Biome-Level Biogeography of Streambed Microbiota

Abstract

A field study was conducted to determine the microbial community structures of streambed sediments across diverse geographic and climatic areas. Sediment samples were collected from three adjacent headwater forest streams within three biomes, eastern deciduous (Pennsylvania), southeastern coniferous (New Jersey), and tropical evergreen (Guanacaste, Costa Rica), to assess whether there is biome control of stream microbial community structure. Bacterial abundance, microbial biomass, and bacterial and microbial community structures were determined using classical, biochemical, and molecular methods. Microbial biomass, determined using phospholipid phosphate, was significantly greater in the southeastern coniferous biome, likely due to the smaller grain size, higher organic content, and lower levels of physical disturbance of these sediments. Microbial community structure was determined using phospholipid fatty acid (PLFA) profiles and bacterial community structure from terminal restriction fragment length polymorphism and edited (microeukaryotic PLFAs removed) PLFA profiles. Principal component analysis (PCA) was used to investigate patterns in total microbial community structure. The first principal component separated streams based on the importance of phototrophic microeukaryotes within the community, while the second separated southeastern coniferous streams from all others based on increased abundance of fungal PLFAs. PCA also indicated that within-and among-stream variations were small for tropical evergreen streams and large for southeastern coniferous streams. A similar analysis of bacterial community structure indicated that streams within biomes had similar community structures, while each biome possessed a unique streambed community, indicating strong withinbiome control of stream bacterial community structure.

Direct and Indirect Influence of Parental Bedrock on Streambed Microbial Community Structure in Forested Streams

“…This support should be tempered by the understanding that while PLFA analysis produces quantitative data, unlike DNA-based methods (50), it is a phenotypic method (see reference 23 for a full discussion of the advantages and disadvantages of the PLFA approach). It should be noted that when PLFA and molecular methods are applied in tandem, they produce very similar analyses of microbial community structure (28,32). These results definitively demonstrated that DOM quality and bedrock composition, via the influence on stream water chemistry, influenced microbial community structure in streambed sediments.…”

“…Variation occurred among biomes, among streams with a biome, and for one biome, within streams. Interestingly, the second component of variation in microbial community structure in the Findlay et al (28) study appeared to be associated with stream water ion concentrations/geology. In our current study, the importance of eukaryotes versus bacteria was evident both seasonally and by bedrock type, with the variation in microbial community structure in the limestone streams characterized by higher relative abundances of microeukaryotic fatty acid markers, while bacterial fatty acids were significant in describing the variation in the sandstone streams.…”

“…Streams flowing over sandstone bedrock consistently showed lower pH and cation concentrations, while streams flowing over limestone bedrock showed higher pH and cation concentrations. Previously, Findlay et al (28) showed differences in microbial community structure in stream sediments at the biome level; while they noted differences in stream water chemistry among biomes they did not determine proximate causes contributing to the variations in microbial community structure. The current study describes variation in stream water chemistry and streambed microbial community structure of six streams within one biome.…”

“…Many studies in the past were limited by methodological tools to elucidate bacterial species, as most bacteria found in the natural environment have yet to be cultured and functional roles and diversity were largely unknown (56,64). With the recent advances in non-culture-dependent techniques, there has been an increase of studies that have shown evidence of varying distributions, abundance, and diversity of microorganisms in the natural environment across spatial and environmental scales, including freshwater lakes and rivers (60,65,70), streams (28), soils (8,21,51,57), and marine ecosystems (33,54). Yet, it is not clear whether limits in distribution or strong environmental selection lead to the observed patterns.…”

Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

“…Several prior studies have demonstrated habitat-driven selection of hyporheic microbial communities, including ones in systems with different hydrology, substratum properties, organic matter inputs, or gradients in heavy-metal contamination (19)(20)(21)(22)(23)(24)(25)(26). Based on this work and recent microbial community assembly studies in the Hanford 300 Area HC (15)(16)(17), deterministic selection imposed by the various DOC sources/ amounts in the three different habitats was expected to lead to distinct microbial assemblages in the colonized sand materials.…”