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.

The chemical composition of natural water is derived from many different sources of solutes, including gases and aerosols from the atmosphere, weathering and erosion of rocks and soil, solution or precipitation reactions occurring below the land surface, and cultural effects resulting from human activities. Broad interrelationships among these processes and their effects can be discerned by application of principles of chemical thermodynamics. Some of the processes of solution or precipitation of minerals can be closely evaluated by means of principles of chemical equilibrium, including the law of mass action and the Nernst equation. Other processes are irreversible and require consideration of reaction mechanisms and rates. The chemical composition of the crustal rocks of the Earth and the composition of the ocean and the atmosphere are significant in evaluating sources of solutes in natural freshwater. The ways in which solutes are taken up or precipitated and the amounts present in solution are influenced by many environmental factors, especially climate, structure and position of rock strata, and biochemical effects associated with life cycles of plants and animals, both microscopic and macroscopic. Taken together and in application with the further influence of the general circulation of all water in the hydrologic cycle, the chemical principles and environmental factors form a basis for the developing science of natural-water chemistry. Fundamental data used in the determination of water quality are obtained by the chemical analysis of water samples in the laboratory or onsite sensing of chemical properties in the field. Sampling is complicated by changes in the composition of moving water and by the effects of particulate suspended material. Some constituents are unstable and require onsite determination or sample preservation. Most of the constituents determined are reported in gravimetric units, usually milligrams per liter or milliequivalents

Study and Interpretation of the Chemical Characteristics of Natural Water

This paper contrasts the natural and anthropogenic controls on the conversion of unreactive N2 to more reactive forms of nitrogen (Nr). A variety of data sets are used to construct global N budgets for 1860 and the early 1990s and to make projections for the global N budget in 2050. Regional N budgets for Asia, North America, and other major regions for the early 1990s, as well as the marine N budget, are presented to highlight the dominant fluxes of nitrogen in each region. Important findings are that human activities increasingly dominate the N budget at the global and at most regional scales, the terrestrial and open ocean N budgets are essentially dis- connected, and the fixed forms of N are accumulating in most environmental reservoirs. The largest uncertainties in our understanding of the N budget at most scales are the rates of natural biological nitrogen fixation, the amount of Nr storage in most environmental reservoirs, and the production rates of N2 by denitrification.

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Nitrogen cycles: past, present, and future

Evolution and measurement of species diversity

As the largest pool of terrestrial organic carbon, soils interact strongly with atmospheric composition, climate, and land cover change. Our capacity to predict and ameliorate the consequences of global change depends in part on a better understanding of the distributions and controls of soil organic carbon (SOC) and how vegetation change may affect SOC distributions with depth. The goals of this paper are (1) to examine the association of SOC content with climate and soil texture at different soil depths; (2) to test the hypothesis that vegetation type, through patterns of allocation, is a dominant control on the vertical distribution of SOC; and (3) to estimate global SOC storage to 3 m, including an analysis of the potential effects of vegetation change on soil carbon storage. We based our analysis on .2700 soil profiles in three global databases supplemented with data for climate, vegetation, and land use. The analysis focused on mineral soil layers. Plant functional types significantly affected the vertical distribution of SOC. The per- centage of SOC in the top 20 cm (relative to the first meter) averaged 33%, 42%, and 50% for shrublands, grasslands, and forests, respectively. In shrublands, the amount of SOC in the second and third meters was 77% of that in the first meter; in forests and grasslands, the totals were 56% and 43%, respectively. Globally, the relative distribution of SOC with depth had a slightly stronger association with vegetation than with climate, but the opposite was true for the absolute amount of SOC. Total SOC content increased with precipitation and clay content and decreased with temperature. The importance of these controls switched with depth, climate dominating in shallow layers and clay content dominating in deeper layers, possibly due to increasing percentages of slowly cycling SOC fractions at depth. To control for the effects of climate on vegetation, we grouped soils within climatic ranges and compared distributions for vegetation types within each range. The percentage of SOC in the top 20 cm relative to the first meter varied from 29% in cold arid shrublands to 57% in cold humid forests and, for a given climate, was always deepest in shrublands, inter- mediate in grasslands, and shallowest in forests ( P , 0.05 in all cases). The effect of vegetation type was more important than the direct effect of precipitation in this analysis. These data suggest that shoot/root allocations combined with vertical root distributions, affect the distribution of SOC with depth. Global SOC storage in the to p3mo fsoil was 2344 Pg C, or 56% more than the 1502 Pg estimated for the first meter (which is similar to the total SOC estimates of 1500-1600 Pg made by other researchers). Global totals for the second and third meters were 491 and 351 Pg C, and the biomes with the most SOC at 1-3 m depth were tropical evergreen forests (158 Pg C) and tropical grasslands/savannas (146 Pg C). Our work suggests that plant functional types, through differences in allocation, help to control SOC distributions with depth in the soil. Our analysis also highlights the potential importance of vegetation change and SOC pools for carbon sequestration strategies.

