Biogeochemical Functioning Research Articles

Chemodiversity of Dissolved Organic Matter and Its Molecular Changes Driven by Rhizosphere Activities in Fe Ore Tailings Undergoing Eco-Engineered Pedogenesis.

Dissolved organic matter (DOM) plays an important role in soil structure and biogeochemical function development, which are fundamental for the eco-engineering of tailings-soil formation to underpin sustainable tailings rehabilitation. In the present study, we have characterized the DOM composition and its molecular changes in an alkaline Fe ore tailing primed with organic matter (OM) amendment and plant colonization. The results demonstrated that microbial OM decomposition dramatically increased DOM richness and average molecular weight, as well as its degree of unsaturation, aromaticity, and oxidation in the tailings. Plant colonization drove molecular shifts of DOM by depleting the unsaturated compounds with a high value of nominal oxidation state of carbon (NOSC), such as tannin-like and carboxyl-rich polycyclic-like compounds. This may be partially related to their sequestration by secondary Fe-Si minerals formed from rhizosphere-driven mineral weathering. Furthermore, the molecular shifts of DOM may have also resulted from plant-regulated microbial community changes, which further influenced DOM molecules through microbial-DOM interactions. These findings contribute to the understanding of DOM biogeochemistry and ecofunctionality in the tailings during early pedogenesis driven by OM input and pioneer plant/microbial colonization, providing an important basis for the development of strategies and technologies toward the eco-engineering of tailings-soil formation.

Stream network variation in dissolved oxygen: Metabolism proxies and biogeochemical controls

An explosion in high frequency dissolved oxygen (DO) observations at river network scales is creating new opportunities to understand dynamic signals in streams and rivers. Among the most informative metrics obtained from DO time series is stream metabolism—comprising gross primary production (GPP) and ecosystem respiration (ER)—but its estimation is non-trivial. There is thus interest in simpler metrics that can capture spatiotemporal patterns in stream metabolism and their consequences for critical ecosystem processes. Using hourly DO time series from 43 agricultural headwater streams reaches (Strahler order 1–5) across five watersheds and two years, we tested the hypothesis that simple DO metrics are useful proxies of stream metabolism, capturing key features of its spatiotemporal variation, and predicting attendant patterns in dissolved organic matter quality and catchment nitrogen processing via denitrification. Our results suggest the diel DO range scaled by stream depth is an excellent proxy for GPP throughout the network, accurately describing its spatial and temporal patterns. In contrast, we found that DO metrics were less successful as proxies for ER, with the maximum daily DO deficit scaled by depth being a good proxy for ER only in higher order streams. We also observed that DO metrics were strongly related to variation in dissolved organic matter quality and denitrification far better than GPP or ER. Finally, we found that DO metrics, GPP, and to a lesser extent ER, had power-law relationships with watershed area (scaling exponents, β = 0.2–0.5), implying increasing downstream metabolic activity. However, because lower order streams occupy ∼75% of network benthic area, total network GPP and ER (g O2 d−1) were disproportionately provided by lower order streams, consistent with recent theoretical modeling. These findings reveal the rich inference space that simple DO metrics can provide, and support their use as proxies for stream metabolism and for inferring network patterns of biogeochemical function.

Nutrient stream attenuation is altered by the duration and frequency of flow intermittency

AbstractRiver flow intermittency affects physical and biological processes in lotic ecosystems, including nutrient attenuation and therefore water purification. We investigated the effect of river flow intermittency, including its duration and occurrence frequency, on the attenuation of dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (P‐PO43−). The net balances of each nutrient form were assessed in artificial streams colonized by biofilms and exposed to six treatments resulting from the combination of two flow intermittency durations (28 or 56 days) and three intermittency frequencies (one, two or four interruption episodes). The respective influences on the nutrient balances were assessed one and eight days after flow resumption, with negative or positive balances indicating net consumption or production, respectively. The P‐PO43− balances ranged from −50.3 to −15.7 μg P‐PO43− h−1 m−2, while for the components of DIN, they varied between −135.6 and −7.3 μg N‐NH4+ h−1 m−2 (ammonium), −1.4 and 4.2 μg N‐NO2− h−1 m−2 (nitrite) and −39.1 and 18.6 μg N‐NO3− h−1 m−2 (nitrate). In general, longer non‐flow durations impaired nutrient attenuation. Overall, while each nutrient form showed specific patterns, our experiment indicated that (1) nutrient attenuation usually decreased with longer non‐flow durations, (2) attenuation generally recovered after frequent events of water flow resumption and when rewetting was longer and (3) longer desiccation periods seemed to persistently affect the biogeochemical responses regardless the number of times flow returned to the system. Our results highlight that more severe conditions (causing dehydration of the substrates and inhibition of biofilm activity) might strongly affect the biogeochemical functioning of temporary streams, with important management implications under accelerating global changes.

