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.

▪ 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.

/pdf/basic-principles-and-ecological-consequences-of-altered-flow-4u5bupofua.pdf

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

This book is written as a reference on organic substances in natural waters and as a supplementary text for graduate students in water chemistry. The chapters address five topics: amount, origin, nature, geochemistry, and characterization of organic carbon. Of these topics, the main themes are the amount and nature of dissolved organic carbon in natural waters (mainly fresh water, although seawater is briefly discussed). It is hoped that the reader is familiar with organic chemistry, but it is not necessary. The first part of the book is a general overview of the amount and general nature of dissolved organic carbon. Over the past 10 years there has been an exponential increase in knowledge on organic substances in water, which is the result of money directed toward the research of organic compounds, of new methods of analysis (such as gas chromatography and mass spectrometry), and most importantly, the result of more people working in this field. Because of this exponential increase in knowledge, there is a need to pull together and summarize the data that has accumulated from many disciplines over the last decade.

Organic geochemistry of natural waters

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

Studies were conducted in four distinct geographic areas (biomes/sites) in northern United States to examine changes in key ecosystem parameters: benthic organic matter (BOM), transported organic matter (TOM), community production and respiration, leaf pack decomposition, and functional feeding-group composition along gradients of increasing stream size. Four stations ranging from headwaters (1st or 2nd order) to midsized rivers (5th to 7th order) were examined at each site using comparable methods. The results for each parameter are presented and discussed in light of the River Continuum Concept of Vannote et al. (1980). The postulated gradual change in a stream ecosystem's structure and function is supported by this study. However, regional and local deviations occur as a result of variations in the influence of: (1) watershed climate and geology, (2) riparian conditions, (3) tributaries, and (4) location-specific lithology and geomorphology. In partic- ular, the continuum framework must be visualized as a sliding scale which is shifted upstream or downstream depending on macroenvironmental forces (1 and 2) or reset following the application of more localized "micro"-environmental influences (3 and 4). Analysis of interactions between BOM and TOM permitted evaluation of stream retentiveness for organic matter. Headwaters generally were most retentive and downstream reaches the least. Estimates of organic matter turnover times ranged between 0.2 and 14 yr, and commonly were 1-4 yr. Both turnover times and distances were deter- mined primarily by the interaction between current velocity and stream retention. Biological processes played a secondary role. However, the streams varied considerably in their spiraling of organic matter due to differences in the interplay between retentiveness and biological activity. Differences in the relative importance of retention mechanisms along the continuum suggest that headwater stream ecosystems may be functionally more stable, at least to physical disturbances, than are their inter- mediate river counterparts.

Interbiome comparison of stream ecosystem dynamics

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

Lotic ecologists share a major goal of explaining the distribution and abundance of biota in the world's rivers and streams, and of predicting how this biota will respond to change in fluvial ecosystems We discuss five areas of research that would contribute to our pursuit of this goal For mechanistic understanding of lotic community dynamics, we need more information on: 1 Physical conditions impinging on lotic biota, measured on temporal and spatial scales relevant to the organisms 2 Responses of lotic biota to discharge fluctuations, including the processes that mediate com- munity recovery following resets caused by spates or droughts 3 Movements of lotic organisms that mediate gene flow, resource tracking, and multilevel species interactions

Biotic and abiotic controls in river and stream communities

Studies were conducted at three locations in the Lower Salmon River, Idaho (USA) and at one Upper Salmon "calibration" site to extend results of previous research (headwater through 5-6th-order [1-814 links] streams) to an 8th-order (15,000 links) river. Transported organic matter (TOM) generally increased downstream. Coarse TOM was prevalent only in the upper 50 km of the system, and ultrafine was the predominant particulate component throughout the system. Stored (benthic) organic matter (OM) was highest in the headwaters and showed a progressive downstream decrease. The headwaters were highly retentive of coarse particulate organic matter (CPOM) but much less so of the fine and ultrafine fractions. Transported and stored OM approached a balance only in the lowermost (deeper) reaches of the river system. Analyses of the components of ecosystem metabolism revealed that gross primary production and respiration (R) both showed a general downstream increase. Overall, the net metabolism measurements showed t...

Colbert E. Cushing

Papers

The River Continuum Concept

Interbiome comparison of stream ecosystem dynamics

Developments in Stream Ecosystem Theory

Biotic and abiotic controls in river and stream communities

Stream Ecosystem Dynamics of the Salmon River, Idaho: An 8th-Order System