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.

1. Using data from 71, mainly shallow (an average mean depth of 3 m), Danish lakes with contrasting total phosphorus concentrations (summer mean 0.02–1.0 mg P L−l), we describe how species richness, biodiversity and trophic structure change along a total phosphorus (TP) gradient divided into five TP classes (class 1–5: 0.4 mg P L−1). 
2. With increasing TP, a significant decline was observed in the species richness of zooplankton and submerged macrophytes, while for fish, phytoplankton and floating-leaved macrophytes, species richness was unimodally related to TP, all peaking at 0.1–0.4 mg P L−1. The Shannon–Wiener and the Hurlbert probability of inter-specific encounter (PIE) diversity indices showed significant unimodal relationships to TP for zooplankton, phytoplankton and fish. Mean depth also contributed positively to the relationship for rotifers, phytoplankton and fish. 
3. At low nutrient concentrations, piscivorous fish (particularly perch, Perca fluviatilis) were abundant and the biomass ratio of piscivores to plankti-benthivorous cyprinids was high and the density of cyprinids low. Concurrently, the zooplankton was dominated by large-bodied forms and the biomass ratio of zooplankton to phytoplankton and the calculated grazing pressure on phytoplankton were high. Phytoplankton biomass was low and submerged macrophyte abundance high. 
4. With increasing TP, a major shift occurred in trophic structure. Catches of cyprinids in multiple mesh size gill nets increased 10-fold from class 1 to class 5 and the weight ratio of piscivores to planktivores decreased from 0.6 in class 1 to 0.10–0.15 in classes 3–5. In addition, the mean body weight of dominant cyprinids (roach, Rutilus rutilus, and bream, Abramis brama) decreased two–threefold. Simultaneously, small cladocerans gradually became more important, and among copepods, a shift occurred from calanoid to cyclopoids. Mean body weight of cladocerans decreased from 5.1 μg in class 1 to 1.5 μg in class 5, and the biomass ratio of zooplankton to phytoplankton from 0.46 in class 1 to 0.08–0.15 in classes 3–5. Conversely, phytoplankton biomass and chlorophyll a increased 15-fold from class 1 to 5 and submerged macrophytes disappeared from most lakes. 
5. The suggestion that fish have a significant structuring role in eutrophic lakes is supported by data from three lakes in which major changes in the abundance of planktivorous fish occurred following fish kill or fish manipulation. In these lakes, studied for 8 years, a reduction in planktivores resulted in a major increase in cladoceran mean size and in the biomass ratio of zooplankton to phytoplankton, while chlorophyll a declined substantially. In comparison, no significant changes were observed in 33 ‘control’ lakes studied during the same period.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2427.2000.00675.x

Trophic structure, species richness and biodiversity in Danish lakes: changes along a phosphorus gradient

Data from the literature suggest that predatory success declines as habitat complexity increases. To explain this phenomenon, we studied the predator-prey interaction between largemouth bass Micropterus salmoides and bluegills Lepomis macrochirus in four laboratory pools (2.4–3.0 m diameter, 0.7 m deep), each with a different density (0, 50, 250, 1,000 stems/m2) of artificial plant stems. Behavior was quantified for both predator and prey during largemouth bass feeding bouts lasting 60 minutes. Predation success (number of captures) by largemouth bass was similar at 0 and 50 stems/m2, then declined to near zero at 250 and 1,000 stems/m2. As stem density increased, predator activity declined due to a decrease in behaviors associated with visual contact with prey. Reduced predation success by largemouth bass in habitats of increased complexity apparently is related to increases in visual barriers provided by plant stems as well as to adaptive changes in bluegill behavior.

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Predator-Prey Interaction between Largemouth Bass and Bluegills as Influenced by Simulated, Submersed Vegetation

