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Ecological distribution and population physiology defined by proteomics in a natural microbial community.

Mueller RS, Denef VJ, Kalnejais LH, Suttle KB, Thomas BC, Wilmes P, Smith RL, Nordstrom DK, McCleskey RB, Shah MB, Verberkmoes NC, Hettich RL, Banfield JF - Mol. Syst. Biol. (2010)

Bottom Line: Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution.Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors.This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

View Article: PubMed Central - PubMed

Affiliation: Earth and Planetary Science Department, University of California, Berkeley, CA 94720, USA.

ABSTRACT
An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

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Correlation of the community structure factor with Leptospirillum Group II proteomes. An MDS separating samples using only Leptospirillum Group II protein abundance data is shown. Symbols for each point represent community structure clusters from Figure 1B and blue and green highlights represent expression groups from Figure 2. All biofilms of the protein expression group labeled green in Figure 2 represent low developmental stage biofilms and correspond to cluster 1 of Figure 1B (i.e. all green samples are small circles). All but two communities (P25 and P33, noted by arrows) from the high developmental stage protein expression group labeled blue in Figure 2 are consistent with biofilms from cluster 2 of Figure 1B (i.e. all but two blue samples are large circles). P25 and P33 are classified as the high developmental stage samples because their whole-community proteomes included many proteins from low abundance organisms and their Leptospirillum Group II proteomes fall at cluster edges. Stress value is reported in top-right corner of the graph.
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f3: Correlation of the community structure factor with Leptospirillum Group II proteomes. An MDS separating samples using only Leptospirillum Group II protein abundance data is shown. Symbols for each point represent community structure clusters from Figure 1B and blue and green highlights represent expression groups from Figure 2. All biofilms of the protein expression group labeled green in Figure 2 represent low developmental stage biofilms and correspond to cluster 1 of Figure 1B (i.e. all green samples are small circles). All but two communities (P25 and P33, noted by arrows) from the high developmental stage protein expression group labeled blue in Figure 2 are consistent with biofilms from cluster 2 of Figure 1B (i.e. all but two blue samples are large circles). P25 and P33 are classified as the high developmental stage samples because their whole-community proteomes included many proteins from low abundance organisms and their Leptospirillum Group II proteomes fall at cluster edges. Stress value is reported in top-right corner of the graph.

Mentions: For Leptospirillum Group II, CS bore the strongest correlation to protein expression patterns (Table Ia). This relationship is illustrated by an MDS created using proteomic data for this organism (Figure 3), with circles superimposed over each sample point representing the two CS clusters from Figure 1B.


Ecological distribution and population physiology defined by proteomics in a natural microbial community.

Mueller RS, Denef VJ, Kalnejais LH, Suttle KB, Thomas BC, Wilmes P, Smith RL, Nordstrom DK, McCleskey RB, Shah MB, Verberkmoes NC, Hettich RL, Banfield JF - Mol. Syst. Biol. (2010)

Correlation of the community structure factor with Leptospirillum Group II proteomes. An MDS separating samples using only Leptospirillum Group II protein abundance data is shown. Symbols for each point represent community structure clusters from Figure 1B and blue and green highlights represent expression groups from Figure 2. All biofilms of the protein expression group labeled green in Figure 2 represent low developmental stage biofilms and correspond to cluster 1 of Figure 1B (i.e. all green samples are small circles). All but two communities (P25 and P33, noted by arrows) from the high developmental stage protein expression group labeled blue in Figure 2 are consistent with biofilms from cluster 2 of Figure 1B (i.e. all but two blue samples are large circles). P25 and P33 are classified as the high developmental stage samples because their whole-community proteomes included many proteins from low abundance organisms and their Leptospirillum Group II proteomes fall at cluster edges. Stress value is reported in top-right corner of the graph.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2913395&req=5

f3: Correlation of the community structure factor with Leptospirillum Group II proteomes. An MDS separating samples using only Leptospirillum Group II protein abundance data is shown. Symbols for each point represent community structure clusters from Figure 1B and blue and green highlights represent expression groups from Figure 2. All biofilms of the protein expression group labeled green in Figure 2 represent low developmental stage biofilms and correspond to cluster 1 of Figure 1B (i.e. all green samples are small circles). All but two communities (P25 and P33, noted by arrows) from the high developmental stage protein expression group labeled blue in Figure 2 are consistent with biofilms from cluster 2 of Figure 1B (i.e. all but two blue samples are large circles). P25 and P33 are classified as the high developmental stage samples because their whole-community proteomes included many proteins from low abundance organisms and their Leptospirillum Group II proteomes fall at cluster edges. Stress value is reported in top-right corner of the graph.
Mentions: For Leptospirillum Group II, CS bore the strongest correlation to protein expression patterns (Table Ia). This relationship is illustrated by an MDS created using proteomic data for this organism (Figure 3), with circles superimposed over each sample point representing the two CS clusters from Figure 1B.

Bottom Line: Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution.Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors.This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

View Article: PubMed Central - PubMed

Affiliation: Earth and Planetary Science Department, University of California, Berkeley, CA 94720, USA.

ABSTRACT
An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

Show MeSH