The use of pyrosequencing and/or DGGE can be used to identify the microbes present.

Microbial succession during a laboratory-scale composting process of garbage was analysed by denaturing gradient gel electrophoresis (DGGE) combined with measurement of physicochemical parameters such as temperature, pH, organic acids, total dissolved organic carbon and water-soluble humic substance. From the temperature changes, a rapid increase from 25 to 58 °C and then a gradual decrease, four phases were recognized in the process as follows; mesophilic (S), thermophilic (T), cooling (C) and maturing (M). The polymerase chain reaction-amplified 16S rDNA fragments with universal (907R) and eubacterial (341F with GC clamp) primers were subjected to DGGE analysis. Consequently, the DGGE band pattern changed during the composting process. The direct sequences from DGGE bands were related to those of known genera in the DNA database. The microbial succession determined by DGGE was summarized as follows: in the S phase some fermenting bacteria, such as lactobacillus, were present with the existing organic acids; in the T phase thermophilic bacillus appeared and, after the C phase, bacterial populations were more complex than in previous phases and the phylogenetic positions of those populations were relatively distant from strains so far in the DNA database. Thus, the DGGE method is useful to reveal microbial succession during a composting process.

http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2672.2000.01177.x/full

Traditionally, the identification and characterization of microbial communities in contaminated soil and water has previously been limited to

those microorganisms that are culturable. The application of molecular techniques to study microbial populations at contaminated sites without the

need for culturing has led to the discovery of unique and previously unrecognized microorganisms as well as complex microbial diversity in

contaminated soil and water which shows an exciting opportunity for bioremediation strategies. Nucleic acid extraction from contaminated sites

and their subsequent amplification by polymerase chain reaction (PCR) has proved extremely useful in assessing the changes in microbial

community structure by several microbial community profiling techniques. This review examines the current application of molecular techniques

for the characterization of microbial communities in contaminated soil and water. Techniques that identify and quantify microbial population and

catabolic genes involved in biodegradation are examined. In addition, methods that directly link microbial phylogeny to its ecological function at

contaminated sites as well as high throughput methods for complex microbial community studies are discussed.

10.1016/j.envint.2007.09.001

meta-omics techniques, RNA-seq and functional gene array coupled with RT-PCR， chemical analytical techniques might be pratical strategy to invesitate microbial activity in contaminated environment.

None of the methods listed above, at least for me and others like me that practice remediation engineering, are useful or informative from an optimization perspective.  For example,  Dr. Sukla describes succession info generated from 16 rDNA analysis but fails to say that this has been known for a long time without any molecular methods lines of evidence.  Although these methods offfer alot of data for the publication of papers, they offer very little in practical terms.  I'm sorry for being such a downer but our biggest problem is the linkage between Phylogeny and in situ metabolism.  We are trying to use pyrosequencing to identify methanotrophic activity and the results have indicated that our negative control has the highest titre of methanotrophs.  Needless to say this will not be published. 

With the development and application of molecular genomic tools, the field of

microbial ecology is undergoing unprecedented changes.

http://www.newbooks-services.de/MediaFiles/Texts/8/9781441979308_Excerpt_001.pdf

So far, I think stable-isotope probing (SIP) combined with metagenomics (16S rRNA amplicon sequencing or shotgun sequencing) is a good way to link microbial functions and microbial identity.  Use stable isotope labeled (such as C-13 or N-15) substrate to feed microbial community in the field or lab and after incubation extract the heavy DNA that bacteria incorporate into their chromosome when growing with that substrate. Then you can do metagemoics analysis and microarray analysis with that DNA. The heavy DNA indicate the active bacteria processing the substrate.

Here are a few review papers talking about that technique. 

http://www.sciencedirect.com/science/article/pii/S0966842X10000193

http://www.nature.com/nrmicro/journal/v3/n6/full/nrmicro1162.html

Since 2005, advances in next-generation sequencing technologies have revolutionized biological science. The analysis of environmental DNA through the use of specific gene markers such as species-specific DNA barcodes has been a key application of next-generation sequencing technologies in ecological and environmental research. Access to parallel, massive amounts of sequencing data, as well as subsequent improvements in read length and throughput of different sequencing platforms, is leading to a better representation of sample diversity at a reasonable cost. New technologies are being developed rapidly and have the potential to dramatically accelerate ecological and environmental research. The fast pace of development and improvements in next-generation sequencing technologies can reflect on broader and more robust applications in environmental DNA research. Here, we review the advantages and limitations of current next-generation sequencing technologies in regard to their application for environmental DNA analysis.

http://www.ncbi.nlm.nih.gov/pubmed/22486820