Estimating Hydrothermal Properties and High-Frequency Fluxes From Geophysical Measurements in the Hyporheic Zone

Located in the critical zone at the intersection between surface water and groundwater, hyporheic zones (HZ) host a variety of hydrological, biological and biogeochemical processes regulating water availability and quality and sustaining riverine ecosystems. However, difficulty in quantifying water fluxes along this interface has limited our understanding of these processes, in particular under dynamic flow conditions where rapid variations can impact large-scale HZ biogeochemical function. In this study, we introduce an innovative measurement assimilation chain for determining uncertainty-quantified hydraulic and thermal HZ properties, as well as associated uncertainty-quantified high-frequency water fluxes. The chain consists in the assimilation of data collected with the LOMOS-mini geophysical device with a process-based, Bayesian approach. The application of this approach on a synthetic case study shows that hydraulic and thermal HZ properties can be estimated from LOMOS-mini measurements, their identifiability depending on the Peclet number – summarizing the hydrological and thermal regime. Hydraulic conductivity values can be estimated with precision when greater than ~10−5m · s−1 when other HZ properties are unknown, with decreasing uncertainty when other HZ properties are known prior to starting the LOMOS-mini measurement assimilation procedure. Water fluxes can be estimated in all regimes with varying accuracy, highest accuracy is reached for fluxes greater than ~10−6m · s−1, except under highly conductive exfiltration regimes. We apply the methodology on in situ datasets by deriving uncertainty-quantified HZ properties and water fluxes for 2 data points collected during field campaigns. This study demonstrates that the LOMOS-mini monitoring technology can be used as complete and stand-alone sampling solution for quantifying water and heat exchanges under dynamic exchange conditions (time resolution < 15 min).

Innovative Instrument for the Field Continuous Monitoring of Dissolved Gases in Environmental Studies

Dissolved gases are particularly relevant tools for the investigation of environmental processes. Indeed, their solubility being a function of the variables of physical state of the medium (temperature, pressure, salinity), the dissolved noble gases are for instance good indicators of equilibrium conditions with the atmosphere and mixing of water bodies. Dissolved gases can also inform the biogeochemical functioning of natural systems by providing information on major processes such as photosynthesis, respiration or denitrification. Classical methods relying on the sampling, the storage and the ex situ analysis of water samples for the measurement of dissolved gases suffer from the difficulty of taking sufficiently frequent and representative samples as well as the analyte preservation. High-frequency in situ measurement of dissolved gases is therefore the most relevant for the study of environmental processes. The use of Membrane Inlet Mass Spectrometer (MIMS) technology provides access to high frequency measurements of a large set of dissolved gases in the field (He, Ne, Ar, Kr, Xe, N2, O2, CO2, CH4, N2O, H2) which offers a real opportunity for environmental studies.

Effect of limited compaction on soil solution chemistry in two acidic forest ecosystems: Changes, recovery and impact of liming

Forest practices are rapidly becoming mechanised in France, resulting in unknown consequences for the current and long-term functioning and functions of ecosystems. Degradation of forest soil porosity cannot be remediated artificially, and restoration via natural processes is slow and not likely to include deep soil layers, where tree roots take up large amounts of water and nutrients. In 2007 and 2008, two experimental sites were set up in the Lorraine Plateau (France). The soils are Ruptic Luvisols and are classified as highly sensitive to compaction. We observed multiple parameters and studied weakly bound soil solutions, which are known to react to changes in ecosystem functioning. We hypothesised that (i) soil solution chemistry is a relevant indicator to assess soil changes after compaction and dynamics of soil recovery in the decade following compaction, (ii) restoration is greater at the more fertile site and (iii) soil pH is a relevant parameter to explain the behaviour of soil solutions. Our results showed that soil solution concentrations changed drastically after compaction and that restoration was more effective in the less fertile soil than in the more fertile one. Finally, a soil pH threshold of 4.5 was relevant for explaining the behaviour of nitrate, which is particularly useful for monitoring solution geochemistry in these acidic soils. Liming at the less fertile site increased the pH to more than 4.5, which changed the behaviour of nitrate and reinforced the utility of this threshold for explaining soil biogeochemical functioning. Soil solution is a relevant indicator of current soil functioning after compaction; however, this study demonstrated that additional information is required to understand its meaning accurately. This study highlights that long-term observation is needed to identify the consequences of soil compaction on long-living ecosystems.

