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Plant, soil, and aquatic microbiomes interact, but scientists often study them independently. Integrating knowledge across these traditionally separate subdisciplines will generate better understanding of microbial ecological properties. Interactions among plant, soil, and aquatic microbiomes, as well as anthropogenic factors, influence important ecosystem processes, including greenhouse gas fluxes, crop production, nonnative species control, and nutrient flux from terrestrial to aquatic habitats. Terrestrial microbiomes influence nutrient retention and particle movement, thereby influencing the composition and functioning of aquatic microbiomes, which, themselves, govern water quality, and the potential for harmful algal blooms. Understanding how microbiomes drive links among terrestrial (plant and soil) and aquatic habitats will inform management decisions influencing ecosystem services. In the present article, we synthesize knowledge of microbiomes from traditionally disparate fields and how they mediate connections across physically separated systems. We identify knowledge gaps currently limiting our abilities to actualize microbiome management approaches for addressing environmental problems and optimize ecosystem services.

Anthropogenic increases in nitrogen (N) and phosphorus (P) concentrations can strongly influence the structure and function of ecosystems. Even though lotic ecosystems receive cumulative inputs of nutrients applied to and deposited on land, no comprehensive assessment has quantified nutrient-enrichment effects within streams and rivers. We conducted a meta-analysis of published studies that experimentally increased concentrations of N and/or P in streams and rivers to examine how enrichment alters ecosystem structure (state: primary producer and consumer biomass and abundance) and function (rate: primary production, leaf breakdown rates, metabolism) at multiple trophic levels (primary producer, microbial heterotroph, primary and secondary consumers, and integrated ecosystem). Our synthesis included 184 studies, 885 experiments, and 3497 biotic responses to nutrient enrichment. We documented widespread increases in organismal biomass and abundance (mean response = +48%) and rates of ecosystem processes (+54%) to enrichment across multiple trophic levels, with no large differences in responses among trophic levels or between autotrophic or heterotrophic food-web pathways. Responses to nutrient enrichment varied with the nutrient added (N, P, or both) depending on rate versus state variable and experiment type, and were greater in flume and whole-stream experiments than in experiments using nutrient-diffusing substrata. Generally, nutrient-enrichment effects also increased with water temperature and light, and decreased under elevated ambient concentrations of inorganic N and/or P. Overall, increased concentrations of N and/or P altered multiple food-web pathways and trophic levels in lotic ecosystems. Our results indicate that preservation or restoration of biodiversity and ecosystem functions of streams and rivers requires management of nutrient inputs and consideration of multiple trophic pathways.

Through litter and root inputs, plants modulate soil properties and the soil microbial communities around them. In turn, these changes in soil properties and microbial community composition can impact plant performance (i.e., plant-soil feedbacks). Many studies have focused on how plant-soil feedbacks affect plant performance and successional patterns, but studies on the impact of plant-soil feedbacks on ecosystem processes are rare. Our research focused on the potential of species-specific plant-soil feedbacks to affect rates of soil organic matter (SOM) decomposition. We conducted a “home vs. away” plant-soil feedback greenhouse experiment using two C3 grass species (Bromus inermis and Pascopyrum smithii) grown in C4 tallgrass prairie soil. We used a closed-circuit CO2 trapping method and isotopic analysis to differentiate between root-derived and SOM-derived CO2 production. Contrary to our predictions, plant-soil feedbacks on plant biomass were independent of the effects of plant-soil interactions on SOM-derived CO2 production, but we did detect a significant legacy of conditioning by B. inermis on subsequent total belowground respiration (i.e., total belowground respiration was higher in soils originally conditioned by B. inermis regardless of which plant species was currently growing in those soils). We attribute these results to the differential effects of these plant species on soil chemistry and soil microbes during the original conditioning phase. This is supported by the observation that differences in soil chemistry and bacterial community composition persisted in soils conditioned by different plant species throughout the entire experiment. Together these results suggest that plant-soil history is important for soil respiration and that differences in soil microbial communities induced by conditioning with different plant species may have lasting effects on ecosystem processes.

