This symbol's kind of general and vague, we know, but that's because there isn't a single type of natural image the writer focuses on throughout the book. Instead, she just kind of throws the kitchen sink at us (only it's all a lot prettier than an actual kitchen sink) when it comes to weaving nature into her metaphorical language.
Here's an example of how the author uses nature to clarify an opinion Manjiro might have:
Wasn't it funny, Manjiro thought, that his countrymen, who so admired the fleeting beauty of cherry blossoms and the maple's momentary burst of fall color, clung so fervently to the past? They were like the last fragile blossoms that tremble on the branch while the wind tears and tears at them. (5.41.5)
The Japanese equal fragile cherry blossoms because they're so unprepared for the world's technological and economic advances. The world, to be clear, is the wind in this passage.
But before this, Manjiro makes a parallel between shells and people:
"These shells are like the people of the world, Okachan […] They come from many different places. They come in many different colors and sizes. But they are all beautiful." (5.40.35)
Here, shells symbolize all the different races of people in the world, beautiful in their differences. It totally works as a means of getting the point across, but as a simile, it has little to do with the cherry blossoms and wind references that shortly follow.
What's the point of all these different ways of comparing human life to nature? It's an aesthetic that goes along with Manjiro's view of the world: to be a harmonious part of a nature rather than be against nature. Natural imagery allows for a closer link between the detached, technological human intellect and the wider, natural world and, by scattering it throughout the pages, we are constantly kept close to Manjiro's relationship with the world around him. For more on this, be sure to check out his analysis over in the "Character" section.