From Nano-Gels to Marine Snow: A Synthesis of Gel Formation Processes and Modeling Efforts Involved with Particle Flux in the Ocean.

Marine gels (nano-, micro-, macro-) and marine snow play important roles in regulating global and basin-scale ocean biogeochemical cycling. Exopolymeric substances (EPS) including transparent exopolymer particles (TEP) that form from nano-gel precursors are abundant materials in the ocean, accounting for an estimated 700 Gt of carbon in seawater. This supports local microbial communities that play a critical role in the cycling of carbon and other macro- and micro-elements in the ocean. Recent studies have furthered our understanding of the formation and properties of these materials, but the relationship between the microbial polymers released into the ocean and marine snow remains unclear. Recent studies suggest developing a (relatively) simple model that is tractable and related to the available data will enable us to step forward into new research by following marine snow formation under different conditions. In this review, we synthesize the chemical and physical processes. We emphasize where these connections may lead to a predictive, mechanistic understanding of the role of gels in marine snow formation and the biogeochemical functioning of the ocean.

The role of soils in the regulation of ocean acidification.

Soils play an important role in mediating chemical weathering reactions and carbon transfer from the land to the ocean. Proposals to increase the contribution of alkalinity to the oceans through ‘enhanced weathering’ as a means to help prevent climate change are gaining increasing attention. This would augment the existing connection between the biogeochemical function of soils and alkalinity levels in the ocean. The feasibility of enhanced weathering depends on the combined influence of what minerals are added to soils, the formation of secondary minerals in soils and the drainage regime, and the partial pressure of respired CO2 around the dissolving mineral. Increasing the alkalinity levels in the ocean through enhanced weathering could help to ameliorate the effects of ocean acidification in two ways. First, enhanced weathering would slightly elevate the pH of drainage waters, and the receiving coastal waters. The elevated pH would result in an increase in carbonate mineral saturation states, and a partial reversal in the effects of elevated CO2. Second, the increase in alkalinity would help to replenish the ocean's buffering capacity by maintaining the ‘Revelle Factor’, making the oceans more resilient to further CO2 emissions. However, there is limited research on the downstream and oceanic impacts of enhanced weathering on which to base deployment decisions.This article is part of the theme issue ‘The role of soils in delivering Nature's Contributions to People’.

Groundwater, Soil, and Vegetation Interactions at Discrete Riparian Inflow Points (DRIPs) and Implications for Boreal Streams

Hydrological processes at hillslope and catchment scales explain a large part of stream chemistry dynamics through source-transport mechanisms from terrestrial to aquatic ecosystems. Riparian zones play a central role, as they exert a strong influence on the chemical signature of groundwater discharge to streams. Especially important are riparian areas where upslope subsurface flow paths converge, because they connect a large part of the catchment to a narrow section of the stream. Recent research shows that both in terrestrial and aquatic ecosystems, riparian convergence zones fulfill important biogeochemical functions that differ from surrounding riparian zones. Most catchment-scale conceptual frameworks focus on generalized hillslope-riparian-stream transects and do not explicitly consider riparian convergence zones. This study integrates collective work on hydrology, groundwater chemistry, vegetation and soils of discrete riparian inflow points (DRIPs) in a boreal landscape. We show that compared to adjacent riparian forests, DRIPs have groundwater levels that are consistently near the surface, and supply organic-rich water to streams. We suggest that interactions between hydrology, wetland vegetation, and peat soil development that occur in DRIPs leads to their unique groundwater chemistry and runoff dynamics. Stream-based studies show that across flow conditions, groundwater inputs from DRIPs to headwater reaches influence stream temperature, water chemistry and biology. As such, accounting for DRIPs can complement existing hillslope and stream observations, which would allow better representation of chemical and biological interactions associated with convergence of subsurface flow paths in riparian zones.

