Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments

In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments

Sediment-Nitrogen (N) connectivity: suspended sediments in streams as N exporters and reactors for denitrification and assimilatory N uptake during storms

Nitrogen (N) pollution in riverine ecosystems has substantial environmental, economic, and policy consequences. Various riverine N removal processes include permanent dissimilatory sinks such as denitrification (Uden) and temporary assimilatory sink such as microbial N uptake (Uassim). Both processes have been extensively evaluated in benthic sediments but only sparsely in the water column, particularly for storm flows producing high suspended sediment (SS) concentrations. Stormflows also increase the sediment bound N (Sed-N) export, and in turn, the overall N exports from watersheds. The balance between N removal by Uden and Uassim vs. Sed-N export has not been studied and is a key knowledge gap. We assessed the magnitude of Uden and Uassim against stormflow Sed-N exports for multiple storm events of varying magnitude and across two drainage areas (750 ha and 15,330 ha) in a mixed landuse mid-Atlantic US watershed. We asked: How do the Uden and Uassim sinks compare with Sed-N exports and how do these N fluxes vary across the drainage areas for sampled storms on the rising and falling limbs of the discharge hydrograph? Mean Uden and Uassim as % of the Sed-N exports ranged between 0.1–40% and 0.6–22%, respectively. Storm event Uassim fluxes were generally slightly lower than the corresponding Uden fluxes. Similarly, comparable but slightly higher Uden fluxes were observed for the second order vs. the fourth order stream, while Uassim fluxes were slightly higher in the fourth-order stream. Both of these N sinks were higher on the falling vs. rising limbs of the hydrograph. This suggests that while the N sinks are not trivial, sediment bound N exports during large stormflows will likely overshadow any gains in N removal by SS associated denitrification. Understanding these N source-sink dynamics for storm events is critical for accurate watershed nutrient modeling and for better pollution mitigation strategies for downstream aquatic ecosystems. These results are especially important within the context of climate change as extreme hydrological events including storms are becoming more and more frequent

A global synthesis of human impacts on the multifunctionality of streams and rivers

Human impacts, particularly nutrient pollution and land-use change, have caused significant declines in the quality and quantity of freshwater resources. Most global assessments have concentrated on species diversity and composition, but effects on the multifunctionality of streams and rivers remain unclear. Here, we analyse the most comprehensive compilation of stream ecosystem functions to date to provide an overview of the responses of nutrient uptake, leaf litter decomposition, ecosystem productivity, and food web complexity to six globally pervasive human stressors. We show that human stressors inhibited ecosystem functioning for most stressor-function pairs. Nitrate uptake efficiency was most affected and was inhibited by 347% due to agriculture. However, concomitant negative and positive effects were common even within a given stressor-function pair. Some part of this variability in effect direction could be explained by the structural heterogeneity of the landscape and latitudinal position of the streams. Ranking human stressors by their absolute effects on ecosystem multifunctionality revealed significant effects for all studied stressors, with wastewater effluents (194%), agriculture (148%), and urban land use (137%) having the strongest effects. Our results demonstrate that we are at risk of losing the functional backbone of streams and rivers if human stressors persist in contemporary intensity, and that freshwaters are losing critical ecosystem services that humans rely on. We advocate for more studies on the effects of multiple stressors on ecosystem multifunctionality to improve the functional understanding of human impacts. Finally, freshwater management must shift its focus toward an ecological function-based approach and needs to develop strategies for maintaining or restoring ecosystem functioning of streams and rivers

The role of Primary Uptake Compartments on stream Nitrogen cycling = El paper dels Compartiments Primaris en el ciclatge del Nitrogen als ecosistemes fluvials

