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The influence of stream alteration on abundance of benthic fish was examined hierarchically by both reach and channel unit scales, in the Makomanai River, in Sapporo City, northern Japan. Study sections of 2km were settled in bank protection, natural, and channel works courses. The density of Cottus nozawae in the channel works reach was significantly lower than that in the natural and bank protection reaches, whereas the abundance of Noemacheilus barbatulus toni was not different among the three reaches. The density of C. nozawae was positively correlated with the abundance of boulders and loose stones, probably because interstitial spaces on river bed provide refuge and critical habitat components for living and spawning. River bed in the channel works reach was covered by fine sediment and with few loose stones, resulting in reduced interstitial spaces and thus a low density of C nozawae. Within the channel unit, the density of C nozawae in riffles was significantly higher than that in pools, which could be attributed to abundant boulders and loose stones in riffles. A reduced tractive force in the stream caused by check dams and bed stabilization works not only promotes the deposition of pebble-sized stones and the creation of a stable channel bed during a flood, but also traps fine sediment during low-flow periods. These physical mechanisms changes, in association with the channel works, greatly altered the habitat required for C. nozawae.
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