Using Plate-Wash PCR and High-Throughput Sequencing to Measure Cultivated Diversity for Natural Product Discovery Efforts.

Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Sequence-based data indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete and more complex, understanding of which organisms were present compared to what was eventually detected during cultivation. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against an already multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.

Ecosystem carbon exchange and nitrogen removal rates in two 33‐year‐old constructed salt marshes are similar to those in a nearby natural marsh

Human activities have led to 1–2% of coastal wetlands lost per year globally, with subsequent losses in ecosystem services such as nutrient filtering and carbon sequestration. Wetland construction is used to mitigate losses of marsh cover and services resulting from human impacts in coastal areas. Though marsh structure can recover relatively quickly (i.e., <10 years) after construction, there are often long‐term lags in the recovery of ecosystem functions in constructed marshes. We conducted a year‐long study comparing seasonal plant productivity, ecosystem respiration (), denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) between two 33‐year‐old constructed marshes (CON‐1, CON‐2) and a nearby natural reference marsh (NAT). We found that CON‐1 and CON‐2 were structurally similar to NAT (i.e., plant aboveground and belowground biomass did not differ). Likewise, gross ecosystem productivity (GEP), , and net ecosystem exchange (NEE) were similar across all marshes. Further, DNRA and denitrification were similar across marshes, with the exception of greater denitrification rates at CON‐2 than at the other two sites. While pore‐water ammonium concentrations were similar across all marshes, organic matter (OM) content, pore‐water phosphate, nitrate + nitrite, and hydrogen sulfide concentrations were greater in NAT than CON‐1 and CON‐2. Collectively, this work suggests that current marsh construction practices could be a suitable tool for recovering plant structure and some ecosystem functions. However, the lag in recovery of pore‐water nutrient stocks and OM content also suggests that some biogeochemical functions may take longer than a few decades to fully recover in constructed marshes.

Revealing the Viral Community in the Hadal Sediment of the New Britain Trench.

Marine viruses are widely distributed and influence matter and energy transformation in ecosystems by modulating hosts’ metabolism. The hadal trenches represent the deepest marine habitat on Earth, for which the viral communities and related biogeochemical functions are least explored and poorly understood. Here, using the sediment samples (8720 m below sea level) collected from the New Britain Trench (NBT), we investigated the viral community, diversity, and genetic potentials in the hadal sediment habitat for the first time by deep shotgun metagenomic sequencing. We found the NBT sediment viral community was dominated by Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, and Phycodnaviridae, which belong to the dsDNA viruses. However, the large majority of them remained uncharacterized. We found the hadal sediment virome had some common components by comparing the hadal sediment viruses with those of hadal aquatic habitats and those of bathypelagic and terrestrial habitats. It was also distinctive in community structure and had many novel viral clusters not associated with the other habitual virome included in our analyses. Further phylogenetic analysis on its Caudovirales showed novel diversities, including new clades specially evolved in the hadal sediment habitat. Annotation of the NBT sediment viruses indicated the viruses might influence microbial hydrocarbon biodegradation and carbon and sulfur cycling via metabolic augmentation through auxiliary metabolic genes (AMGs). Our study filled in the knowledge gaps on the virome of the hadal sediment habitats and provided insight into the evolution and the potential metabolic functions of the hadal sediment virome.

Predicting arctic-alpine lake dissolved oxygen responses to future tree line advance at the Swedish forest-tundra transition zone.

High latitude regions of the globe are experiencing higher warming rates than many other areas and are expected to undergo dramatic change with future warming (Carpenter et al., 2011; Kuhn et al., 2021). One such change is the poleward advance of tree line into prior tundra environments. While nominally a terrestrial ecosystem change, this advance may dramatically alter aquatic ecosystems, with lakes in particular being highly responsive to events that occur in the surrounding landscape. Klaus et al. (2021) address this important issue by using a space-for-time substitution across 40 Swedish arctic-alpine lakes to understand how a transition from tundra to forested watersheds will influence lake dissolved oxygen (DO).

