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Four New Studies Shed Light on Microbial Ecology

NEW YORK (GenomeWeb News) – Four studies published today in Science used genetics and metagenomics to tease apart the characteristics of diverse microbial communities — from microbes in acidic mine waste and deep beneath the sea to those in the human gut.
The first, by researchers at the University of California, Berkeley, peeked into microbial genomes to find the genetic underpinnings of bacterial and archeal resistance to viruses. By reconstructing the genomes of microbes found in acidic biofilms on mine waste, the researchers were able to predict which viruses the bacteria and archea had encountered.
Their results suggest that viruses and their bacterial and archael hosts take turns using offensive and defensive strategies, with microbes silencing viral genes using small inhibitory RNAs and viruses rearranging their own genomes to evade this silencing.
“Viruses play a critical role in all ecosystems, but because they can lower the fitness of, or kill, cells, cells had to find a way around the viruses, leading both to evolve to arm themselves against one another,” senior author Jillian Banfield, a geomicrobiologist at the University of California, Berkeley, said in a statement. “This is one of the first studies to link viruses with their hosts and to show a major component of how the virus responds.” 
Key players in this battle are stretches of DNA in microbial genomes called “clustered regularly interspaced short palindromic repeats,” or CRISPRs, that contain dozens or even hundreds of pieces of repeated DNA. When bacteria become infected with viruses, they apparently chop up viral DNA and pop bits of it into these CRISPR sequences where they become “spacers.” Then, when bacteria encounter these, or similar viruses, they use the spacer sequence to produce small RNAs that silence viral messenger RNA. 
The tactic “may be the evolutionary precursor of our RNA interference system,” Banfield said. The biofilm microbes they tested seem to get rid of spacers that are no longer necessary relatively quickly, replacing them with new ones corresponding to rearranged viral genomes.
“These populations are dynamic,” Banfield said. “Potentially, a microbe may add one or more spacers per division cycle, which makes for a very fast arms race and perhaps a complete turnover of spacers in just a few months’ time.”
Another study, led by Jeffrey Gordon at Washington University’s Center for Genome Sciences, used metagenomics and network-based analyses to investigate how microbes living deep within the guts of mammals have co-evolved with and contributed to their hosts’ evolution.
The team looked at 20,000 16S rRNA sequences from microbes in fecal samples from 106 different animals representing 60 types of mammals, including humans. The results suggest host diet has a profound effect on the communities of microorganisms living in mammalian guts. And gut microbe biodiversity seems to have increased in mammalian species as they evolved from meat-based diets to omnivory to plant-based diets.
In a third study appearing in Science today, an international team of scientists led by Massachusetts Institute of Technology researchers Eric Alm and Martin Polz used a combination of gene sequencing and mathematical modeling to define populations of marine bacteria with distinct lifestyles and resource partitioning. Based on their analysis of Vibrionaceae family bacteria collected from the wild, the team suggested that ecological selection can influence evolution and speciation in these microbes.
“Although we cannot determine whether the clusters represent transiently adapted populations or nascent species,” the authors wrote, “our observations of different distributions of genotypes suggest that there exists a small-scale adaptive landscape in the water column allowing the initiation of (sympatric) speciation within this community.” In the future, they noted, comparing whole genomes of ecologically diverged microbes will help unravel the specific genetic changes involved in this adaptive evolution.
Finally, in a brief published online today in Science, French and British researchers reported on the deepest microbial community found yet, living about a mile beneath the sea floor. The team detected the microbes in 46 to 111 million-year-old sediments obtained from a drilling project on the Newfoundland Margin and used 16S rRNA sequencing to identify bugs found at different depths.
For instance, they found that thermophilic Pyrococcus were the most common microbe in the sample taken from 958 meters (~0.6 miles) below the sea floor. As the methane content increased with depth, anaerobic methane-oxidizing archaea became more common — though these disappeared at the greatest depths, where Pyrococcus and Thermococcus samples were most common.

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