119 Small invertebrates are functionally important in many terrestrial and aquatic ecosystems (Wilson 1992, Freckman et al. 1997, Palmer et al. 1997, Postel and Carpenter 1997). In freshwater sediments, benthic invertebrates are diverse and abundant, but they are often patchily distributed and relatively difficult to sample, especially when they live in deep subsurface sediments. Thus, the species richness and functional importance of freshwater benthic invertebrates generally go unnoticed until unexpected changes occur in ecosystems. Unanticipated changes in freshwater ecosystems are often due to alterations in the complex connections among sediment-dwelling species and associated food webs (e.g., Goedkoop and Johnson 1996, Lodge et al. 1998b, Stockley et al. 1998) or to disturbances, such as floods or drought (e.g., Covich 1993, Power 1995, Johnson et al. 1998), that alter the species composition of the benthos. In addition, benthic species can themselves constitute a disturbance, such as when they transmit diseases. For example, certain benthic invertebrate species (e.g., Tubifex tubifex) serve as parasite-transmitting vectors; if these invertebrates increase in abundance in stream sediments, they may spread a lethal disease to trout, causing trout populations to decline (Brinkhurst 1997). Fish kills may also occur because of increased accumulation of nutrients, which cause formation of toxic algal blooms, deoxygenation of deeper, density-stratified waters, and high concentrations of ammonia or hydrogen sulfide (Covich 1993). The bottom muds of lakes and streams may at first glance appear to be uniform and, therefore, unlikely habitats for high biodiversity. However, physical, chemical, and biological processes create significant horizontal and vertical heterogeneities in the substrata (Figure 1) that provide a physical template for distinct niches (Hutchinson 1993). These sedimentary processes include changes in direction and rates of flows, differential deposition of sediment grain sizes and dead organisms, growth and death of roots, burrowing and sediment reworking, and fecal production by benthic consumers. Microhabitats are also created by chemical gradients and microzonation in concentrations of dissolved oxygen, hydrogen sulfide, ammonia, phosphorus, and other critical chemicals (Groffman and Bohlen 1999). Colwell (1998) emphasizes that such “biocomplexity” of habitats and biological relationships is an important aspect of biodiversity. Bioturbation and other biotic interactions create extensive biocomplexity in freshwater sediments (Charbonneau and Hare 1998). These biocomplexities must be better understood if clean drinking water and recreational uses of fresh waters are to be maintained. Science-based policies require an ecosystem perspective on the multiple roles of many diverse benthic species. Previous studies have often dealt with the “goods” produced by benthic species, such as the quantity of prey items consumed by fish. These goods are clearly important components of food webs, but how their functional relationships respond to changes in species composition are also important. In this article, we highlight examples of how some species have a disproportionately large impact on food-web dynamics and how particular species provide essential ecosystem services. These ecosystem functions include sediment mixing, nutrient cycling, and energy flow through food webs. The Role of Benthic Invertebrate Species in Freshwater Ecosystems

https://www.jstor.org/stable/10.1525/bisi.1999.49.2.119

The Role of Benthic Invertebrate Species in Freshwater Ecosystems: Zoobenthic species influence energy flows and nutrient cycling

Impact of submerged macrophytes including charophytes on phyto- and zooplankton communities: allelopathy versus other mechanisms

Lake Zwemlust (area 1.5 ha, Zm 1.5 m) has been the object of an extensive limnological study since its biomanipulation involving removal of planktivorous fish (bream) in March 1987 and emptying of the lake. In the subsequent summer period of 1987 the Secchi depth increased to the lake bottom (2.5 m), compared with ca 30 cm in the earlier summers. The reaction of submerged macrophytes to improving under-water light climate was rapid. In summer 1987, besides the introduced Chara globularis, 5 species of submerged macrophytes occurred and colonized 10% of the lake area. In 1988 and 1989 only quantitative changes were observed; new species did not appear, but the area colonized by macrophytes increased by 7 and 10 times, respectively. Elodea nuttallii was dominant among the macrophytes and Mougeotia sp. among the filamentous green algae. Their abundance, contributed to transient N-limination of phytoplankton causing a persistent clear water phase in 1988 and 1989, unlike in 1987 when zooplankton grazing contributed chiefly to the water clarity. Laboratory bioassays on macrophytes confirmed nitrogen limitation.

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Can macrophytes be useful in biomanipulation of lakes? The Lake Zwemlust example

Waters of Lake Luknajno (623 ha, 3 m max. depth postglacial basin in Masurian Lakeland) are of meso-eutrophic type in spite of an intensive land impact and substantial phosphorus loading. The reason of this peculiarity is an abundance of 4 species of charophytes (Chara aculeolata, C. aspera, C. contraria and C. tomentosa) which dominate the submerged vegetation of the lake and yielded 417 g m−2 dry biomass in summer 1991. The plants have high potential for phosphorus uptake and accumulation as was checked in laboratory experiments. Due to this potential Chara can outcompete planktonic algae in mixed cultures at different mineral P supplies.

Can Chara control phosphorus cycling in Lake Łuknajno (Poland)

The capacity of Elodea nuttallii (Planch.) St. John and Elodea canadensis Michx. to remove nitrogen from water was evaluated in laboratory experiment. The growth rate of plants and their effect on the nitrogen level of hypertrophic Lake Zwemlust (the Netherlands) as well as on lake water enriched with nitrogen were investigated. The plants grew best in water enriched with up to 2 mg NH4-Nl−1 and 2 mg NH4-Nl−1 plus 2 mg NO3 Nl−1. During a 14 day experiment, plants absorbed from 75% to 90% of nitrogen. Higher nitrogen concentration than 4 mg l−1 had a negative effect on growth of both species. Elodea nuttallii and E. canadensis prefer NOinf4/p+ over NOinf4/p− when both ions were present in water in equal concentrations.

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Teresa Ozimek

Papers

Can macrophytes be useful in biomanipulation of lakes? The Lake Zwemlust example

Can Chara control phosphorus cycling in Lake Łuknajno (Poland)

Growth and nutrient uptake by two species of Elodea in experimental conditions and their role in nutrient accumulation in a macrophyte-dominated lake

Long-term changes of the submerged macrophytes in eutrophic lake Mikołajskie (North Poland)

The effect of sewage sludge flooding on growth and morphometric parameters of Phragmites australis (Cav.) Trin. ex Steudel