Sediment and Nutrient Retention in Ponds on an Agricultural Stream: Evaluating Effectiveness for Diffuse Pollution Mitigation

The creation of ponds and wetlands has the potential to alleviate stream water quality impairment in catchments affected by diffuse agricultural pollution. Understanding the hydrological and biogeochemical functioning of these features is important in determining their effectiveness at mitigating pollution. This study investigated sediment and nutrient retention in three connected (on-line) ponds on a lowland headwater stream by sampling inflowing and outflowing concentrations during base and storm flows. Sediment trapping devices were used to quantify sediment and phosphorus accumulations within ponds over approximately monthly periods. The organic matter content and particle size composition of accumulated sediment were also measured. The ponds retained dissolved nitrate, soluble reactive phosphorus and suspended solids during baseflows. During small to moderate storm events, some ponds were able to reduce peak concentrations and loads of suspended solids and phosphorus; however, during large magnitude events, resuspension of deposited sediment resulted in net loss. Ponds filtered out larger particles most effectively. Between August 2019 and March 2020, the ponds accumulated 0.306 t ha−1 sediment from the 30 ha contributing area. During this period, total sediment accumulations in ponds were estimated to equal 7.6% of the suspended flux leaving the 340 ha catchment downstream. This study demonstrates the complexity of pollutant retention dynamics in on-line ponds and highlights how their effectiveness can be influenced by the timing and magnitude of events.

The information system of the French Peatland Observation Service: Service National d'Observation Tourbières – A valuable tool to assess the impact of global changes on the hydrology and biogeochemistry of temperate peatlands through long term monitoring

AbstractMitigating and adapting to global changes requires a better understanding of the response of the Biosphere to these environmental variations. Human disturbances and their effects act in the long term (decades to centuries) and consequently, a similar time frame is needed to fully understand the hydrological and biogeochemical functioning of a natural system. To this end, the ‘Centre National de la Recherche Scientifique’ (CNRS) promotes and certifies long‐term monitoring tools called national observation services or ‘Service National d'Observation’ (SNO) in a large range of hydrological and biogeochemical systems (e.g., cryosphere, catchments, aquifers). The SNO investigating peatlands, the SNO ‘Tourbières’, was certified in 2011 (https://www.sno-tourbieres.cnrs.fr/). Peatlands are mostly found in the high latitudes of the northern hemisphere and French peatlands are located in the southern part of this area. Thus, they are located in environmental conditions that will occur in northern peatlands in coming decades or centuries and can be considered as sentinels. The SNO Tourbières is composed of four peatlands: La Guette (lowland central France), Landemarais (lowland oceanic western France), Frasne (upland continental eastern France) and Bernadouze (upland southern France). Thirty target variables are monitored to study the hydrological and biogeochemical functioning of the sites. They are grouped into four datasets: hydrology, fluvial export of organic matter, greenhouse gas fluxes and meteorology/soil physics. The data from all sites follow a common processing chain from the sensors to the public repository. The raw data are stored on an FTP server. After operator or automatic processing, data are stored in a database, from which a web application extracts the data to make them available (https://data-snot.cnrs.fr/data-access/). Each year at least, an archive of each dataset is stored in Zenodo, with a digital object identifier (DOI) attribution (https://zenodo.org/communities/sno_tourbieres_data/).

Nature development in degraded landscapes: How pioneer bioturbators and water level control soil subsidence, nutrient chemistry and greenhouse gas emission

The restoration of degraded ecosystems and landscapes is challenging, because returning to the original state is often socio-economically unfeasible. A novel approach is to construct new ecosystems to improve the functioning of degraded landscapes. However, the development of novel ecosystems is largely driven by the pre-construction hydrogeophysical and ecological conditions of the soil. In Lake Markermeer, a deteriorating freshwater lake in the Netherlands, a large archipelago is currently being constructed to boost the ecological functioning of the lake. Hence, islands – with wetlands and with more elevated and dryer areas – have been created to sustain biodiversity and key biogeochemical functions such as nutrient cycling. The islands are constructed from lake-bottom sediments. To study how two potentially important drivers, water level and bioturbation, affect soil characteristics in a novel wetland ecosystem, we experimentally tested the effects of water level (-30, -10 and 5 cm), and bioturbation by earthworms (Lumbricus rubellus) and Tubifex spp. in a microcosm experiment. We demonstrate that a high water level prevents soil subsidence, soil crack formation and carbon dioxide (CO2) emissions, and affects nitrogen cycling. In dryer soils, the presence of earthworms strongly increases CO2 emissions next to reducing soil crack formation, while Tubifex spp. in wetter soils hardly affect soil characteristics. Our findings highlight the important roles of both water level and bioturbation for the functioning of novel soils, which likely affects vegetation development in novel ecosystems. This knowledge can be used to aid the construction and nature development of novel wetlands.

