PublicClodなどの音声認識サービスにおいてSDKで実装しようとするとインターフェースとしてInputStreamとなっている事があります。
byte[] で扱いたい場合にはPipedOutputStream/PipedInputStreamを使うと実装の幅が広がったりします。

import static java.lang.System.out;

import java.io.IOException;
import java.io.PipedInputStream;
import java.io.PipedOutputStream;

import javax.sound.sampled.AudioFormat;
import javax.sound.sampled.AudioSystem;
import javax.sound.sampled.DataLine;
import javax.sound.sampled.LineUnavailableException;
import javax.sound.sampled.TargetDataLine;

public class PipedSoundStreamExample {

	public static final int PIPE_SIZE = 1024 * 32;

	public static final AudioFormat format = new AudioFormat(8000, 16, 1, true, false);
	public static final DataLine.Info info = new DataLine.Info(TargetDataLine.class, format);

	static boolean finish = false;

	static long senderSize = 0;
	static long receiverSize = 0;

	public static void main(String[] args) throws IOException, InterruptedException {

		if (!AudioSystem.isLineSupported(info)) {
			out.println("Line not supported");
			System.exit(0);
		}

		final PipedOutputStream sender = new PipedOutputStream();
		final PipedInputStream receiver = new PipedInputStream(sender, PIPE_SIZE);

		Thread WriterThread  = new Thread(() -> {
			TargetDataLine line = null;
			try {
				line = (TargetDataLine) AudioSystem.getLine(info);// ### read from microphone
				line.open(format);
				line.start();
				long end = System.currentTimeMillis() + (3 * 1000);// ### run for 3 seconds
				byte[] bytes = new byte[1024];
				while (line.isOpen()) {
					if (System.currentTimeMillis() > end)
						break;
					int numBytesRead = line.read(bytes, 0, bytes.length);
					if ((numBytesRead <= 0) && (line.isOpen()))
						continue;
					senderSize += bytes.length;
					sender.write(bytes);// ### send byte.
				}
			} catch (LineUnavailableException | IOException e) {
				e.printStackTrace();
			} finally {
				if (line != null) {
					line.stop();
					line.close();
				}
				// Thread.sleep(100);
				finish = true;
			}
		});

		Thread ReaderThread = new Thread(() -> {
			try {
				int ready;
				byte[] buffer;
				while (!finish) {
					ready = receiver.available();
					if (ready <= 0)
						continue;
					buffer = new byte[ready];
					receiver.read(buffer);// ### read byte.
					// out.println(Arrays.toString(buffer));
					receiverSize += buffer.length;
				}
			} catch (IOException e) {
				e.printStackTrace();
			}
		});

		WriterThread.start();
		ReaderThread.start();

		WriterThread.join();
		ReaderThread.join();

		sender.close();
		receiver.close();

		out.println(senderSize + " => " + receiverSize);

	}
}