from IanGoddard Website
Imagine stepping out into a rain shower only to find it was raining blood!
That's what it looked like to residents of Kerala, India in 2001 when red rains fell in scattered areas over three months. Some rains were even yellow, green, or black.  Experts scrambling for answers first suggested that fallout from a hypothetical meteor explosion may have colored the rain.
More recently, news reports suggest such a meteor burst may
have colored the rain with extraterrestrial cells. [2-4]
They found that the rainwater was colored by spores from a locally prolific aerial algae of the Trentepohlia genus.  Accounting for all the observed colors, Trentepohlia spores can be red or green, and degrees of their dilution can make rainwater appear yellow or black.
Sampath et al. estimated that at least one ton of the spores fell in the rain  and they cited the still-unanswered question: How did so many local spores contaminate the rain, and why in only scattered areas during the 2001 monsoon? 
Frames (1) and (2) show the microscopic spores that colored the Keralan rains;
(3) rain samples with (a) spores settled to the bottom, (b) rainwater evaporated, and (c) spores suspended in the rainwater;
algae grown from the spores. 
Regarding the extraterrestrial-microbe hypothesis, Sampath et al found no meteor debris in the colored rainwater.
Moreover, the extraterrestrial hypothesis rests on the assumption that a loud thunder and flash of light during a storm was an exploding meteor. However, a better causal explanation for a thunderous sound and flash of light during a storm is thunder.
Additionally, just the fact that the
colored rains fell sporadically over three months refutes a
meteor-burst event as the cause. Finally, given that the spores grew
in culture into a known species of algae, the extraterrestrial
hypothesis seems to be without factual grounding.
While rains colored red by desert sands or yellow by pollen have been reported and analyzed around the world over several centuries, [7-12] the Keralan rains may be the only cases of rain colored exclusively by spores.
So what might cause such a proliferation
of spores? Unique rain patterns in Kerala during 2001 may have
played a role. Given a period of above-average rainfall weeks before
and then below-average rainfall just prior to and during the colored
rains,  there may have been an algae bloom and then a build-up
Yet raindrops in Kerala were so
thoroughly contaminated by spores that in some cases they were as
red as blood. The rain was also reported to have been clear for some
time prior to the sudden onset of colored rain. 
So by precisely what mechanism could such local aerosol input and output occur?
The anatomy of a self-propagating storm provides an attractive causal model. 
Such anatomy is depicted in the following illustration showing by way of arrows the possible paths that might be taken by accumulated spores lofted up by the warm updraft flowing from ground-level forward of a storm up and into the storm.
Anatomy of a self-propagating storm.
Accumulated spores forward of a storm cloud are lofted up and carried into the cloud via its warm updraft.
Spores within the
cloud may follow one of the many possible paths (depicted by arrows)
before they rainout.
It is useful to think of such a storm as a machine that inputs airborne spores, processes them into rain droplets by absorption or nucleation, and then outputs spore-colored rain.
Given the variable proclivities of machines or of the input thereto, it could happen on rare occasion that the output is atypically concentrated.
In this case such atypical output may
have been due to an atypical input of built up local spores.
Furthermore, given the likelihood of scattered showers due to
below-average rainfall within the timeframe of the colored rains,
such concentrated spore-rain output might be expected to occur only
over scattered areas as reported.