Proteomics in environmental and technical microbiology

Abstract

Nowadays, the field of proteomics encompasses various techniques for the analysis of the entirety of proteins in biological samples. Not only 2D electrophoresis as the primary method, but also MS‐based workflows and bioinformatic tools are being increasingly applied. In particular, research in microbiology was significantly influenced by proteomics during the last few decades. Hence, this review presents results of proteomic studies carried out in areas, such as fundamental microbiological research and biotechnology. In addition, the emerging field of metaproteomics is addressed because high‐throughput genome sequencing and high‐performance MS facilitate the access to such complex samples from microbial communities as found in sludge from wastewater treatment plants and biogas plants. Both current technical limitations and new concepts in this growing and important area are discussed. Moreover, it was convincingly shown that future prospective applications of proteomics in technical and environmental microbiology might also be closely connected with other Omics approaches as well as bioinformatics for systems biology studies.

Metaproteomics of activated sludge from a wastewater treatment plant – A pilot study

“…Major proteins were keratins and the pancreatic enzyme elastase. The latter one is released into the colon and was also detected previously in activated sludge samples [1,3]. Small fractions of archaeal (2%) and viral (0.4%) meta-proteins were also identified.…”

“…In order to understand its function without isolating single strains, metaproteomic analysis has been applied to activated sludge samples . Major challenges for this approach are the presence of humic compounds interfering with protein separation, the high complexity of the community, and the lack of sufficient genomic sequences for protein identification .…”

“…The high number of identified proteins compared to the peptides was mainly attributed to redundant assignments of peptides to highly conserved proteins from different species, e.g. chaperones, elongation factors or keratins as discussed by Benndorf and Reichl (2014) . In order to remove redundancy, all proteins sharing at least one peptide were combined to meta‐proteins (Fig.…”

Environmental Microbiology and Biotechnology: Progress and Prospects

“…Examples of environmental proteomics applied to model organisms were presented [13] along with discussions on microbial community proteomics, named as metaproteomics [14]. 2D electrophoresis, MS-based workflows and bioinformatic tools are being applied nowadays for the analysis of total proteins in environmental microbiological samples [15]. 2D electrophoresis, MS-based workflows and bioinformatic tools are being applied nowadays for the analysis of total proteins in environmental microbiological samples [15].…”

“…Proteomics can further be employed for phylogenetic classification of bacterial species through 2D maps. 2D electrophoresis, MS-based workflows and bioinformatic tools are being applied nowadays for the analysis of total proteins in environmental microbiological samples [15]. Proteomic data can be used to correct genome annotations of model organisms, an area of study called proteogenomics [16].…”