David Siminoff, now former general partner at Venrock, has left the venture firm after a little over a year and a half. The move, confirmed by the firm, is significant considering Siminoff’s stature in the Silicon Valley venture community. It’s unclear what prompted the change — whether he left of his own accord or was somehow caught up in the wave of downsizing hitting funds of Venrock’s caliber. Further details have yet to be disclosed.

It’s highly likely he decided to quit — he certainly has the wealth and prestige necessary to operate independently from an established firm. One of the heroes of the late-90s tech bubble, he made several billion-dollar investments in Yahoo, America Online and eBay before retiring stylishly early. He made his comeback in April 2007, joining Venrock’s $600 million fund, but had already financed a few enterprises of his own, including mobile search service 4INFO. During his time at the firm, he worked with video messaging provider Tapioca Mobile, presentation-sharing site SlideShare and anime streaming site Crunchyroll.

There’s an outside chance his area of expertise — media companies — contributed to his departure. As former chief executive of dating-site umbrella Spark Networks, he was clearly closely-tied to the area. But the challenges facing this sector, flagging advertising models chief among them, are formidable and highly visible. And many firms are turning their attention, preferring instead to place safer bets on cleantech companies that continue to perform well despite the downturn. Even when Siminoff first joined, a good chunk of the fund was devoted to alternative enery development. Other marquee names like Kleiner Perkins have grown their green activity, and Steve Jurvetson of DFJ just spoke to us about shifting his focus to cleantech.

Then again, Venrock just drafted David Pakman in October to work on digital media investments in New York, so the firm doesn’t seem to be shying away from media startups. More on Siminoff’s plans is sure to be released in the next day.

Aria Systems, perhaps the first company to offer billing and subscription management through a software-as-a-service business model (i.e., online subscriptions), has raised a $10 million second round.

The Media, Pa.-based company has been around since 2003, but interest in online billing software seems to have taken off this year — and it’s not just Aria chief executive Ed Sullivan who says so. A new competitor called Zuora, led by an early employee of SaaS pioneer Salesforce.com, launched several products this year, and has attracted funding from some big-name investors, including Benchmark Capital and Salesforce chief executive Marc Benioff.

Zuora may have high-profile investors, but Sullivan says Aria has the advantage of being first. It boasts customers in 238 countries, and the third quater of 2008 saw sales bookings double from the second, which saw bookings quadruple from the first. Aria’s customers, who used to be “startup guys” for the most part,  have also changed dramatically this year, Sullivan says, with many more big companies looking for an affordable way to handle the many moving parts that go into billing and subscriptions.

“I think in six months it’s going to be a different world,” he says. “The SaaS waters are rising and the winners are going to be the companies that are positioned and ready that have a product that can sell into those mainstream companies that are publicly traded … or have to go through public audits.”
The new round comes from Venrock, with participation from previous investors Hummer Winblad Venture Partners and Dave Labuda, an industry veteran Sullivan previously described as “the Michael Jordan of billing.” Aria has raised a total of $14 million.

A technology that might offer some respite to first-generation ethanol makers like Verasun and Pacific Ethanol has received a significant $25 million from backers including oil giant BP and George Soros’s investment fund. The company in question is Qteros, formerly called SunEthanol, a little-known startup placing big bets on a plucky microbe.

Qteros is one of a large group of companies trying to engineer a microorganism to cheaply break down woody matter, including everything from corn husks and grass to actual wood, into fuels. The general tack of these companies is to find a naturally occurring microbe and change its genes until it becomes a perfect production unit.

But Qteros claims to have a vital difference, saying that its proprietary organism, the Q Microbe, was nearly perfect for the job in nature, with an unusual ability to dynamically adjusts to the type of organic matter it’s processing. So instead of trying to patch together “Frankenbugs” incorporating the useful parts of different organisms, as Battery Ventures investor Jason Matlof put it to me, the company is only engaged in “classical genetic engineering”, which basically means selective breeding.

The Qteros bug requires about a year of development work, in which time the company will build its own pilot facility. However, that pilot will likely be the last facility Qteros builds on its own, possibly forever. Unlike rivals like Coskata and Mascoma, Qteros primary plans involve licensing its technology out.

If the pilot facility proves the Q Microbe works as expected at scale, first-gen ethanol makers could line up to sign deals. The Q Microbe could be useful to those companies because in the ethanol making process, the parts of the feedstock that have cellulosic matter — like corn husks and bagasse, or left over sugar cane husks — are often wasted or underutilized.

Employing a cellulose-eating microbe, then, would give such companies access to more of the plant’s energy. Existing plants could tap into an additional profit source by using microbes, thus pushing up the returns of an industry that has often has razor-thin margins, or outright loses money.

For Qteros, if all goes according to plan, the company’s growth should explode as it signs contracts. Unlike other startups that build their own plants, Qteros only needs to secure a deal with an engineering firm that can nail down a design and help deploy it, Matlof says: “After that, it’s cookie cutter.” This approach isn’t totally innovative, by the way; green chemical manufacturer Genomatica also plans to develop “bolt-on” facilities for larger companies.

Licensing its technology for bolt-ons and entire cellulosic ethanol facilities should also let Qteros slip by with much less funding than its rivals, according to Matlof, who says the company will only need $30 to $50 million to reach its objectives. With this funding and its previous $3.6 million round, the company has taken almost $29 million to date.

Venrock led this round, with previous investors Battery Ventures, Long River Ventures and Camros Capital joining. BP and Soros Fund Management are new investors. Qteros is based in Hadley, Mass.