Managing landscapes to maintain climate refugia is likely the best strategy to promote persistence of temperature-sensitive species with limited dispersal capacity. Rare, cold-stenothermic taxa occupy mosaic mountain stream networks due largely to hydrological source heterogeneity. We collected environmental and biological data from alpine streams in the Teton Range, Wyoming representing runoff from snowpack (N=3), glaciers (N=4) and subterranean ice (N=4), every summer from 2015-2017. We quantified differences in habitat among the streams according to a glaciality index that included bed stability, suspended solids, temperature and conductivity, and by comparing annual water temperature profiles for each stream. We measured to what degree macroinvertebrate and diatom assemblages varied by stream type. Abiotic and biotic characteristics appeared to differ among sources. Notably, streams fed by subterranean ice (icy seeps) maintained extremely low (mean

Alpine streams are threatened as meltwater sources diminish. We established baseline monitoring efforts of alpine streams in the Teton Range during 2015 by describing biotic and abiotic conditions of surface glacier and snowmelt streams. Our results indicated a third alpine stream type, icy seeps. Icy seeps are fed by subterranean ice melt, extremely cold but stable water temperature (summer mean 50 μS cm-1). In 2016, we documented several icy seeps in the Teton massif, and our data suggest that they have the potential to serve as climate refugia for organisms and processes associated with extremely cold meltwater, due to the subterranean ice sources being more insulated from atmospheric conditions than surface glaciers and snowpack. Our 2016 work focused on locating icy seeps and documenting physical conditions, invertebrates, diatoms, and microbes in these alpine streams. We are processing the biological data, but microbial assemblages in icy seeps are similar to those found in streams fed by dwindling surface glacier ice. We are preparing to submit a paper about the microbial patterns, including how they compare to alpine streams representing comparable hydrological sources in Glacier National Park. Featured photo by Nicole Y-C on Unsplash. https://unsplash.com/photos/9XixVlnUCbk

Closing nutrient loops in terrestrial and aquatic ecosystems is integral to achieve resource security in the food-energy-water (FEW) nexus. We performed multiyear (2005-2008), monthly sampling of instream dissolved inorganic nutrient concentrations (NH4-N, NO3-N, soluble reactive phosphorus-SRP) along a ∼ 300-km arid-land river (Rio Grande, NM) and generated nutrient budgets to investigate how the net source/sink behavior of wastewater and irrigated agriculture can be holistically managed to improve water quality and close nutrient loops. Treated wastewater on average contributed over 90% of the instream dissolved inorganic nutrients (101 kg/day NH4-N, 1097 kg/day NO3-N, 656 kg/day SRP). During growing seasons, the irrigation network downstream of wastewater outfalls retained on average 37% of NO3-N and 45% of SRP inputs, with maximum retention exceeding 60% and 80% of NO3-N and SRP inputs, respectively. Accurate quantification of NH4-N retention was hindered by low loading and high variability. Nutrient retention in the irrigation network and instream processes together limited downstream export during growing seasons, with total retention of 33-99% of NO3-N inputs and 45-99% of SRP inputs. From our synoptic analysis, we identify trade-offs associated with wastewater reuse for agriculture within the scope of the FEW nexus and propose strategies for closing nutrient loops in arid-land rivers.

Alpine streams are dynamic habitats harboring substantial biodiversity across small spatial extents. The diversity of alpine stream biota is largely reflective of environmental heterogeneity stemming from varying hydrological sources. Globally, alpine stream diversity is under threat as meltwater sources recede and stream conditions become increasingly homogeneous. Much attention has been devoted to macroinvertebrate diversity in alpine headwaters, yet to fully understand the breadth of climate change threats, a more thorough accounting of microbial diversity is needed. We characterized microbial diversity (specifically Bacteria and Archaea) of 13 streams in two disjunct Rocky Mountain subranges through 16S rRNA gene sequencing. Our study encompassed the spectrum of alpine stream sources (glaciers, snowfields, subterranean ice, and groundwater) and three microhabitats (ice, biofilms, and streamwater). We observed no difference in regional (γ) diversity between subranges but substantial differences in diversity among (β) stream types and microhabitats. Within-stream (α) diversity was highest in groundwater-fed springs, lowest in glacier-fed streams, and positively correlated with water temperature for both streamwater and biofilm assemblages. We identified an underappreciated alpine stream type-the icy seep-that are fed by subterranean ice, exhibit cold temperatures (summer mean

Technological advances in sequencing technologies and bioinformatics analysis tools now enable the generation of a metagenome from soil, although the ultimate goal of obtaining the entire complement of all genes of all organisms in a given sample of soil still lies in the future. The rich information obtained from a soil metagenome will undoubtedly provide new insights into the taxonomic and functional diversity of soil microorganisms; the question is whether it will also yield greater understanding of how C, N, and other nutrients cycle in soil. The purpose of this review is to describe the steps involved in producing a soil metagenome, including some of the potential pitfalls associated with its production and annotation. Possible solutions to some of these challenges are presented. Selected examples from published soil metagenomic studies are discussed, with an emphasis on clues that they have provided about biogeochemical cycling.

