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: 7.12). 06/2012; 23(3):431-6. DOI: 10.1016/j.copbio.2011.11.017
Source: PubMed


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
  • Source
    • "Antarctic fjords (Grange & Smith, 2013)) and to test hypotheses about dispersal and colonisation (such as the airborne dispersal of soil organisms in the Antarctic Dry Valleys ()) (Gonzalez et al., 2012). The upscaling of small-scale processes is not likely to respond in a linear fashion (Schimel & Potter, 1995) and thus may lead to uncertainties, and this must be kept in mind when interpreting model output. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Advances in microbial ecology in the cryosphere continue to be driven by empirical approaches including field sampling and laboratory-based analyses. Although mathematical models are commonly used to investigate the physical dynamics of Polar and Alpine regions, they are rarely applied in microbial studies. Yet, integrating modelling approaches with ongoing observational and laboratory-based work is ideally suited to Polar and Alpine microbial ecosystems given their harsh environmental and biogeochemical characteristics, simple trophic structures, distinct seasonality, often difficult accessibility, geographical expansiveness, and susceptibility to accelerated climate changes. In this opinion paper, we explain how mathematical modelling ideally complements field and laboratory-based analysis. We thus argue that mathematical modelling is a powerful tool for the investigation of these extreme environments and that fully integrated, interdisciplinary model-data approaches could help the Polar and Alpine microbiology community address some of the great research challenges of the 21st century (e.g. assessing global significance, response to climate change). However, a better integration of field and laboratory work with model design and calibration/validation, as well as a stronger focus on quantitative information is required to advance models that can be used to make predictions and upscale processes and fluxes beyond what can be captured by observations alone.
    Preview · Article · Jan 2016 · FEMS Microbiology Ecology
  • Source
    • "Simulation of light conditions in a laboratory experiment with microcosms proved that the level of light and its penetration into the anaerobic zone defined the dominant composition of the microbial community in the chemocline zone, and therefore the dominant type of metabolism-phototrophic or chemotrophic (Matyugina et al., 2014). Next-generation '-omics' technologies such as high-throughput amplicon sequencing allow collection of billions of sequences (Green et al., 2008; DeLong, 2009) and application of statistical methods enables the detection of the numerically dominant as well as uncommon organisms in a system (Bent and Forney, 2008; Gonzalez et al., 2012). The first group may be responsible for the majority of metabolic activity and energy flux, but uncommon organisms serve as a reservoir of genetic and functional diversity (Yachi and Loreau, 1999; Nandi et al., 2004), they often play key roles in ecosystems (Phillips et al., 2000), and they can become numerically important if environmental conditions change (Bent and Forney, 2008). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Meromictic soda and saline lakes are unique ecosystems characterized by the stability of physical, chemical and biological parameters, and they are distributed all over the world. Lakes located in regions with average annual negative air temperature are of particular interest because of the presence of two periods with intensive and dynamic processes: the so-called biological summer and the long ice season with the biological spring. Soda Lake Doroninskoe is located in Eastern Transbaikalia (51°14′N, 112°14′E) in the permafrost zone in an extreme continental climate, and is covered by ice for seven months per year. The structure and diversity of the microbial communities throughout the water column of the lake was studied by 16S rRNA gene amplicon metasequencing. Different species with specific functions were found to dominate at different depths. Metabolically flexible bacteria with a capacity to switch between anoxygenic photosynthesis and aerobic chemotrophic metabolism dominate in soda Lake Doroninskoe. © 2015, Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag Berlin Heidelberg.
    Full-text · Article · Nov 2015 · Chinese Journal of Oceanology and Limnology
  • Source
    • "The w value was low across the 6-year experiment, but we still observed a significantly linear decrease in the microbial similarity with time (log transformed) for the in situ samples and the northward and southward transplants. The results strongly support the claim that the community similarity decays over time (time–decay), which underlies key ecological principles; this decay appears to be universal in biology (Chytry et al., 2001; Korhonen et al., 2010; Gonzalez et al., 2012; Shade et al., 2013). We compared the microbial temporal turnover in different habitats and across different temporal scales (SupplementaryFigure S6). "
    [Show abstract] [Hide abstract]
    ABSTRACT: To understand soil microbial community stability and temporal turnover in response to climate change, a long-term soil transplant experiment was conducted in three agricultural experiment stations over large transects from a warm temperate zone (Fengqiu station in central China) to a subtropical zone (Yingtan station in southern China) and a cold temperate zone (Hailun station in northern China). Annual soil samples were collected from these three stations from 2005 to 2011, and microbial communities were analyzed by sequencing microbial 16S ribosomal RNA gene amplicons using Illumina MiSeq technology. Our results revealed a distinctly differential pattern of microbial communities in both northward and southward transplantations, along with an increase in microbial richness with climate cooling and a corresponding decrease with climate warming. The microbial succession rate was estimated by the slope (w value) of linear regression of a log-transformed microbial community similarity with time (time-decay relationship). Compared with the low turnover rate of microbial communities in situ (w=0.046, P<0.001), the succession rate at the community level was significantly higher in the northward transplant (w=0.058, P<0.001) and highest in the southward transplant (w=0.094, P<0.001). Climate warming lead to a faster succession rate of microbial communities as well as lower species richness and compositional changes compared with in situ and climate cooling, which may be related to the high metabolic rates and intense competition under higher temperature. This study provides new insights into the impacts of climate change on the fundamental temporal scaling of soil microbial communities and microbial phylogenetic biodiversity.The ISME Journal advance online publication, 19 May 2015; doi:10.1038/ismej.2015.78.
    Full-text · Article · May 2015 · The ISME Journal
Show more