Characterizing microbial communities through space and time

Department of Computer Science, University of Colorado at Boulder, Boulder, CO 80309, USA.
Current Opinion in Biotechnology (Impact Factor: 8.04). 06/2012; 23(3):431-6. DOI: 10.1016/j.copbio.2011.11.017
Source: PubMed

ABSTRACT Until recently, the study of microbial diversity has mainly been limited to descriptive approaches, rather than predictive model-based analyses. The development of advanced analytical tools and decreasing cost of high-throughput multi-omics technologies has made the later approach more feasible. However, consensus is lacking as to which spatial and temporal scales best facilitate understanding of the role of microbial diversity in determining both public and environmental health. Here, we review the potential for combining these new technologies with both traditional and nascent spatio-temporal analysis methods. The fusion of proper spatio-temporal sampling, combined with modern multi-omics and computational tools, will provide insight into the tracking, development and manipulation of microbial communities.

Download full-text


Available from: Michael Scott Robeson, Aug 19, 2015
1 Follower
  • Source
    • "In fact, bacterial diversityis clearly affected by certain environmentalfactors, such as pH, water temperature, water chemistry,nutrient condition, geographical and seasonal variations(Lindstrom et al., 2005; Hahn, 2006; Zeng et al., 2009).However, to predict and describe microbially mediated processes, spatial and temporal patterns of diversity at multiple levels could be investigated.Because of the high diversity of microbial communities, the ability to characterize their fine-scale vertical distribution has only become achievable within the past decade (Scholz et al., 2012). Next-generation 'omics' technologies such as high-throughput amplicon sequencing allow collection of thousands to millions of sequences (Green et al., 2008; DeLong, 2009) and following bystatistical methods detection of numerically dominant as well as uncommon organisms in a system (Bent, Forney, 2008; Gonzalez et al., 2012). The first ones are seem to be responsible for the majority of metabolic activity and energy flux, but uncommon organisms serve as a reservoir of genetic and functional diversity (Yachi,Loreau, 1999; Nandi et al., 2004), often play key roles in ecosystems (Phillips et al., 2000), and can become numerically important if environmental conditions change (Bent, Forney, 2008). "
    Acta Geologica Sinica 12/2014; 88(s1). DOI:10.1111/1755-6724.12266_5 · 1.25 Impact Factor
  • Source
    • "Candida tropicalis has been reported to have the ability to produce ethanol at high temperatures (Jamai et al. 2001) similar to those recorded in the areas where taberna is produced. Thus, the high environmental temperature may explain the dominance of the non-Saccharomyces yeasts in taberna production because, for instance, the local environmental conditions influence the composition of the microorganism community (Gonzalez et al. 2012). The yeast count was similar among the three palms, and their values decreased in the later samples where the ethanol content was high, pH values and sugar content were low (Table 1); the data indicates that, most likely, the microorganisms were inhibited by these conditions. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The aim of this study was to isolate and identify the yeasts present in taberna, a traditional palm wine from Mexico, which is produced by natural fermentation of the palm sap obtained from Acrocomia aculeata. A total of 450 yeast isolates were obtained from 45 taberna samples collected over 15 days of tapping at the end of fed-batch fermentation (12 hours of feeding and fermentation of the sap in the canoe) from three coyol palm trees. The yeast isolates were identified using restriction pattern analysis of the internal transcribed spacer region 5.8S-ITS and by sequence analysis of the D1/D2 divergent domain of the 26S rRNA gene. Nine different yeast species were identified in the taberna samples tested, namely, Saccharomyces cerevisiae, Hanseniaspora guilliermondii, Candida tropicalis, Candida intermedia, Kazachstania unispora, Kazachstania exigua, Meyerozyma guilliermondii, Pichia kudriavzevii (Issatchenkia orientalis) and Pichia kluyveri. The non-Saccharomyces yeasts H. guilliermondii and C. tropicalis were detected in samples from all three palm trees, while S. cerevisiae was detected in samples from only two of the palm trees. The frequency and distribution of the yeast species were different in the samples of each palm tree, which indicated that the inoculum in the palm sap may be deposited randomly by different vectors. This study is the first to characterize the yeast population associated with the palm wine named taberna.
    Annals of Microbiology 02/2014; DOI:10.1007/s13213-014-0861-8 · 1.04 Impact Factor
  • Source
    • "raditional culture - based techniques ( Pace , 1997 ; Schloss and Handelsman , 2007 ) . Fortunately , the ongoing development of culture - independent tools and high - throughput sequencing technologies has made it feasible to describe the temporal dynamics of microbial communities at time scales and resolutions that were previously unattainable ( Gonzalez et al . , 2012 ) . We conducted a meta - analysis of newly available time series of microbial communities assessed via high - throughput sequencing of the 16S rRNA gene , which permits the detailed analysis of microbial community changes through time . Our objective was to characterize temporal dynamics of microbial communities from a suite of habitat"
    [Show abstract] [Hide abstract]
    ABSTRACT: Ecologists have long studied the temporal dynamics of plant and animal communities with much less attention paid to the temporal dynamics exhibited by microbial communities. As a result, we do not know if overarching temporal trends exist for microbial communities or if changes in microbial communities are generally predictable with time. Using microbial time series assessed via high-throughput sequencing, we conducted a meta-analysis of temporal dynamics in microbial communities, including 76 sites representing air, aquatic, soil, brewery wastewater treatment, human- and plant-associated microbial biomes. We found that temporal variability in both within- and between-community diversity was consistent among microbial communities from similar environments. Community structure changed systematically with time in less than half of the cases, and the highest rates of change were observed within ranges of 1 day to 1 month for all communities examined. Microbial communities exhibited species-time relationships (STRs), which describe the accumulation of new taxa to a community, similar to those observed previously for plant and animal communities, suggesting that STRs are remarkably consistent across a broad range of taxa. These results highlight that a continued integration of microbial ecology into the broader field of ecology will provide new insight into the temporal patterns of microbial and 'macro'-bial communities alike.The ISME Journal advance online publication, 11 April 2013; doi:10.1038/ismej.2013.54.
    The ISME Journal 04/2013; 7(8). DOI:10.1038/ismej.2013.54 · 9.27 Impact Factor
Show more