Effect of Different Carbon Sources on Community Composition of Bacterial Enrichments from Soil

Abstract

Soil is a highly heterogeneous matrix, which can contain thousands of different bacterial species per gram. Only a small component of this diversity (maybe <1%) is commonly captured using standard isolation techniques, although indications are that a larger proportion of the soil community is in fact culturable. Better isolation techniques yielding greater bacterial diversity would be of benefit for understanding the metabolic activity and capability of many soil microorganisms. We studied the response of soil bacterial communities to carbon source enrichment in small matrices by means of terminal restriction fragment length polymorphism (TRFLP) analysis. The community composition of replicate enrichments from soil displayed high variability, likely attributable to soil heterogeneity. An analysis of TRFLP data indicated that enrichment on structurally similar carbon sources selected for similar bacterial communities. The same analysis indicated that communities first enriched on glucose or benzoate and subsequently transferred into medium containing an alternate carbon source retained a distinct community signature induced by the carbon source used in the primary enrichment. Enrichment on leucine presented a selective challenge that was able to override the imprint left by primary enrichment on acetate. In a time series experiment community change was most rapid 18 hours after inoculation, corresponding to exponential growth. Community composition did not stabilize even 4 days after secondary enrichment. Four different soil types were enriched on four different carbon sources. TRFLP analysis indicated that in three out of four cases communities enriched on the same carbon source were more similar regardless of which soil type was used. Conversely, the garden soil samples yielded similar enrichment communities regardless of the enrichment carbon source. Our results indicate that in order to maximize the diversity of bacteria recovered from the environment, multiple enrichments should be performed using a chemically diverse set of carbon sources.

Biogeography of Actinomycete Communities and Type II Polyketide Synthase Genes in Soils Collected in New Jersey and Central Asia

“…The two methods produced analogous results. Pairwise similarity values were calculated using two different methods, as previously described (33,34). The Sorenson index was calculated as follows:…”

Technicalities and Glitches of Terminal Restriction Fragment Length Polymorphism (T-RFLP)

“…Past study showed that researchers often do not have a very good idea about data normalization, data transformation and statistical methods to be applied for the data generated [36]. Several points must be reckoned before analyzing the data of community analysis and some of them being: (1) setting of accurate fluorescence threshold to discriminate true peaks from baseline noise; (2) alignment of replicate profiles to a single consensus profile; (3) normalization of data for clustering and statistical analysis [13,34,[36][37][38][39]; and (4) matching against databases for confirmation of specificity of T-RFs from clone libraries [24].…”

“…Abdo et al [37] reported that injudicious choice of minimum peak height may lead to difficulties in data analysis. Initially, a method for selection of minimum peak height based on variability and % similarity of T-RFs in replicated profiles was also proposed [13,34]. Discarding of the peaks with a relative peak area (calculated by dividing the area of individual peak by the cumulative area of all peaks in the sample) of less than 1 % also helps in eliminating the background noise [35].…”

“…It is an inexpensive, robust, reproducible, and rapid method for the study of microbial community structure. The potential of T-RFLP method for the study of community dynamics and structure is extensively studied for diverse habitats [5][6][7][8][9][10][11][12][13][14]. In addition to 16S rRNA gene, T-RFLP analysis also included genes representing a variety of functional groups [15][16][17].…”

Suppression of Bacterial Wilt and Fusarium Wilt by a <i>Burkholderia nodosa</i> Strain Isolated from Kalimantan Soils, Indonesia

“…The addition of carbon substrates is considered one effective method to enhance the colonization of BCAs. Carbon sources can increase growth rates of certain types of rhizosphere microorganisms and thereby affect competition for space and nutrients, resulting in a modified community of microorganisms 9,15,16,19,41 ). Our previous study also found that the addition of organic compounds such as glucose and lysine had a conducive suppressive effect against bacterial wilt of tomato, possibly through modification of the indigenous microbial community 26) .…”