of Terrestrial Ecosystem Ecology

The flow regime is regarded by many aquatic ecologists to be the key driver of river and floodplain wet- land ecosystems. We have focused this literature review around four key principles to highlight the important mech- anisms that link hydrology and aquatic biodiversity and to illustrate the consequent impacts of altered flow regimes: Firstly, flow is a major determinant of physical habitat in streams, which in turn is a major determinant of biotic com- position; Secondly, aquatic species have evolved life history strategies primarily in direct response to the natural flow regimes; Thirdly, maintenance of natural patterns of longitu- dinal and lateral connectivity is essential to the viability of populations of many riverine species; Finally, the invasion and success of exotic and introduced species in rivers is facilitated by the alteration of flow regimes. The impacts of flow change are manifest across broad taxonomic groups including riverine plants, invertebrates, and fish. Despite growing recognition of these relationships, ecologists still struggle to predict and quantify biotic responses to altered flow regimes. One obvious difficulty is the ability to distin- guish the direct effects of modified flow regimes from im- pacts associated with land-use change that often accom- panies water resource development. Currently, evidence about how rivers function in relation to flow regime and the flows that aquatic organisms need exists largely as a series of untested hypotheses. To overcome these problems, aquatic science needs to move quickly into a manipulative or experimental phase, preferably with the aims of restora- tion and measuring ecosystem response.

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Basic principles and ecological consequences of altered flow regimes for aquatic biodiversity.

From headwaters to mouth, the physical variables within a river system present a continuous gradient of physical conditions. This gradient should elicit a series of responses within the constituent...

The River Continuum Concept

The detritus pathway is that in which plant or animal material dies and is then attacked by microorganisms. More of the energy fixed by autotrophic organisms is probably transferred through this route than through the grazing pathway (98). Detritus cannot be precisely defined in terms of its chemical composition or associated microorganisms. As an operational definition, Boling et al (16) defined it as all particulate (>0.45-μm particle diameter) organic matter (reduced carbon compounds) together with associated microbiota—fungi, bacteria, protozoa, and other microinvertebrates. Microbes are included as part of the detritus because the relationship between them and the organic substrate is so intimate that independence is never observed in nature; also, efficient separation techniques applicable to field-collected detritus are nonexistent. The role of detritus in aquatic ecosystems was discussed in two recent symposia (1, 109). Studies of biological decomposition are interdisciplinary in nature and were a theme of the International Biological Programs in freshwater, marine, and terrestrial projects (1). Thus, with the upsurge of interest in this topic, it is timely to review contributions, especiajly on the

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Detritus Processing by Macroinvertebrates in Stream Ecosystems

Four significant areas of thought, (1) the holistic approach, (2) the linkage between streams and their terrestrial setting, (3) material cycling in open systems, and (4) biotic interactions and in...

Developments in Stream Ecosystem Theory

https://www.fs.fed.us/pnw/pubs/pnw_gtr118.pdf

James R. Sedell

Papers

The River Continuum Concept

Ecology of Coarse Woody Debris in Temperate Ecosystems

Detritus Processing by Macroinvertebrates in Stream Ecosystems

Developments in Stream Ecosystem Theory

Ecological Characteristics of Old-Growth Douglas-Fir Forests