Biology subjects

Graham, E. B.

Publications and source records attributed to Graham, E. B..

22 records · Page 2Linked to original sources

bioRxiv2018

Forfeiting the founder effect: turnover defines biofilm community succession

Microbial community succession is a fundamental process that effects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are poorly understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the roles of founder species? We performed a succession experiment within a hypersaline microbial mat ecosystem to investigate how ecological processes contributed to the turnover of founder species. Bacterial and micro-eukaryotic founder species were identified from primary succession and tracked through a defined maturation period using 16S and 18S rRNA gene amplicon sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate basic functional capabilities. The majority of the founder species did not maintain high relative abundances in later stages of succession. Turnover (versus nestedness) was the dominant process shaping the final community structure. We also asked if different ecological processes acted on bacteria versus eukaryotes during successional stages and found that deterministic and stochastic forces corresponded more with eukaryote and bacterial colonization, respectively. Our results show that taxa from different kingdoms, that share habitat in the tight spatial confines of a biofilm, were influenced by different ecological forces and time scales of succession.

ecology↗

bioRxiv2017

Stochastic microbial community assembly decreases biogeochemical function

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative influence of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function, which we define generically to represent any biogeochemical reaction of interest. We used an ecological simulation model to evaluate this hypothesis. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by deterministic selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal rates high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer its biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.

ecology↗

bioRxiv2017

Riparian vegetation limits oxidation of thermodynamically unfavorable bound-carbon stocks along an aquatic interface

In light of increasing terrestrial carbon (C) transport across aquatic boundaries, the mechanisms governing organic carbon (OC) oxidation along terrestrial-aquatic interfaces are crucial to future climate predictions. Here, we investigate the biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor using ultra-high resolution C characterization. We leverage natural vegetative differences to encompass variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition associated with diminished riparian vegetation induce oxidation of physically -bound OC. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and--in direct conflict with the priming concept--that inputs of water-soluble and thermodynamically favorable terrestrial OC protects bound-OC from oxidation. In both environments, the most thermodynamically favorable compounds appear to be preferentially oxidized regardless of which OC pool microbiomes metabolize. In turn, we suggest that the extent of riparian vegetation causes sediment microbiomes to locally adapt to oxidize a particular pool of OC, but that common thermodynamic principles govern the oxidation of each pool (i.e., water-soluble or physically-bound). Finally, we propose a mechanistic conceptualization of OC oxidation along terrestrial-aquatic interfaces that can be used to model heterogeneous patterns of OC loss under changing land cover distributions.\n\nKey pointsO_LIRiparian vegetation protects bound-OC stocks\nC_LIO_LIBiochemical processes associated with OC oxidation vary with vegetation conditions\nC_LIO_LICommon thermodynamic principles underlie OC oxidation regardless of vegetation conditions\nC_LI

ecology↗

bioRxiv2016

Deterministic assembly processes govern seasonal and spatial variation in microbiomes across hydrologically-connected hyporheic zones

Subsurface groundwater-surface water mixing zones (hyporheic zones) have enhanced biogeochemical activity, but assembly processes governing subsurface microbiomes remain a critical uncertainty in understanding hyporheic biogeochemistry. To address this obstacle, we investigated (a) biogeographical patterns in attached and waterborne microbiomes across three hydrologically-connected, physicochemically-distinct zones (inland hyporheic, nearshore hyporheic, and river); (b) assembly processes that generated these patterns; (c) groups of organisms that corresponded to deterministic changes in the environment; and (d) correlations between these groups and hyporheic metabolism. All microbiomes remained dissimilar through time, but consistent presence of similar taxa suggested dispersal and/or common selective pressures among zones. Further, we demonstrated a pronounced impact of deterministic assembly in all microbiomes as well as seasonal shifts from heterotrophic to autotrophic microorganisms associated with increases in groundwater discharge. The abundance of one statistical cluster of organisms increased with active biomass and respiration, revealing organisms that may strongly influence hyporheic biogeochemistry. Based on our results, we propose a conceptualization of hyporheic zone metabolism in which increased organic carbon concentrations during surface water intrusion support heterotrophy, which succumbs to autotrophy under groundwater discharge. These results provide new opportunities to enhance microbially-explicit ecosystem models describing hyporheic zone biogeochemistry and its influence over riverine ecosystem function.\n\nOriginality-Significance StatementSubsurface zones of groundwater and surface water mixing (hyporheic zones) are hotspots of biogeochemical activity and strongly influence carbon, nutrient and contaminant dynamics within riverine ecosystems. Hyporheic zone microbiomes are responsible for up to 95% of riverine ecosystem respiration, yet the ecology of these microbiomes remains poorly understood. While significant progress is being made in the development of microbially-explicit ecosystem models, poor understanding of hyporheic zone microbial ecology impedes development of such models in this critical zone. To fill the knowledge gap, we present a comprehensive analysis of biogeographical patterns in hyporheic microbiomes as well as the ecological processes that govern their composition and function through space and time. Despite pronounced hydrologic connectivity throughout the hyporheic zone--and thus a strong potential for dispersal--we find that ecological selection deterministically governs microbiome composition within local environments, and we identify specific groups of organisms that correspond to seasonal changes in hydrology. Based on our results, we propose a conceptual model for hyporheic zone metabolism in which comparatively high-organic C conditions during surface water intrusion into the hyporheic zone support heterotrophic metabolisms that succumb to autotrophy during time periods of groundwater discharge. These results provide new opportunities to develop microbially-explicit ecosystem models that incorporate the hyporheic zone and its influence over riverine ecosystem function.

ecology↗