[Paul] recalled another thing the [Reverend Mother] had said about a world being the sum of many things—the people, the dirt, the growing things, the moons, the tides, the suns—the unknown sum called nature, a vague summation without any sense of the now. (4.72)
An environment may not have any sense of the now, but we use many aspects of nature to create our own sense of time. It's just one of many human institutions we create from our environment—more to come as we explore the other themes.
"Those are date palms," [Yueh] said. "One date palm requires forty liters of water a day. A man requires but eight liters. A palm, then, equals five men. There are twenty palms out there—one hundred men." (8.24)
Wow, that's pretty dark, but it raises a good point. The competition for resources between organisms is super important to consider when studying ecology. Bet you never thought of yourself as competing with trees, huh?
Kynes stared at [Duke Leto], seeing the water-fat flesh. (15.32)
Beauty tips from an ecologist? Yep. Here, we see that what's an acceptable body-type on Caladan is not the same as on Arrakis. Can you imagine any other instances where environment might affect our image of beauty?
"It's a rule of ecology," Kynes said, "that the young Master appears to understand quite well. The struggle between life elements is the struggle for the free energy of a system. Blood's an efficient energy source." (16.145)
Kynes notes another fun fact of ecology. Blood is an important energy resource for us to consume, but since we also have blood in us, our bodies also provide an important energy resource. It's one of those circle of life things. A blood-drenched circle of life.
[Paul's] voice lowered and he repeated: "A poison—so subtle, so insidious… so irreversible. It won't even kill you unless you stop taking it. We can't leave Arrakis unless we take part of Arrakis with us." (22.147)
For a zoo to be successful, its habitats must replicate the animals' environments. This is because the animals' bodies have adjusted to a certain environment, and they need that environment to survive. Humans are the same way, only our habitat is planet-sized.
Jessica felt that the night was dominated by degrees of smallness in substances beneath their feet and hands—boulders or pea gravel or flaked rock or pea sand or sand itself or grit or dust or gossamer powder. (27.80)
There's an urban legend that Inuit think about snow more than other peoples because they have more words for "snow." It's been largely debunked now (source), but the idea has spread through our culture like the Slender Man meme. Herbert taps into something like the Inuit legend here to show that Jessica's thoughts are being shaped by Arrakis's environment.
A thought spread across [Kynes's] mind—clear, distinct: The real wealth of a planet is in its landscape, how we take part in that basic source of civilization—agriculture. (30.8)
Agriculture helped grow the first civilizations in the Fertile Crescent (source). It keeps our civilization going, and it looks like that won't change in the far-flung future. That is, until we develop those food replicators.
"To the working planetologist, his most important tool is human beings," [Kynes's] father said. "You must cultivate ecological literacy among the people. That's why I've created this entirely new form of ecological notion." (30.24)
Herbert goes totally meta here. Pardot creates a new ecological notion; Herbert writes a new type of ecology book.
It came to [Paul] that he was surrounded by a way of life that could only be understood by postulating an ecology of ideas and values. He felt that this Fremen world was fishing for him, trying to snare him in its ways. And he knew what lay in that snare—the wild jihad, the religious war he felt he should avoid at any cost. (36.116)
If Paul is ensnared in the Fremen religion, he'll become locked in the complete ecology of Arrakis, including the environment. It's just like the ecology of a dance club. You go to hang out with friends, but the next thing you know, you're twirling glow sticks to some trance on the dance floor. Only in this case, there's less trance and more jihad.
We try to copy these patterns [of the universe] in our lives and our society, seeking the rhythms, the dances, the forms that comfort. Yet, it is possible to see peril in the finding of ultimate perfection. It is clear that the ultimate pattern contains its own fixity. In such perfection, all things move toward death. (40.Intro)
Okay, this one can get a little complicated. Physics has this concept called entropy. The basic idea is that any ordered system will eventually break down into disorder. So, if we manage to balance our society perfectly with nature, the system will only last so long. It will always, in time, break down. Well, that's depressing, but does that mean we shouldn't try? We'll leave that one up to you.