Agricultural and urban development alters nitrogen and other biogeochemical cycles in rivers worldwide. Because such biogeochemical processes cannot be measured empirically across whole river networks, simulation models are critical tools for understanding river-network biogeochemistry. However, limitations inherent in current models restrict our ability to simulate biogeochemical dynamics among diverse river networks. We illustrate these limitations using a river-network model to scale up in situ measures of nitrogen cycling in eight catchments spanning various geophysical and land-use conditions. Our model results provide evidence that catchment characteristics typically excluded from models may control river-network biogeochemistry. Based on our findings, we identify important components of a revised strategy for simulating biogeochemical dynamics in river networks, including approaches to modeling terrestrial-aquatic linkages, hydrologic exchanges between the channel, floodplain/riparian complex, and subsurface waters, and interactions between coupled biogeochemical cycles.

Canalization and incision are common morphological alterations associated with human land use that reduce hydrological/hydrodynamic linkages between surtace and ground waters in stream ecosystems. To explore the impacts of these anthropogenic changes on nutrient spiraling in streams, we measured the linkage between hyporheic and surface zones of reference and human-altered streams using 15 N-nitrate ( 15 NO 3 ― ) and bromide (Br ― ) tracer injection experiments. Experiments were conducted in 7 streams (3 reference, 3 agricultural and 1 urban) in Arizona and New Mexico, USA, over a 3 yr period during the Lotic Intersite Nitrogen eXperiment (LINX II). Groundwater wells (6―9 in each stream) were inserted to 30cm depth and multilevel samplers (MLS) were installed downstream from injection sites to measure inorganic nitrogen (N) and Br ― concentrations in hyporheic water. There was measurable surface water-ground water (SW-GW) connectivity, as indicated by Br ― concentrations in shallow alluvial ground water (0―30 cm depth) at all sites. SW-GW connectivity was higher in reference than in human-altered streams. Concentrations of NO 3 ― and NH 4 + in MLS cells (0―10, 10―20, and 20―30 cm below streambed) were inversely correlated, and 15 N-enrichment of both N species was measurable in groundwater wells. Hyporheic zones with lower surface-water infiltration had higher quantities of 15 NH 4 + than of 15 NO 3 ― . Whole stream uptake (k tot ; calculated during the LINX II experiments) was correlated with δ 15 NH 4 + in wells; i.e., high δ 15 NH 4 + in wells was associated with high stream uptake, and both whole stream NO 3 ― uptake and δ 15 NH 4 + were highest in the human-altered streams. The presence of enriched 15 NH 4 + in many of the wells within 24 h of injection suggested that dissimilatory nitrate reduction to ammonium (DNRA) was occurring in the hyporheic zone.

In desert ecosystems, microbial activity and associated nutrient cycles are driven primarily by water availability and secondarily by nutrient availability. This is especially apparent in the extremely low productivity cold deserts of the McMurdo Dry Valleys, Antarctica. In this region, sediments near streams and lakes provide the seasonally wet conditions necessary for microbial activity and nutrient cycling and thus transfer energy to higher organisms. However, aside from a few studies of soil respiration, rates of microbial activity throughout the region remain unexplored. We measured extracellular enzyme activity potentials (alkaline phosphatase, leucine-aminopeptidase, beta-glucosidase, phenol oxidase, and peroxidase) in soils adjacent to lakes and streams, expecting activity to be primarily related to soil water content, as well as time of season and organic matter supply. Phosphatase and beta-glucosidase activities were higher in shoreline than upland soils; however, potential rates were not correlated with soil water content. Instead, soil organic matter, salinity, and pH were the best predictors of microbial activity. Microbial nutrient limitation metrics estimated from extracellular enzyme activity were correlated with pH and salinity and exhibited similar patterns to previously published trends in soil P and N content. Compared to other terrestrial ecosystems, organic matter specific rates for leucine-aminopeptidase and oxidative enzyme activities were high, typical of alkaline desert soils. Phosphatase activity was close to the global mean whereas beta-glucosidase activity was extremely low, which may reflect the lack of vascular plant derived organic matter in the Dry Valleys. In this cold desert ecosystem, water availability promotes microbial activity, and microbial nutrient cycling potentials are related to soil geochemistry.

