Emily B. Graham

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.

Linking microbial community structure and microbial processes: an empirical and conceptual overview

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009-13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearsons correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

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.

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.The well-documented significance of microorganisms to the function of virtually all ecosystems has led to the assumption that more information on microbiomes will improve our ability to understand and predict system-level processes. Notably, the importance of the microbiome has become increasingly evident in the environmental sciences and in particular ecosystem ecology. However, translating the ever-increasing wealth of information on environmental microbiomes to advance ecosystem science is proving exceptionally challenging. One reason for this challenge is that correlations between microbiomes and the ecosystem processes they influence are often reported without the underlying causal mechanisms. This limits the predictive power of each correlation to the time and place at which it was identified. In this paper, we assess the assumptions and approaches currently used to establish links between environmental microbiomes and the ecosystems they influence, propose a framework to more effectively harness our understanding of microbiomes to advance ecosystem science, and identify key challenges and solutions required to apply the proposed framework. Specifically, we suggest identifying each microbial process that contributes to the ecosystem process of interest a priori. We then suggest linking information on microbial community membership through microbial community properties (such as biomass elemental ratios) to the microbial processes that drive each ecosystem process (e.g. N -mineralization). A key challenge in this framework will be identifying which microbial community properties can be determined from the constituents of the community (community aggregated traits, CATs) and which properties are unable to be predicted from a list of their constituent taxa (emergent properties, EPs). We view this directed approach as a promising pathway to advance our understanding of how microbiomes influence the systems they inhabit.

Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology

The hyporheic corridor (HC) encompasses the river–groundwater continuum, where the mixing of groundwater (GW) with river water (RW) in the HC can stimulate biogeochemical activity. Here we propose a novel thermodynamic mechanism underlying this phenomenon and reveal broader impacts on dissolved organic carbon (DOC) and microbial ecology. We show that thermodynamically favorable DOC accumulates in GW despite lower DOC concentration, and that RW contains thermodynamically less-favorable DOC, but at higher concentrations. This indicates that GW DOC is protected from microbial oxidation by low total energy within the DOC pool, whereas RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW–RW mixing overcomes these protections and stimulates respiration. Mixing models coupled with geophysical and molecular analyses further reveal tipping points in spatiotemporal dynamics of DOC and indicate important hydrology–biochemistry–microbial feedbacks. Previously unrecognized thermodynamic mechanisms regulated by GW–RW mixing may therefore strongly influence biogeochemical and microbial dynamics in riverine ecosystems.The mechanisms responsible for stimulating biogeochemical activity in the hyporheic corridor (HC) are poorly understood. Here, the authors find that previously unrecognized thermodynamic mechanisms regulated by groundwater-river water mixing may strongly influence HC biogeochemical and microbial dynamics.

Dissolved organic matter and inorganic mercury loadings favor novel methylators and fermentation metabolisms in oligotrophic sediments

Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (unvegetated and vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings on microbiomes, DOM cycling, and MeHg production in the St. Louis River Estuary, which has a legacy of mercury contamination. Overall, our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments in this environment. Further, oligotrophic unvegetated sediments receiving leachate produced more MeHg than unamended microcosms, pointing to the role of organic matter and vegetation patterns as an important control on MeHg production in these sediments.We also show that while leachate influenced the microbiome in both environment types, sediment with high organic carbon content was more resistant to change than oligotrophic sediment. Our work supports emerging research suggesting that Clostridia may be important methylators in oligotrophic environments. We demonstrate changes in community structure towards Clostridia and metagenomic shifts toward fermentation as well as degradation of complex DOM and MeHg production in unvegetated microcosms receiving leachate. Together, our work shows the importance of wetland vegetation in driving MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in the composition of microbiomes associated with higher DOM levels.Advances in genetics have allowed for greater investigation into the complex microbial communities mediating mercury methylation in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury production both through direct chemical interactions with mercury and through substrate effects on the environmental microbiome. We conducted microcosm experiments in two chemically disparate wetland environments (unvegetated and vegetated sediments) to examine the impact of DOM from leachate of local vegetation and inorganic mercury loadings on microbial community membership, metagenomic potential, DOM processing, and methylmercury production. We show that while DOM loadings impacted the microbiome in both environment types, sediment with high organic carbon content was more resistant than oligotrophic sediment to changes in microbial community structure and methylmercury production. We identify putative chemoorganotrophic methylators within the class Clostridia as primary community members associated with methylation rates in contrast to previous work focusing on microorganisms involved in sulfur, iron, and methane cycling. Metagenomic shifts toward fermentation, and secondarily iron metabolisms, as well as degradation of complex DOM indicated by fluorescence indices further support the involvement of rarely acknowledged biogeochemical pathways in mercury toxicity. We therefore propose that DOM addition in our system generates methylmercury production either 1) via direct methylation by fermenting bacteria or 2) via enhancing the bioavailability of simple carbon compounds for sulfate- and iron-reducing bacteria through breakdown of complex DOM. Our results demonstrate variation in sediment methylmercury production in response to DOM loading across geochemical environments and provide a mechanistic framework for understanding linkages between environmental microbiomes, carbon cycling, and mercury toxicity.Advances in genetics have allowed for greater investigation into the complex microbial communities mediating mercury methylation in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury production both through direct chemical interactions with mercury and through substrate effects on the environmental microbiome. We conducted microcosm experiments in two chemically disparate wetland environments (unvegetated and vegetated sediments) to examine the impact of DOM from leachate of local vegetation and inorganic mercury loadings on microbial community membership, metagenomic potential, DOM processing, and methylmercury (MeHg) production. We show that while DOM loadings impacted the microbiome in both environment types, sediment with high organic carbon content was more resistant than oligotrophic sediment to changes in microbiomes. Oligotrophic sediments receiving DOM produced significantly more MeHg than unamended microcosms, coincident with an increase in putative chemoorganotrophic methylators within the class Clostridia. Further, metagenomic shifts toward fermentation, and secondarily iron metabolisms, in these microcosms as well as degradation of complex DOM indicated by fluorescence indices also support a possible association between rarely acknowledged microbial metabolisms and MeHg production. Our research provides a basis for future investigation into the role of fermenting organisms in mercury toxicity and generates a new hypothesis that DOM can stimulate mercury methylation in oligotrophic environments either 1) via direct methylation by fermenting bacteria or 2) via enhancing the bioavailability of simple carbon compounds for sulfate- and iron-reducing bacteria through breakdown of complex DOM.Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (unvegetated and vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings on microbiomes, DOM cycling, and MeHg production. We show that while leachate influenced the microbiome in both environment types, sediment with high organic carbon content was more resistant to change than oligotrophic sediment. Oligotrophic unvegetated sediments receiving leachate produced more MeHg than unamended microcosms, coincident with an increase in putative chemoorganotrophic methylators belonging to Clostridia. Further, metagenomic shifts toward fermentation, and secondarily iron metabolisms, in these microcosms as well as degradation of complex DOM also support a possible association between rarely acknowledged microorganisms and MeHg. Our research provides a basis for future investigation into the role of fermenting organisms in mercury toxicity and generates a new hypothesis that DOM can stimulate mercury methylation either 1) via direct methylation by fermenting bacteria or 2) via enhancing carbon bioavailability for sulfate- and iron-reducing bacteria through breakdown of complex DOM.

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;

Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition

Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (oligotrophic unvegetated and high-C vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings (20 mg/L HgCl2) on microbiomes and MeHg production in the St. Louis River Estuary. Our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments. Further, our work shows how mercury cycling in oligotrophic unvegetated sediments may be susceptible to DOM inputs in the St. Louis River Estuary: unvegetated microcosms receiving leachate produced substantially more MeHg than unamended microcosms. We also demonstrate (1) changes in microbiome structure towards Clostridia, (2) metagenomic shifts toward fermentation, and (3) degradation of complex DOM; all of which coincide with elevated net MeHg production in unvegetated microcosms receiving leachate. Together, our work shows the influence of wetland vegetation in controlling MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in microbiome composition.

Understanding how microbiomes influence the systems they inhabit

Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.This Review Article discusses the importance of considering known microbial processes to inform our understanding of the role of microbial communities in ecosystem processes, and a move away from approaches based solely on correlation analyses.