[eng] The main goal of this thesis is to investigate how (15)N natural abundances can help understanding the role of different primary uptake compartments (i.e., biofilm, filamentous algae, bryophytes, macrophytes; PUCs) on stream nutrient retention. The experimental design of this thesis involved the examination of patterns of variability in the (15)N signatures of Dissolved Inorganic Nitrogen (DIN) and PUCs at three different spatial scales: the watershed/global scale, the reach scale, and the habitat scale; as well as the (15)N transfer between them. At each level of organization, a common goal of examining how intrinsic (i.e., among PUCs) and extrinsic (i.e., environmental) factors influence (15)N signatures of DIN and PUCs was addressed, but quite different tools and experimental approaches were used depending on each scale. At the global scale, results showed that land use in the catchment is a key driver of the variability in (15)N signatures of both DIN and PUCs. In particular, (15)N signatures of DIN and PUC are higher in streams draining catchments with agriculture and urban activities than in those draining forested catchments; whereas within each stream, major among-compartments differences in (15)N signatures are between photoautotrophic and detrital-based compartments. At the reach scale, results for the different functional groups of macrophytes in streams indicate that direct assimilation of stream water DIN is occurring by submersed and amphibious species; while species of macrophytes located at the stream-riparian edge most likely rely on DIN sources other than those provided by stream water DIN. Moreover, in streams influenced by inputs from wastewater treatment plants (WWTP), DIN uptake by submersed and amphibious macrophytes seems to be mainly in the form of N03• On the other hand, results for the (15)N transfer between photoautotrophic PUCs and stream water DIN showed that variation in DIN uptake of photoautotrophic PUCs is principally driven by nutrient concentration and light incidence, rather than by the particular characteristics of each PUc. On the contrary, variation in autotrophic N turnover is more remarkable among photoautotrophic PUCs than among study reaches, suggesting an intrinsic control by the particular characteristics of each PUC on N turnover, and being relatively independent of environmental influences. Finally, results from tracer (15)N additions at the habitat and microhabitat scales revealed that spatial heterogeneity of microbial N uptake at the microhabitat scale is characterized by a mosaic of patches dominated by microhabitats of low N, with hot spots of highly active N uptake accounting for the 20% of the reach coverage. Particularly, spatial variation of epilithon N uptake at microhabitat scale is principally driven by flow velocity, while spatial variation of N uptake by detrital compartments is controlled bya combination of biophysical factors, indicating the relevance of organic matter characteristics on their role of stream water N uptake. Overall, these results indicate that the extent to which spatial variation in microbial N uptake at fine scales is integrated at the whole-reach scale is potentially affected by factors operating at the ecosystem level, such as the degree of canopy cover, which determines the relative abundance of each PUc. Results from this present thesis highlights that changes in the major land uses within the catchment, changes in the degree of riparian vegetation and/or in the DIN loads of stream ecosystems caused by WWTP inputs, or losses of spatial heterogeneity in the stream channel can have a significant incidence on the way that PUCs contribute to N cycling at the reach scale, which ultimately dictates the N dynamics of stream ecosystems

Variability in d15N natural abundance of basal resources in fluvial ecosystems: a meta-analysis

13 páginas,3 figuras, 3 tablas.Variation in N stable isotope (d15N) signatures of basal resources can influence interpretation of trophic relationships in ecosystems, and significant variation in d15N signatures has been reported in streams and rivers. However, a comprehensive understanding of the main factors driving d15N variability is lacking, and this variability confounds the consumer’s trophic-level position during d15N analysis. We conducted a meta-analysis to examine the variability in d15N natural abundance of basal resources and dissolved inorganic N (DIN) in streams and rivers in relation to the environmental factors that may drive this variability. The meta-analysis was based on a literature review over the last 20 y (1989–2009) and contained signatures of d15N-DIN (d15N-NO3 and d15N-NH4) and d15N-basal resources (d15N-detrital compartments, d15N-biofilm, d15N-algae, and d15N-macrophytes) from .100 rivers or streams. Signatures of d15N-DIN varied widely (28.4–19.4%), and we found fewer values for d15N-NH4 than d15N-NO3, even though NH4 + is assimilated rapidly by basal resources. The range of d15N-basal resources was also broad (24–16%) within and among compartments. Human land use was the most significant factor explaining variability in d15N-DIN and d15N-basal resource signatures. We found significant differences between d15N signatures of photoautotrophic (i.e., autochthonous) and detrital (i.e., allochthonous) basal resources. Our results point out the difficulty in defining a baseline d15N signature of the food web, and provide a basis to explain confounding results in studies using d15N analysis to identify trophic linkages in fluvial food webs.Financial support was provided by the ISONEF project (Iso´ - topos estables de nitro´geno en ecosistemas fluviales, papel de los componentes bio´ ticos como indicadores de fuentes y procesos del nitro´geno, ref: CGL2008- 05504-C02-02/BOS) funded by the Spanish Ministry of Science and Innovation. MP was funded by a Formacio´n de Personal Investigador PhD fellowship from the Spanish Ministry of Science and Innovation.Peer reviewe

Variability in δ15N natural abundance of dissolved inorganic nitrogen and biotic compartments in streams: a meta-analysis

Peer reviewe

Influence of nitrate and ammonium availability on uptake kinetics of stream biofilms

