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/).

/pdf/construction-of-escherichia-coli-k-12-in-frame-single-gene-4c68fx6pb1.pdf

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

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time. SDMs are now widely used across terrestrial, freshwater, and marine realms. Differences in methods between disciplines reflect both differences in species mobility and in “established use.” Model realism and robustness is influenced by selection of relevant predictors and modeling method, consideration of scale, how the interplay between environmental and geographic factors is handled, and the extent of extrapolation. Current linkages between SDM practice and ecological theory are often weak, hindering progress. Remaining challenges include: improvement of methods for modeling presence-only data and for model selection and evaluation; accounting for biotic interactions; and assessing model uncertainty.

/pdf/species-distribution-models-ecological-explanation-and-1szux2yl31.pdf

Species Distribution Models: Ecological Explanation and Prediction Across Space and Time

Acts in what Hutchinson (1965) has called the 'ecological theatre' are played out on various scales of space and time. To understand the drama, we must view it on the appropriate scale. Plant ecologists long ago recognized the importance of sampling scale in their descriptions of the dispersion or distribution of species (e.g. Greig-Smith, 1952). However, many ecologists have behaved as if patterns and the processes that produce them are insensitive to differences in scale and have designed their studies with little explicit attention to scale. Kareiva & Andersen (1988) surveyed nearly 100 field experiments in community ecology and found that half were conducted on plots no larger than 1 m in diameter, despite considerable differences in the sizes and types of organisms studied. Investigators addressing the same questions have often conducted their studies on quite different scales. Not surprisingly, their findings have not always matched, and arguments have ensued. The disagreements among conservation biologists over the optimal design of nature reserves (see Simberloff, 1988) are at least partly due to a failure to appreciate scaling differences among organisms. Controversies about the role of competition in structuring animal communities (Schoener, 1982; Wiens, 1983, 1989) or about the degree of coevolution in communities (Connell, 1980; Roughgarden, 1983) may reflect the

https://www.jstor.org/stable/info/2389612

Spatial Scaling in Ecology

Human alteration of the global environment has triggered the sixth major extinction event in the history of life and caused widespread changes in the global distribution of organisms. These changes in biodiversity alter ecosystem processes and change the resilience of ecosystems to environmental change. This has profound consequences for services that humans derive from ecosystems. The large ecological and societal consequences of changing biodiversity should be minimized to preserve options for future solutions to global environmental problems.

Consequences of changing biodiversity

https://www.jstor.org/stable/10.1641/0006-3568%282002%29052%5B0905%3AUPADLO%5D2.0.CO%3B2

Understanding Processes and Downstream Linkages of Headwater Systems

In this paper we review, develop, and differentiate among concepts associated with environmental patterning (patch, division, and heterogeneity), spatial and temporal scales of ecological processes (ecological neighborhoods), and responses of organisms to environmental patterning (relative patch size, relative patch duration, relative patch isolation, and grain response). We generalize the concept of ecological neighborhoods to represent regions of activity or influence during periods of time appropriate to particular ecological processes. Therefore, there is no single ecological neighborhood for any given organism, but rather a number of neighborhoods, each appropriate to different processes. Neighborhood sizes can be estimated by examining the cumulative distribution of activity or influence of an organism as a function of increasingly large spatial units. The spatial and temporal dimensions of neighborhoods provide the scales necessary for assessing environmental patterning relative to particular ecological processes for a given species. Consistent application of the neighborhood concept will assist in the choice of appropriate study units, comparisons among different studies, and comparisons between empirical studies and theoretical postulates.

Ecological neighborhoods: scaling environmental patterns

Studies of the effects of cross-habitat resource subsidies have been a feature of food web ecology over the past decade. To date, most studies have focused on demonstrating the magnitude of a subsidy or documenting its effect in the recipient habitat. Ecologists have yet to develop a satisfactory framework for predicting the magnitude of these effects. We used 115 data sets from 32 studies to compare consumer responses to resource subsidies across recipient habitat type, trophic level, and functional group. Changes in consumer density or biomass in response to subsidies were inconsistent across habitats, trophic, and functional groups. Responses in stream cobble bar and coastline habitats were larger than in other habitats. Contrary to expectation, the magnitude of consumer response was not affected by recipient habitat productivity or the ratio of productivity between donor and recipient habitats. However, consumer response was significantly related to the ratio of subsidy resources to equivalent resources in the recipient habitat. Broad contrasts in productivity are modified by subsidy type, vector, and the physical and biotic characteristics of both donor and recipient habitats. For this reason, the ratio of subsidy to equivalent resources is a more useful tool for predicting the possible effect of a subsidy than coarser contrasts of in situ productivity. The commonness of subsidy effects suggests that many ecosystems need to be studied as open systems.