The vertical distribution of soil organic carbon and its relation to climate and vegetation

Boreal and subarctic peatlands comprise a carbon pool of 455 Pg that has accumulated during the postglacial period at an average net rate of 0.096 Pg/yr (1 Pg = 1015g). Using Clymo's (1984) model, the current rate is estimated at 0.076 Pg/yr. Longterm drainage of these peatlands is estimated to be causing the oxidation to CO2 of a little more than 0.0085 Pg/yr, with conbustion of fuel peat adding °0.026 Pg/yr. Emissions of CH4 are estimated to release ° 0.046 Pg of carbon annually. Uncertainties beset estimates of both stocks and fluxes, particularly with regard to Soviet peatlands. The influence of water table alterations upon fluxes of both CO2 and CH4 is in great need of investigation over a wide range of peatland environments, especially in regions where permafrost melting, thermokarst erosion, and the development of thaw lakes are likely results of climatic warming. The role of fire in the carbon cycle of peatlands also deserves increased attention. Finally, satellite—monitoring of the abundance of open water in the peatlands of the West Siberian Plain and the Hudson/James Bay Lowland is suggested as a likely method of detecting early effects of climatic warming upon boreal and subarctic peatlands.

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Northern Peatlands: Role in the Carbon Cycle and Probable Responses to Climatic Warming.

Publisher Summary In this chapter, the litter production in forests of the world is discussed. The study of quantitative aspects of litter–fall is an important part of forest ecology, dealing with a major pathway for both energy and nutrient transfer in ecosystem. This chapter collates the available data on the quantity of litter produced by forests in different parts of the world. It demonstrates the importance of litter–fall in the nutrient cycle of the forest, and the significance in soil development is investigated in the types of forest humus layer. Harvest methods are used to commercially utilize litter. The various sources, selection criteria, arrangement, and presentation of data are provided. The annual production of leaf and total litter by forests of the world are tabulated. The detailed litter separation components, percentage of non–leaf litter in different climates, understory litter, mineral material, and organic material are also described. Major factors affecting litter–fall are evergreen gymnosperms and deciduous angiosperms, and the environment. The proposed treatments for litter–fall are also discussed. The seasonal litter–fall of in forests is graphically represented and the dry weight of standing crops of leaves on an annual production basis is tabulated.

Litter production in forests of the world

Globally, lakes are currently accumulating organic carbon (OC) at an estimated annual rate of about 42 Tgṁyr −1 . Most of the OC in all but the most oligotrophic of these lakes is autochthonous, produced by primary production in the lakes. The sediments of reservoirs accumulate an additional 160 Tg annually, and peatlands contribute 96 Tg annually. These three carbon pools collectively cover less than 2% of the Earth9s surface and constitute a carbon sink of about 300 Tgṁyr −1 . Although the oceans cover 71% of the Earth9s surface, they accumulate OC at a rate of only about 100 Tgṁyr −1 .

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Magnitude and significance of carbon burial in lakes, reservoirs, and peatlands

Northern (>40°N) wetlands have been suggested as the largest natural source of methane (CH4) to the troposphere. To refine our estimates of source strengths from this region and to investigate climatic controls on the process, fluxes were measured from a variety of Minnesota peatlands during May, June, and August 1986. Sites included forested and unforested ombrotrophic bogs and minerotrophic fens in and near the U.S. Department of Agriculture Marcell Experimental Forest and the Red Lake peatlands. Late spring and summer fluxes ranged from 11 to 866 mg CH4 m−2 d−1, averaging 207 mg CH4 m−2 d−1 overall. At Marcell Forest, forested bogs and fen sites had lower fluxes (averages of 77 ± 21 mg CH4 m−2 d−1 and 142 ± 19 mg CH4 m−2 d−1) than open bogs (average of 294 ± 30 mg CH4 m−2 d−1). In the Red Lake peatland, circumneutral fens, with standing water above the peat surface, produced more methane than acid bog sites in which the water table was beneath the moss surface (325 ± 31 and 102 ± 13 mg CH4 m−2 d−1, respectively). Peat temperature was an important control. Methane flux increased in response to increasing soil temperature. For example, the open bog in the Marcell Forest with the highest CH4 flux exhibited a 74-fold increase in flux over a three-fold increase in temperature. We estimate that the methane flux from all peatlands north of 40° may be on the order of 70 to 90 Tg/yr though estimates of this sort are plagued by uncertainties in the areal extent of peatlands, length of the CH4 producing season, and the spatial and temporal variability of the flux.

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Eville Gorham

Papers

Northern Peatlands: Role in the Carbon Cycle and Probable Responses to Climatic Warming.

Litter production in forests of the world

Magnitude and significance of carbon burial in lakes, reservoirs, and peatlands

Methane flux from Minnesota Peatlands

The patterned mires of the Red Lake Peatland, northern Minnesota: vegetation, water chemistry, and landforms