57
understanding about microbial recruiting, organism interactions, cooperation and
competence for nutrient resources, and metabolic activities (Hettich et al. 2013). At
a somewhat higher level, the information is crucial for depiction of host–microbe
crosstalk such as microorganism–plant or microorganism–human interactions
(Hettich et al. 2013). In a nutshell, environmental metaproteomics perspectives have
founded a “proof- of- concept” that can facilitate applications to numerous significant research areas such as bioremediation, carbon cycling, bioenergy, and human
health (Hettich et al. 2013). Until now, most of the proteomics experiments are
focused on the analysis of single species under different conditions, leaving the
perspective of microbial community proteomics almost totally unexplored (Lacerda
et al. 2007). Furthermore, metaproteome analysis from different environmental conditions allows (1) identification of novel genes and cellular pathways and (2) recognition of stress-responsive proteins (Maron et al. 2007). There exist numerous
challenges in microbial community proteomics such as representative protein
extraction, sample complexity for separation (including even thousands of bacterial
proteomes), and an almost total absence of genomic sequences for microbes in ecological communities (Lacerda et al. 2007). Metaproteomics analysis of diverse environments such as the natural microbial biofilm (Ram et al. 2005), water (Kan et al.
2005; Ogunseitan 1993, 1996, 1997), sediment (Ogunseitan 1993), soil (Ogunseitan
1993; Singleton et al. 2003), and processed sludge (Wilmes and Bond 2004) have
led to the discovery that the protein complement of the metagenome was much
more complex and variable depending on the target environment (Ogunseitan 1993)
and surroundings (Ogunseitan 1996; Singleton et al. 2003).
5.2.2 Metaproteomics Approaches
Metaproteome analysis involves various technical processes such as microbial protein extraction from the samples and subsequent identification and functionality
assessment of the protein networks. Similar to in situ nucleic acid-based approaches,
in metaproteomics analysis also the most critical process is making sure that the
isolated proteins truly represent the sample (Maron et al. 2007). The success of any
metaproteome experiments depends upon three factors: (i) efficient protein isolation
from the sample, (ii) protein segregation and fractionation before detection, and (iii)
robust protein identification (Hettich et al. 2013). It is largely applicable in the case
of proteomic analysis of the environment as their highly heterogeneous and complex nature makes the specific isolation of the microbial proteome difficult. The
extraction methodology differs according to selected proteins (which could potentially be from prokaryotes or eukaryotes, cellular or extracellular in nature) and by
the successive techniques of proteome study (i.e., comparable 2-D protein maps,
identification of proteins and enzyme activities) (Maron et al. 2007).
After the isolation of protein samples, diverse biochemical approaches are
employed for the metaproteome study depending upon the required resolution and
information. To obtain a “proteofingerprint” of the microorganisms, environmental
5.2 Metaproteomics
understanding about microbial recruiting, organism interactions, cooperation and
competence for nutrient resources, and metabolic activities (Hettich et al. 2013). At
a somewhat higher level, the information is crucial for depiction of host–microbe
crosstalk such as microorganism–plant or microorganism–human interactions
(Hettich et al. 2013). In a nutshell, environmental metaproteomics perspectives have
founded a “proof- of- concept” that can facilitate applications to numerous significant research areas such as bioremediation, carbon cycling, bioenergy, and human
health (Hettich et al. 2013). Until now, most of the proteomics experiments are
focused on the analysis of single species under different conditions, leaving the
perspective of microbial community proteomics almost totally unexplored (Lacerda
et al. 2007). Furthermore, metaproteome analysis from different environmental conditions allows (1) identification of novel genes and cellular pathways and (2) recognition of stress-responsive proteins (Maron et al. 2007). There exist numerous
challenges in microbial community proteomics such as representative protein
extraction, sample complexity for separation (including even thousands of bacterial
proteomes), and an almost total absence of genomic sequences for microbes in ecological communities (Lacerda et al. 2007). Metaproteomics analysis of diverse environments such as the natural microbial biofilm (Ram et al. 2005), water (Kan et al.
2005; Ogunseitan 1993, 1996, 1997), sediment (Ogunseitan 1993), soil (Ogunseitan
1993; Singleton et al. 2003), and processed sludge (Wilmes and Bond 2004) have
led to the discovery that the protein complement of the metagenome was much
more complex and variable depending on the target environment (Ogunseitan 1993)
and surroundings (Ogunseitan 1996; Singleton et al. 2003).
5.2.2 Metaproteomics Approaches
Metaproteome analysis involves various technical processes such as microbial protein extraction from the samples and subsequent identification and functionality
assessment of the protein networks. Similar to in situ nucleic acid-based approaches,
in metaproteomics analysis also the most critical process is making sure that the
isolated proteins truly represent the sample (Maron et al. 2007). The success of any
metaproteome experiments depends upon three factors: (i) efficient protein isolation
from the sample, (ii) protein segregation and fractionation before detection, and (iii)
robust protein identification (Hettich et al. 2013). It is largely applicable in the case
of proteomic analysis of the environment as their highly heterogeneous and complex nature makes the specific isolation of the microbial proteome difficult. The
extraction methodology differs according to selected proteins (which could potentially be from prokaryotes or eukaryotes, cellular or extracellular in nature) and by
the successive techniques of proteome study (i.e., comparable 2-D protein maps,
identification of proteins and enzyme activities) (Maron et al. 2007).
After the isolation of protein samples, diverse biochemical approaches are
employed for the metaproteome study depending upon the required resolution and
information. To obtain a “proteofingerprint” of the microorganisms, environmental
5.2 Metaproteomics