The 29-year-old centre-back was seen yelling at his compatriot when the former Real Madrid playmaker refused to applaud the travelling Arsenal fans after the club's 6-3 loss to Manchester City at the Etihad Stadium.
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“It can't just be all happiness, peace and pancakes,” the Germany international told Bild. “If it is then you won't develop as a team.
“The good thing is that Mesut and I know each other well from our time at (Werder) Bremen. We can be honest with each other.”
The Gunners were handed a tough Champions League last-16 draw against reigning champions Bayern Munich, but Mertesacker believes the side can take heart from their victory at the Allianz Arena last season.
“It's a good draw,” continued the Arsenal centre-back. “I still remember how paralysed Bayern were when we made it 2-0 (last season). We nearly toppled them then.”