March 18th. -- We sailed from Bahia. A few days afterwards, when not far distant from the Abrolhos Islets, my; attention was called to a reddish-brown appearance in the sea. The whole surface of the water, as it appeared under a weak lens, seemed as if covered by chopped bits of hay, with their ends jagged. These are minute cylindrical confervae, in bundles or rafts of from twenty to sixty in each. Mr. Berkeley informs me that they are the same species (Trichodesmium erythraeum) with that found over large spaces in the Red Sea, and whence its name of Red Sea is derived.  Their numbers must be infinite: the ship passed through several bands of them, one of which was about ten yards wide, and, judging from the mud-like colour of the water, at least two and a half miles long. In almost every long voyage some account is given of these confervae. They appear especially common in the sea near Australia; and off Cape Leeuwin I found an allied but smaller and apparently different species. Captain Cook, in his third voyage, remarks, that the sailors gave to this appearance the name of sea-sawdust.
Near Keeling Atoll, in the Indian Ocean, I observed many little masses of confervae a few inches square, consisting of long cylindrical threads of excessive thinness, so as to be barely visible to the naked eye, mingled with other rather larger bodies, finely conical at both ends. Two of these are shown in the woodcut united together. They vary in length from .04 to .06, and even to .08 of an inch in length; and in diameter from .006 to .008 of an inch. Near one extremity of the cylindrical part, a green septum, formed of granular matter, and thickest in the middle, may generally be seen. This, I believe, is the bottom of a most delicate, colourless sac, composed of a pulpy substance, which lines the exterior case, but does not extend within the extreme conical points. In some specimens, small but perfect spheres of brownish granular matter supplied the places of the septa; and I observed the curious process by which they were produced. The pulpy matter of the internal coating suddenly grouped itself into lines, some of which assumed a form radiating from a common centre; it then continued, with an irregular and rapid movement, to contract itself, so that in the course of a second the whole was united into a perfect little sphere, which occupied the position of the septum at one end of the now quite hollow case. The formation of the granular sphere was hastened by any accidental injury. I may add, that frequently a pair of these bodies were attached to each other, as represented above, cone beside cone, at that end where the septum occurs.
I will add here a few other observations connected with the discoloration of the sea from organic causes. On the coast of Chile, a few leagues north of Concepcion, the Beagle one day passed through great bands of muddy water, exactly like that of a swollen river; and again, a degree south of Valparaiso, when fifty miles from the land, the same appearance was still more extensive. Some of the water placed in a glass was of a pale reddish tint; and, examined under a microscope, was seen to swarm with minute animalcula darting about, and often exploding. Their shape is oval, and contracted in the middle by a ring of vibrating curved ciliae. It was, however, very difficult to examine them with care, for almost the instant motion ceased, even while crossing the field of vision, their bodies burst. Sometimes both ends burst at once, sometimes only one, and a quantity of coarse, brownish, granular matter was ejected. The animal an instant before bursting expanded to half again its natural size; and the explosion took place about fifteen seconds after the rapid progressive motion had ceased: in a few cases it was preceded for a short interval by a rotatory movement on the longer axis. About two minutes after any number were isolated in a drop of water, they thus perished. The animals move with the narrow apex forwards, by the aid of their vibratory ciliae, and generally by rapid starts. They are exceedingly minute, and quite invisible to the naked eye, only covering a space equal to the square of the thousandth of an inch. Their numbers were infinite; for the smallest drop of water which I could remove contained very many. In one day we passed through two spaces of water thus stained, one of which alone must have extended over several square miles. What incalculable numbers of these microscopical animals! The colour of the water, as seen at some distance, was like that of a river which has flowed through a red clay district, but under the shade of the vessel's side it was quite as dark as chocolate. The line where the red and blue water joined was distinctly defined. The weather for some days previously had been calm, and the ocean abounded, to an unusual degree, with living creatures.