Flexible Community Structure Correlates with Stable Community Function in Methanogenic Bioreactor Communities Perturbed by Glucose

Abstract

Methanogenic bioreactor communities were used as model ecosystems to evaluate the relationship between functional stability and community structure. Replicated methanogenic bioreactor communities with two different community structures were established. The effect of a substrate loading shock on population dynamics in each microbial community was examined by using morphological analysis, small-subunit (SSU) rRNA oligonucleotide probes, amplified ribosomal DNA (rDNA) restriction analysis (ARDRA), and partial sequencing of SSU rDNA clones. One set of replicated communities, designated the high-spirochete (HS) set, was characterized by good replicability, a high proportion of spiral and short thin rod morphotypes, a dominance of spirochete-related SSU rDNA genes, and a high percentage of Methanosarcina-related SSU rRNA. The second set of communities, designated the low-spirochete (LS) set, was characterized by incomplete replicability, higher morphotype diversity dominated by cocci, a predominance of Streptococcus-related and deeply branching Spirochaetales-related SSU rDNA genes, and a high percentage of Methanosaeta-related SSU rRNA. In the HS communities, glucose perturbation caused a dramatic shift in the relative abundance of fermentative bacteria, with temporary displacement of spirochete-related ribotypes by Eubacterium-related ribotypes, followed by a return to the preperturbation community structure. The LS communities were less perturbed, with Streptococcus-related organisms remaining prevalent after the glucose shock, although changes in the relative abundance of minor members were detected by morphotype analysis. A companion paper demonstrates that the more stable LS communities were less functionally stable than the HS communities

CMEIAS: A Computer-Aided System for the Image Analysis of Bacterial Morphotypes in Microbial Communities

“…This information reveals the shared dominance of regular rods and spirals in reactor HS-6 in contrast to the sole dominance of cocci in reactor LS-4 (reflected in their Simpson dominance values of 0.346 and 0.445, and J evenness values of 0.642 and 0.537, respectively). These results concur with differences in relative abundance of 16S rDNA phylogenetic probes hybridizing to corresponding whole community samples, indicating both Methanosaeta-like and Treponema-like ribotypes dominating in the high-spiral reactors and Streptococcus-like ribotypes dominating in the low-spiral reactors [15]. When provided with an appropriate sized community sample, CMEIAS can distinguish morphotype frequencies at a resolution of 0.1%.…”

“…Samples varying significantly in object counts are normalized by a percent transformation for comparison to one another. This application is currently being used to augment other methods of community analysis (e.g., profiles of metabolic volatile fatty acids, phospholipid fatty acids, ARDRA, and 16S rDNA sequencing) to develop models that predict the persistence and functional stability of complex microbial communities following nutrient up-shift perturbations in glucose-fed anaerobic bioreactors [11,15,18,19]. Figures 17a-d illustrate this application of CMEIAS in analysis of microbial community structure in two different steady-state bioreactors (labeled "high spiral" reactor HS-6 and "low spiral" reactor LS-4).…”

“…Such diversity indices are attractive because they reduce large amounts of data to single indicator numbers, but the drawback of this summarization of data is that information is lost. However, when supplemented with other characteristics of microbial communities (e.g., metabolic profiling, ribotype diversity), this CMEIAS-derived morphological information can become very useful in developing ecological models of community persistence, function, and stability [15,19].…”

Bacterial community structure corresponds to performance during cathodic nitrate reduction

“…Because 16S rRNA is considered a proxy for bacterial activity, these bacteria are significantly enriched in the biofilm community, and these data are consistent with described ecological role of these bacteria as putative denitrifiers, we find this explanation unlikely. Alternatively, we propose that the replacement of Proteobacteria with Firmicutes in the ANL reactor over time without a corresponding change in operation indicates these bacteria are functionally redundant and thus a change in composition does not affect reactor performance (Fernandez et al, 2000;Wohl et al, 2004).…”

Bioaugmentation of overloaded anaerobic digesters restores function and archaeal community

“…A lower number of clones in all samples were most similar to Methanosarcinales (family Methanosataceae), members of which metabolize acetate ( Patel andSprott, 1990 andFernandez et al, 2000). Since methane production from propionate typically involves conversion of acetate to methane, the detection of organisms classified as Methanosarcinales (family Methanosaetaceae) in all communities was expected.…”