foreach ($paragraph->childNodes as $child) {
    $node .= $paragraph->ownerDocument->saveHTML($child);
}

$node = trim($node); // Does not work

$breaks = array("rn", "n", "r");
$node = str_replace($breaks, " ", $node); // Doesn't work

$paragraph->ownerDocument->formatOutput = false;
$paragraph->ownerDocument->preserveWhiteSpace = false;

<b>Keywords: </b>marine fungus; sediment; anthranilic acid; <i>Penicillium&#13; paneum</i>; cytotoxicity

$node = preg_replace(array('/r/', '/n/'), '', $node);

$string =  preg_replace("#<brs*/?>#i", "", $string);

preg_replace( "/r|n/", "", $yourString);

$node .= $paragraph->ownerDocument->saveHTML($child);

$buffer = $paragraph->ownerDocument->saveHTML($child);
$node .= substr($buffer, 0, strlen($buffer) - 1);  // strip last byte