In class on the 9th we:
1- set up our Winogradsky column experiments by table
Table 1 – 6 homogenized soil cores assigned to 1 of 3 saltwater treatments (fresh, 1/2 strength seawater, full strength seawater) and 1 of 2 light treatments (full spectrum, infrared)
Table 2 – collected 6 intact soil cores from 3 distances away from a road (near, far, farther) and assigned 1 in each pair to a high NO3 enrichment treatment)
Table 3 – used soils from 4 restored wetlands varying in soil organic matter content to prepare 8 cores (a pair from each wetland). One core in each wetland received supplemental C as potassium acetate.
THEN – we checked out how to identify our cultured specimens from sequence data. We learned how to decide whether a sequence read is useful or not and how to trim it to improve its quality. We then learned how to submit a sequence to BLAST (Basic Local Alignment Search Tool, the wikipedia of sequence data) or to use a more rigorous database system for bacterial DNA – the Ribosomal Database Project. We used 2 of your sequences, but [HOMEWORK] you guys are supposed to now figure out the identity (or likely identity) of all the sequences run by your table.
Finally – we discussed 3 papers selected by Alyse that examined bigoeographic variation in microbial diversity across the worlds oceans (Fuhrman et al. 2008); the response of microbial community structure to experimental manipulations of redox (Pett-Ridge & Fireston 2005); and an experimental test of whether there is a “home team advantage” whereby microbial communities are best able to degrade the organic matter from which they are isolated or whether microbial communities are sufficiently diverse that they are functionally redundant (Strickland et al. 2009).
