Culturing captures members of the soil rare biosphere

Abstract

Summary The ecological significance of rare microorganisms within microbial communities remains an important, unanswered question. Microorganisms of extremely low abundance (the ‘rare biosphere’) are believed to be largely inaccessible and unknown. To understand the structure of complex environmental microbial communities, including the representation of rare and prevalent community members, we coupled traditional cultivation with pyrosequencing. We compared cultured and uncultured bacterial members of the same agricultural soil, including eight locations within one apple orchard and four time points. Our analysis revealed that soil bacteria captured by culturing were in very low abundance or absent in the culture‐independent community, demonstrating unexpected accessibility of the rare biosphere by culturing.

Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods

“…None of the bacteria isolated using several types of culturing media were representative of the major bacterial operational taxonomic units (OTUs) recovered by 454-pyrosequencing. Similar results were also observed in fresh water sample, soil samples and Montasio cheese manufacturing (Carraro et al, 2011;Vaz-Moreira et al, 2011;Shade et al, 2012). While high-throughput sequencing has typically been applied to analyze microbial communities in the environment, community enrichment during the isolation of contaminate degrading strains is seldom reported.…”

Use of CMEIAS Image Analysis Software to Accurately Compute Attributes of Cell Size, Morphology, Spatial Aggregation and Color Segmentation that Signify in Situ Ecophysiological Adaptations in Microbial Biofilm Communities

“…The smaller niche apportionment for abundant classes (2/7 and 2/9 for assemblages A and B, respectively) compared to "rare" classes (<25% relative abundance) frequently occurs when the ecology of the assemblage is dominated by only a few factors [30]. A prominent implication is that "rarity" among class membership in microbial communities is "conditional" [42] without necessarily implying unimportance, since members of rare morphotypes can be very active and significantly contribute to community stability and resilience after environmental perturbation [4,31,32].…”

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

“…The convergence points to the resilience of the alkane-degradation function through a potential 'seed bank' formed by dormant or rare alkane degraders in times of low substrate availability (Giebler et al, 2013). These microbes might be reactivated when the system experiences more favourable environmental conditions (Epstein, 2009;Shade et al, 2012). Their existence is furthermore indicated by high-abundant T-RFs formerly not detected in matured T12 soils (for example, 88,94,95,239,463,Supplementary Material S1.3 and S3).…”