13 páginas, 3 figuras, 2 tablas.Human activity has significantly increased dissolved inorganic N (DIN) availability and has modified the relative proportion of NO3 2 and NH4 + species in many streams. Understanding the relationship between DIN concentration and DIN uptake is crucial to predicting how streams will respond to increased DIN loading. Nonetheless, this relationship remains unclear because of the complex interactions governing DIN uptake. We aimed to evaluate how biofilms from 2 streams differing in background DIN concentration would respond to increases in availability and changes in speciation (NO3 2 or NH4 +) of DIN. We measured DIN uptake by biofilms in artificial flumes in each stream, using separate 15N-NO3 2 and 15N-NH4 + additions in a graded series of increasing DIN concentrations. The ambient uptake rate (U) was higher for NO3 2 than for NH4 + in both streams, but only U for NH4 + differed between streams. Uptake efficiency (UN-specific) at ambient conditions was higher in the low-N than in the high-N stream for both DIN species. A Michaelis–Menten model of uptake kinetics best fit the relationship between uptake and concentration in the case of NH4 + (for both streams) but not in the case of NO3 2 (neither stream). Moreover, saturation of NH4 + uptake occurred at lower rates (lower Umax) in the low-N than in the high-N stream, but affinity for NH4 + was higher (lower Ks) in the low-N stream. Together, these results indicate that the response capacity of biofilm communities to short-term increases of DIN concentration is determined primarily by the ambient DIN concentrations under which they develop. Our study also shows that DIN uptake by benthic biofilms varies with DIN availability and with DIN speciation, which often is modified by human activities.This study was funded by the Spanish Ministry of Education and Science through the NICON project (ref: CGL2005-7362). MR was supported by a contract with the Spanish Ministry of Science and Innovation through the ISONEF project (CGL2008-05504-C02-02/BOS). MP was funded by a 1164 M. RIBOT ET AL. [Volume 32 Formacio´n de Personal Investigador PhD fellowship from the Spanish Ministry of Science and Innovation. DvS’s work was also funded by a Juan de la Cierva postdoctoral contract (JCI-2010-06397) from the Spanish Ministry of Science and Innovation. NB Grimm was supported by funds from the Spanish Council for Scientific Research (CSIC).Peer reviewe

Spatial drivers of ecosystem structure and function in a floodplain riverscape: springbrook nutrient dynamics

On riverine flood plains, reorganization by fluvial processes creates and maintains a mosaic of aquatic and riparian landscape elements across a biophysical gradient of disturbance and succession. Across flood plains of gravel-bottom rivers, spring brooks emerge from points of groundwater discharge that may occur in distinct landscape positions. We investigated how ecosystem processes in spring brooks differ spatially across biophysical zones, reflecting how landscape position dictates severity of flood disturbance, allochthonous loading from riparian forests, and inputs from groundwater systems. Between July and October 2011, we quantified aspects of ecosystem structure and function among 6 spring brooks of the Nyack flood plain, Flathead River, Montana. Structural features varied predictably across near-channel (i.e., parafluvial) and late successional (i.e., orthofluvial) biophysical zones. Large wood standing stocks increased >40× (0.19–9.19 kg/m2), dominant particle size class differed by an order of magnitude (median particle size [D50] = 2–27), and measures of vertical hydraulic gradient (–0.06 to +0.12 cm/cm) reflected differences in landscape position. We found fine sediment accumulation, stronger groundwater inputs, and greater benthic and large wood standing stocks in orthofluvial than in parafluvial spring brooks. Algal biomass was negatively correlated with insolation and positively related to vertical hydraulic gradient. Results from microcosm experiments showed increasing N uptake across the gradient from parafluvial to orthofluvial spring brooks. Functional response to landscape-scale organization of springbrook structure underscores the need for a spatially explicit model of floodplain ecology.Peer reviewe

Biofilm diversity patterns across the hierarchical organization of river-floodplain systems.

<p>Data points for each river-floodplain system represent mean values ± SEM of Shannon-Wiener (A) and beta-diversity (B) indices of biofilm communities at each hierarchical level. Diversity indices for each specific identity at each hierarchical level were calculated from group-averaged OTUs abundances within the next lower level (e.g., diversity indices at the floodplain level are calculated using zone-specific OTUs abundances). Prior to diversity indices calculations, 1000 bootstrap iterations were applied to normalize the number of sequenced samples per river at 10. Results associated with the Clark Fork River (orange), Boulder River (blue), Bitterroot River (red), and Madison River (green) are shown separately.</p

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes

<div><p>River-floodplain systems are among the most diverse and productive ecosystems, but the effects of biophysical complexity at multiple scales on microbial biodiversity have not been studied. Here, we investigated how the hierarchical organization of river systems (i.e., region, floodplain, zone, habitats, and microhabitats) influences epilithic biofilm community assemblage patterns by characterizing microbial communities using 16S rRNA gene sequence data and analyzing bacterial species distribution across local and regional scales. Results indicate that regional and local environmental filters concurrently sort bacterial species, suggesting that spatial configuration of epilithic biofilms resembles patterns of larger organisms in floodplain ecosystems. Along the hierarchical organization of fluvial systems, floodplains constitute a vector of maximum environmental heterogeneity and consequently act as a major landscape filter for biofilm species. Thus, river basins and associated floodplains may simply reflect very large scale ‘patches’ within which environmental conditions select for community composition of epilithic biofilms.</p></div