Alex R. Crump

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes: Deterministic assembly of hyporheic microbiomes

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.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures—imposed by sediment and porewater physicochemistry—integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound Organic Carbon Via Biochemical and Thermodynamic Processes

1 In light of increasing terrestrial carbon (C) transport across aquatic boundaries, the 2 mechanisms governing organic carbon (OC) oxidation along terrestrial-aquatic interfaces are 3 crucial to future climate predictions. Here, we investigate the biochemistry, metabolic pathways, 4 and thermodynamics corresponding to OC oxidation in the Columbia River corridor using ultra5 high resolution C characterization. We leverage natural vegetative differences to encompass 6 variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition 7 associated with diminished riparian vegetation induce oxidation of physically -bound OC. We 8 also find that contrasting metabolic pathways oxidize OC in the presence and absence of 9 vegetation and—in direct conflict with the ‘priming’ concept—that inputs of water-soluble and 10 thermodynamically favorable terrestrial OC protects bound-OC from oxidation. In both 11 environments, the most thermodynamically favorable compounds appear to be preferentially 12 oxidized regardless of which OC pool microbiomes metabolize. In turn, we suggest that the 13 extent of riparian vegetation causes sediment microbiomes to locally adapt to oxidize a particular 14 pool of OC, but that common thermodynamic principles govern the oxidation of each pool (i.e., 15 water-soluble or physically-bound). Finally, we propose a mechanistic conceptualization of OC 16 oxidation along terrestrial-aquatic interfaces that can be used to model heterogeneous patterns of 17 OC loss under changing land cover distributions. 18 19 20 21 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/105486 doi: bioRxiv preprint first posted online Feb. 2, 2017;

Effects of Integrated Pest Management on Pest Damage and Yield Components in a Rice Agro-Ecosystem in the Barisal Region of Bangladesh

Recently, recognition of negative environmental impacts associated with overuse of pesticides in the agricultural regions of Bangladesh has made it clear that unsustainable pest-control strategies must change. Integrated Pest Management (IPM) was developed for use as a tool in the production of healthy, sustainably grown food. A strategic approach to crop-pest control, IPM aims to minimize pest populations by combining environmentally friendly pest-control methods and economically viable farming practices. This study examined the impact of IPM on insect damage to crop-yield parameters in a rice agro-ecosystem. IPM methods tested were: 1) collection of egg masses; 2) sweeping (using a funnel shaped net to capture insects); 3) perching (installing a branch or pole which serves as a resting place for predatory birds); and 4) Economic Threshold Level (ETL) based insecticide application (The ETL is the point at which the value of the crop destroyed exceeds the cost of controlling the pest). We also examined the effects of prophylactic insecticide application and current management practices on rice yield. Rice-yield indicators included number of healthy tillers, number of hills, central leaf drying (Dead Heart), and grain-less panicles (White Head). For two consecutive years, the lowest percentages of Dead Heart (1.23 and 1.55) and White Head (2.06) were found in the IPM-treated plots. Further, the IPM-treated plots had higher yields (7.3-7.5 ton/ha) compared with the non-IPM treatments (6.28-7.02 ton/ha). The location of the plots appeared to be non-significant for all measured yield components. The effect of treatment on the percentage of Dead Heart, White Head, number of hills, and yield was statistically significant (p ≤ 0.05). We concluded that IPM is an effective strategy for obtaining high rice yields in sustainable rice agro-ecosystems.

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of nutrients and organic carbon have been shown to stimulate microbial activity and transformations of carbon and nitrogen. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the Columbia River HZ, the grain size distributions for sediment samples were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of microbial heterotrophic and nitrifying communities partially explained the variability in many biogeochemical attributes such as C:N ratio and %TOC. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae. Network analysis showed negative relationships between sets of co-varying organisms and sand and mud contents, and positive relationships with total organic carbon. Our results indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Relationships between facies and hydrobiogeochemical properties enable facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.

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 biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor. 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 (i.e., mineral and microbial) OC at terrestrial-aquatic interfaces. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and—in direct conflict with the concept of ‘priming’—that inputs of water-soluble and thermodynamically-favorable terrestrial OC protects bound-OC from oxidation. Based on our results, 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.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 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 (e.g., 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.

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. Originality-Significance Statement Subsurface 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.Subsurface zones of groundwater and surface water mixing (hyporheic zones) are regions of enhanced rates of biogeochemical cycling, but ecological processes influencing hyporheic microbiomes through space and time remain unknown. We sampled attached and planktonic microbiomes in the Columbia River hyporheic zone across seasonal hydrologic change within three hydrologically-connected, yet physicochemically-distinct geographic zones (inland, nearshore, river). Although microbiomes remained dissimilar through time across all zones and habitat types (attached vs. planktonic), consistent presence of certain heterotrophic taxa suggested dispersal and/or common selective pressures among all zones. We used statistical null models and co-occurrence network analysis, respectively, to demonstrate a pronounced impact of deterministic assembly on microbiomes in all data subsets and to elucidate taxa most affected by these processes. The composition of one network cluster of nearshore organisms exhibited a seasonal shift from heterotrophic to autotrophic microorganisms, and the abundance of taxa within this cluster also correlated positively with active microbial biomass and metabolism, possibly indicating that these taxa have strong influences over biogeochemical reactions within the hyporheic zone. Taken together, our research demonstrates a predominant role for deterministic assembly across highly-connected environments and provides insight into niche dynamics associated with seasonal changes in hyporheic microbiome composition and metabolism.

Investigation into the Stabilization of Soil Organic Matter by Microbes

A better understanding of below ground carbon (C) flux is of fundamental importance to predict how changing climate will influence the C balance of forest (and other) ecosystems [1]. The root system of higher plants is associated not only with soil environment composed of inorganic and organic matter, but also with a vast community of metabolically active microorganisms. Rhizosphere is the zone of soil immediately surrounding the plant roots, with the microbial population considerably higher than that of root free soil environment. Soil organic carbon pools are often defined either as labile or as recalcitrant, referring to its stability against decomposition of soil organic matter (SOM). We studied the microbial role in production and stabilization of SOM in laboratory setup of column-grown Pinus resinosa mesocosm systems [2], by (a) imaging by light and electron microscopy, with (b) high resolution chemical analysis by Fourier transform ion cyclotron resonance-mass spectroscopy (FTICR-MS), and (c) crystallographic X-ray analyses of the microbially-induced mineral weathering, to determine SOM resistance to decomposing activities.