Summary 1 Aridland ecosystems cover about one-third of terrestrial environments globally, yet the extent to which models of carbon (C) and nitrogen (N) cycling, developed largely from studies of mesic ecosystems, apply to aridland systems remains unclear. 2 Within aridland ecosystems, C and N dynamics are often described by a pulse-reserve model in which episodic precipitation events stimulate biological activity that generate reserves of biomass, propagules and organic matter that prime the ecosystem to respond rapidly to subsequent precipitation events. 3 The role of microbial C and N processing within the pulse-reserve paradigm has not received much study. We present evidence suggesting that fungi play a critical and underappreciated role in aridland soils, including efficient decomposition of recalcitrant C compounds, N-transformations such as nitrification, and nutrient storage and translocation of C and N between plants and biotic soil crusts. While fungi may perform some of these functions in other ecosystems, this ‘fungal loop’ assumes particular importance in the N cycle in aridlands because water availability imposes even greater restrictions on bacterial activity and physicochemical processes limit accumulation of soil organic matter (SOM). 4 We incorporate these findings into a Threshold-Delay Nutrient Dynamics (TDND) model for aridland ecosystems in which plant responses to pulsed precipitation events are mediated by a fungal loop that links C and N cycling, net primary production (NPP) and decomposition in aridland soils. 5 Synthesis. Arid ecosystems are highly sensitive to global environmental change including N deposition and altered precipitation patterns; yet, models from mesic ecosystems do not adequately apply to aridland environments. Our ‘fungal loop’ N cycle model integrates spatial structure with pulse dynamics and extends the pulse-reserve paradigm to include the key role of microbial processes in aridland ecosystem dynamics.

Nutrient spiraling in theory and application provides a framework for comparing nutrient retention efficiency of urban streams to relatively unaltered streams. Previous research indicated that streams of the southwestern USA deserts are highly retentive of N because of N limitation, high productivity, and high channel complexity (in particular, extensive transient storage associated with the hyporheic zone). Most southwestern urban streams have extensively modified channels and experience N loading from urban runoff and inputs of NO3−-contaminated groundwater. Therefore, we predicted southwestern urban streams are neither N-limited nor retentive. For some urban streams, however, restoration efforts reestablish flow in long-dry channels, create nonstructural flood-management solutions, and design riparian areas as a public recreation amenity. These human modifications may, in part, restore N retention functions if channel complexity and heterogeneity are as important to N retention efficiency as be...

Soils process and store large amounts of C; however, considerable uncertainty still exists about the details of that influence microbial partitioning of C into soil C pools, and what are the main influential forces that control the fraction of the C input that is stabilized. The soil microbial community is genotypically and phenotypically diverse. Despite our ability to predict the kinds of regional environmental changes that will accompany global climate change, it is not clear how the microbial community will respond to climate-induced modification of precipitation and inter-precipitation intervals, and if this response will affect the fate of C deposited into soil by the local plant community. Part of this uncertainty lies with our ignorance of how the microbial community adapts genotypically and physiologically to changes in soil moisture brought about by shifts in precipitation. Our overarching goal is to harness the power of multiple meta-omics tools to gain greater understanding of the functioning of whole-soil microbial communities and their role in C cycling. We will do this by meeting the following three objectives: 1. Further develop and optimize a combination of meta-omics approaches to study how environmental factors affect microbially-mediated C cycling processes. 2. Determine the impacts of long-termmore » changes in precipitation timing on microbial C cycling using an existing long-term field manipulation of a tallgrass prairie soil. 3. Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes. We took advantage of our state-of-the-art expertise in community “omics” to better understand the functioning soil C cycling within the Great Prairie ecosystem, including our ongoing Konza Prairie soil metagenome flagship project at JGI and the unique rainfall manipulation plots (RaMPs) established at this site more than a decade ago. We employed a systems biology approach, considering the complex soil microbial community as a functioning system and using state-of-the-art metatranscriptomic, metaproteomic, and metabolomic approaches. These omics tools were refined, applied to field experiments, and confirmed with controlled laboratory studies. Our experiments were designed to specifically identify microbial community members and processes that are instrumental players in processing of C in the prairie soils and how these processes are impacted by wetting and drying events. This project addresses a key ecosystem in the United States that current climate models predict will be subjected to dramatic changes in rainfall patterns as a result of global warming. Currently Mollisols, such as those of the tallgrass prairie, are thought to sequester more C than is released into the atmosphere, but it is not known what changes in rainfall patterns will have on future C fluxes. Through an analysis of the molecular response of the soil microbial community to shifts in precipitation cycles that are accompanied by phenologically driven changes in quality of plant C rhizodeposits, we gained deeper insight into how the metabolism of microbes has adapted to different precipitation regimes and the impact of this adaption on the fate of C deposited into soil. In doing so, we addressed key questions about the microbial cycling of C in soils that have been identified by the DOE.« less

