I want to identify microbial communities in cultures isolated from activated sludge. How can I select suitable primers for carrying out DNA extraction and sequencing?
For fungal amplification use ITS1/ITS4 and 16S-28F/16S-1526R for bacteria. You can find similar work in 'Oligo-DNA Custom Macroarray for Monitoring Major Pathogenic and Non-Pathogenic Fungi and Bacteria in the Phyllosphere of Apple Trees' PLoS One 1012, 7, e34249.
I personally do not rely on the primers originally designed by lane et al. They are just too old and designed based on a limited dataset. Most studies have used these primers so designing primers using this dataset won't help anyways. However, primers that are designed using genomic sequences are the best bet and you won't miss many taxa. This has also been covered excellently by Frank et al. 2008. See here doi:10.1128/aem.02272-07
I use a complex cocktail of 4 degenerate primers as suggested in this paper and a closer 515 reverse primer that i've modified myself to increase its coverage published here doi:10.1016/j.biortech.2011.04.098.
Similarly for fungi, there is a more recent updated primer set that i use. See this doi:10.1128/aem.03870-12