Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter

Abstract

Understanding the ecological principles underlying the structure and function of microbial communities remains an important goal for microbial ecology. We examined two biogeochemically important taxa, the sulfate-reducing bacterial genus, Desulfobulbus, and the methanogenic archaeal genus, Methanosaeta, to compare and contrast niche partitioning by these two taxa that are ecologically linked as anaerobic terminal oxidizers of organic material. An observational approach utilizing functional gene pyrosequencing was combined with a community-based reciprocal incubation experiment and characterization of a novel Desulfobulbus isolate. To analyze the pyrosequencing data, we constructed a data analysis pipeline, which we validated with several control data sets. For both taxa, particular genotypes were clearly associated with certain portions of an estuarine gradient, consistent with habitat or niche partitioning. Methanosaeta genotypes were generally divided between those found almost exclusively in the marine habitat (B30% of operational taxonomic units (OTUs)), and those which were ubiquitously distributed across all or most of the estuary (B70% of OTUs). In contrast to this relatively monotonic distribution, for Desulfobulbus, there were many more genotypes, and their distributions represented a wide range of inferred niche widths from specialist genotypes found only at a single site, to ubiquitous or generalist genotypes found in all 10 sites examined along the full estuarine gradient. Incubation experiments clearly showed that, for both taxa, communities from opposite ends of the estuary did not come to resemble one another, regardless of the chemical environment. Growth of a Desulfobulbus isolated into pure culture indicated that the potential niche of this organism is significantly larger than the realized niche. We concluded that niche partitioning can be an important force structuring microbial populations, with biotic and abiotic components having very different effects depending on the physiology and ecology of each taxon.

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces

“…S5b and S5c) lending support to the generality of the principle of emergence of spatial self-assembly of interacting microbial populations. The results reflect the importance of specific metabolic stoichiometry within multi-nutrients environments that result in trophic-induced niche partitioning3233 for promoting stable microbial spatial patterns.…”

Genotypic Distribution of a Specialist Model Microorganism, Methanosaeta, along an Estuarine Gradient: Does Metabolic Restriction Limit Niche Differentiation Potential?

“…This variability, which is not apparent on the DGGE pattern, can be explained by the limited scale of the clone libraries from each site, a perennial problem in microbial ecology. The use of functional gene targeted pyrosequencing confirms that Methanosaeta genotypes were not sequentially distributed along the estuary [22]. Therefore, the Methanosaeta distribution pattern can be described as monotonic, which contrasts markedly with that observed for Desulfobulbus.…”

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

“…The surface freshwater from the littoral zone and from the middle of the lake along with the deepest mineral layer from the shore site may be less hospitable or more favorable to competitive non-generalist microorganisms, constituting particular niches where few habitat generalists could establish. As previously observed, niche partitioning can strongly structure microbial communities45. Habitat specialists are known to have a limited niche, but the highest fitness in their optimal habitat40.…”