Climate change models predict that future precipitation patterns will entail lower-frequency but larger rainfall events, increasing the duration of dry soil conditions. Resulting shifts in microbial C cycling activity could affect soil C storage. Further, microbial response to rainfall events may be constrained by the physiological or nutrient limitation stress of extended drought periods; thus seasonal or multiannual precipitation regimes may influence microbial activity following soil wet-up. We quantified rainfall-driven dynamics of microbial processes that affect soil C loss and retention, and microbial community composition, in soils from a long-term (14-year) field experiment contrasting ''Ambient'' and ''Altered'' (extended intervals between rainfalls) precipitation regimes. We collected soil before, the day following, and five days following 2.5-cm rainfall events during both moist and dry periods (June and September 2011; soil water potential ¼� 0.01 and � 0.83 MPa, respectively), and measured microbial respiration, microbial biomass, organic matter decomposition potential (extracel- lular enzyme activities), and microbial community composition (phospholipid fatty acids). The equivalent rainfall events caused equivalent microbial respiration responses in both treatments. In contrast, microbial biomass was higher and increased after rainfall in the Altered treatment soils only, thus microbial C use efficiency (CUE) was higher in Altered than Ambient treatments (0.70 6 0.03 . 0.46 6 0.10). CUE was also higher in dry (September) soils. C-acquiring enzyme activities (b-glucosidase, cellobiohydrolase, and phenol oxidase) increased after rainfall in moist (June), but not dry (September) soils. Both microbial biomass C:N ratios and fungal : bacterial ratios were higher at lower soil water contents, suggesting a functional and/or population-level shift in the microbiota at low soil water contents, and microbial community composition also differed following wet-up and between seasons and treatments. Overall, microbial activity may directly (C respiration) and indirectly (enzyme potential) reduce soil organic matter pools less in drier soils, and soil C sequestration potential (CUE) may be higher in soils with a history of extended dry periods between rainfall events. The implications include that soil C loss may be reduced or compensated for via different mechanisms at varying time scales, and that microbial taxa with better stress tolerance or growth efficiency may be associated with these functional shifts.

The McMurdo Dry Valleys (MDV) comprise a mosaic of habitats at scales ranging from micrometers to the kilometer scale. The varied landscape of the valleys, combined with strong physical and chemical gradients within and across the terrestrial and aquatic habitats, yields an ecosystem dominated by microbes that is both complex and diverse (Gordon et al.,2000; Smith et al., 2006; Mikucki and Priscu, 2007). The cold desert environment is analogous to icy conditions found on other icy worlds. For example, the low organic carbon, cold, arid soils of the MDV are similar to Mars' present-day terrestrial environment and the glaciers and ice-covered lakes of the MDV are comparable to conditions that existed on Mars in the past (Priscu et al., 1998; Wynn-Williams and Edwards, 2000; McKay et al., 2005). If there are extant or extinct life forms on Mars, they likely experience similar physical constraints and environmental challenges as do microbial communities in the MDV. Therefore, the MDV provide a unique earthly setting to gain insight into the diversity, adaptation, and function of life on other icy worlds. Here we describe the ecological processes and conditions that contribute to the microbial diversity observed in the MDV and relate these to potential life on Mars. The McMurdo Dry Valley ecosystem The MDV include a variety of unique habitats that are connected physically, chemically, and energetically (Fig. 8.1). Solar radiation and wind are the underlying forces that determine the existence and distribution of biota throughout the valleys (Dana et al., 1998; Nkem et al., 2006).