Sensitivity of 21st-century projected ocean new production changes to idealized biogeochemical model structure

Abstract. While there is agreement that global warming over the 21st century is likely to influence the biological pump, Earth system models (ESMs) display significant divergence in their projections of future new production. This paper quantifies and interprets the sensitivity of projected changes in new production in an idealized global ocean biogeochemistry model. The model includes two tracers that explicitly represent nutrient transport, light- and nutrient-limited nutrient uptake by the ecosystem (new production), and export via sinking organic particles. Globally, new production declines with warming due to reduced surface nutrient availability, as expected. However, the magnitude, seasonality, and underlying dynamics of the nutrient uptake are sensitive to the light and nutrient dependencies of uptake, which we summarize in terms of a single biological timescale that is a linear combination of the partial derivatives of production with respect to light and nutrients. Although the relationships are nonlinear, this biological timescale is correlated with several measures of biogeochemical function: shorter timescales are associated with greater global annual new production and higher nutrient utilization. Shorter timescales are also associated with greater declines in global new production in a warmer climate and greater sensitivity to changes in nutrients than light. Future work is needed to characterize more complex ocean biogeochemical models in terms of similar timescale generalities to examine their climate change implications.

High sulfate concentrations maintain low methane emissions at a constructed fen over the first seven years of ecosystem development

Wetlands comprise a large expanse of the pre-disturbance landscape in the Athabasca Oil Sands Region (AOSR) and have become a focus of reclamation in recent years. An important aspect of wetland reclamation is understanding the biogeochemical functioning and carbon exchange, including methane (CH4) emissions, in the developing ecosystem. This study investigates the drivers of CH4 emissions over the first seven years of ecosystem development at a constructed fen in the AOSR and looks towards future CH4 emissions from this site. Specifically, the objectives were to: 1) investigate the environmental controls on CH4 emissions measured using manual static chambers between 2013 and 2019 and 2) investigate the relationship between water table depth, sulfate (SO42−) concentrations and CH4 emissions during the 2019 growing season. Methane emissions remained low throughout the majority of the measurement period; however, in later years, a small but significant increase became apparent. High levels of SO42− are likely the cause of the low CH4 emissions, despite the high-water tables and dominance of vegetation with aerenchyma such as Carex aquatilis and Typha latifolia in later years. Although low CH4 emissions may be beneficial from a climate warming perspective, the results also suggest that this constructed peatland is not functioning similarly to regional reference fens. Future climate scenarios across Western Boreal Canada could lead to higher air temperatures and changing precipitation patterns, influencing the direction of future CH4 emissions from this site. However, given the likelihood of this site maintaining extremely high SO42− concentrations over the next decade, it is expected that CH4 emissions will remain low.

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

BackgroundBiogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.ResultsWe intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor.ConclusionsThe disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.AU1kaDmL5ojSw8dBEKS2i-Video abstract

Effects of chronic exposure of antibiotics on microbial community structure and functions in hyporheic zone sediments

Microbial communities in hyporheic zones (HZ) provide vital biogeochemical functions such as contaminant degradation for river ecosystems. Antibiotics are contaminants that have been increasingly detected in HZ sediments. In this study, sediments from different HZ locations in a contaminated river, Maozhou river, China were sampled and analyzed using qPCR and high-throughput sequencing to investigate the effect of antibiotic contamination on microbial community structures and functions in HZ sediments. Results indicated that types and concentrations of antibiotics in HZ sediments were heterogeneously distributed that were largely consistent with the distribution of antibiotic sources. Sediments near animal farm and hospital contained higher antibiotic concentrations compared with those from mainstream. The distribution of ARGs was well correlated with antibiotics. Bacterial indicator genera indicating differences between mainstream area and other sampling areas were positively correlated with antibiotics, suggesting the influences of antibiotics on reshaping microbial community structures. PICRUSt revealed positive relationships between antibiotics and predicted functional genes involved in defense, signal transduction, and recombination and repair. This imply the defensive response of microbial communities on antibiotic attack. These results indicated that antibiotic contamination in the watershed posed a potential risk on HZ microbial community structures and functions, which may further threaten river ecosystem functions.