https://www.jstor.org/stable/pdfplus/27651075.pdf

Meta-analysis: trophic level, habitat, and productivity shape the food web effects of resource subsidies

Many species of detritivorous invertebrates in small streams depend almost entirely on inputs of leaf litter for their nutritional requirements, however the concentration of this resource varies considerably seasonally. An experiment designed to test the hy- pothesis that productivity of coarse particle detritus feeders (shredders) is seasonally food limited was performed using replicate streamside channels that received one of three input rates of whole leaf detritus (rates equal to those naturally falling into montane streams, and two levels of increased inputs). Seven of the nine common shredder species attained significantly higher adult mass, higher densities, or both when food was supplemented. Larval densities of Malenka spp. and Brillia retifinis were significantly higher when additional food was added. Brillia retifinis densities were more than 10 x greater in high food additions than in the "natural" treatment; B. retifinis apparently fills a role as a fugitive in this system and is better able to track shifts in resource abundance by virtue of its short generation time. Zapada cinctipes and Z. haysi were more dense in high and intermediate food input treatments during the last half of the summer. Other taxa had nonsignificant trends to higher densities when extra food was provided. Most of the change in benthic densities can be attributed to decreased rates of emigration with increased food supply. Six of the eight taxa for which adult mass at emergence was measured were significantly more massive (4-46%) when food was added. Both sexes exhibited this increase in mass, but females gained proportionally more in most species. There were no detectable changes in the timing of adult emergence due to food manipulations. The biomass of most taxa increased in proportion to the overall increase in biomass of the common coarse-detritus consumers. The main exceptions to that pattern were a disproportionate increase in the percentage of the biomass represented by Brillia retifinis and a decrease in the representation of Zapada cinctipes. The responses of this community to food supplementation demonstrate food limitation of detritivores. The exponential increase in benthic biomass under food addition shows the scope for productivity if food were not limiting. These coexisting species benefitted from enhanced food supply on a spatial scale that is relevant for population level processes. The large seasonal variation in resource abundance under natural conditions creates bot- tlenecks during periods of low food supply, which constrain subsequent production even during periods when food is abundant.

Seasonal Food Limitation of Detritivores in a Montane Stream: An Experimental Test

Headwater streams make up a large proportion of the total length and watershed area of fluvial networks, and are partially characterized by the large volume of organic matter (large wood, detritus, and dis- solved organic matter) and invertebrate inputs from the riparian forest, relative to stream size. Much of those inputs are exported to downstream reaches through time where they potentially subsidize river communities. The relative rates, timing, and conversion processes that carry inputs from small streams to downstream rea- ches are reasonably well quantified. For example, larger particles are converted to smaller particles, which are more easily exported. Also, dissolved organic matter and surface biofilms are converted to larger particles which can be more easily intercepted by consumers. However, the quality of these materials as it affects biological activity downstream is not well known, nor is the extent to which timing permits biological use of those parti- cles. These ecological unknowns need to be resolved. Further, land uses may disrupt and diminish material transport to downstream reaches by removing sources (e.g., forest harvest), by affecting transport and decompo- sition processes (e.g., flow regulation, irrigation, changes in biotic communities), and by altering mechanisms of storage within headwaters (e.g., channelization). We present conceptual models of energy and nutrient fluxes that outline small stream processes and pathways important to downstream communities, and we identify infor- mational gaps that, if filled, could significantly advance the understanding of linkages between headwater streams and larger rivers. The models, based on empirical evidence and best professional judgment, suggest that navigable waters are significantly influenced by headwater streams through hydrological and ecological connec- tivities, and land use can dramatically influence these natural connectivities, impacting downstream riverine ecosystems.

http://mostreamteam.org/documents/research/function/ecolinks.pdf

John S. Richardson

Papers

Understanding Processes and Downstream Linkages of Headwater Systems

Ecological neighborhoods: scaling environmental patterns

Meta-analysis: trophic level, habitat, and productivity shape the food web effects of resource subsidies

Seasonal Food Limitation of Detritivores in a Montane Stream: An Experimental Test

Ecological linkages between headwaters and downstream ecosystems: Transport of organic matter, invertebrates, and wood down headwater channels