Biogeochemical Functioning Research Articles

Disentangling the Functional Role of Fungi in Cold Seep Sediment.

Cold seeps are biological oases of the deep sea fueled by methane, sulfates, nitrates, and other inorganic sources of energy. Chemolithoautotrophic bacteria and archaea dominate seep sediment, and their diversity and biogeochemical functions are well established. Fungi are likewise diverse, metabolically versatile, and known for their ability to capture and oxidize methane. Still, no study has ever explored the functional role of the mycobiota in the cold seep biome. To assess the complex role of fungi and fill in the gaps, we performed network analysis on 147 samples to disentangle fungal-prokaryotic interactions (fungal 18S and prokaryotic 16S) in the Haima cold seep region. We demonstrated that fungi are central species with high connectivity at the epicenter of prokaryotic networks, reduce their random-attack vulnerability by 60%, and enhance information transfer efficiency by 15%. We then scavenged a global metagenomic and metatranscriptomic data set from 10 cold seep regions for fungal genes of interest (hydrophobins, cytochrome P450s, and ligninolytic family of enzymes); this is the first study to report active transcription of 2,500+ fungal genes in the cold seep sediment. The genera Fusarium and Moniliella were of notable importance and directly correlated with high methane abundance in the sulfate-methane transition zone (SMTZ), likely due to their ability to degrade and solubilize methane and oils. Overall, our results highlight the essential yet overlooked contribution of fungi to cold seep biological networks and the role of fungi in regulating cold seep biogeochemistry. IMPORTANCE The challenges we face when analyzing eukaryotic metagenomic and metatranscriptomic data sets have hindered our understanding of cold seep fungi and microbial eukaryotes. This fact does not make the mycobiota any less critical in mediating cold seep biogeochemistry. On the contrary, many fungal genera can oxidize and solubilize methane, produce methane, and play a unique role in nutrient recycling via saprotrophic enzymatic activity. In this study, we used network analysis to uncover key fungal-prokaryotic interactions that can mediate methane biogeochemistry and metagenomics and metatranscriptomics to report that fungi are transcriptionally active in the cold seep sediment. With concerns over rising methane levels and cold seeps being a pivotal source of global methane input, our holistic understanding of methane biogeochemistry with all domains of life is essential. We ultimately encourage scientists to utilize state-of-the-art tools and multifaceted approaches to uncover the role of microeukaryotic organisms in understudied systems.

Hydrological Controls on Dissolved Organic Matter Composition throughout the Aquatic Continuum of the Watershed of Selin Co, the Largest Lake on the Tibetan Plateau.

Alpine river and lake systems on the Tibetan Plateau are highly sensitive indicators and amplifiers of global climate change and important components of the carbon cycle. Dissolved organic matter (DOM) encompasses organic carbon in aquatic systems, yet knowledge about DOM variation throughout the river-lake aquatic continuum within alpine regions is limited. We used optical spectroscopy, ultrahigh-resolution mass spectrometry (Fourier transform ion cyclotron resonance mass spectrometry), and stable water isotopic measurements to evaluate linkages between DOM composition and hydrological connection. We investigated glacial influences on DOM composition throughout the watershed of Selin Co, including upstream glacier-fed rivers and downstream-linked lakes. We found that the dissolved organic carbon concentration increased, whereas specific ultraviolet absorbance (SUVA254) decreased along the river-lake continuum. Relative to rivers, the downstream lakes had low relative abundances of polyphenolic and condensed aromatic compounds and humic-like substances but increased relative abundances of aliphatics and protein-like compounds. SUVA254 decreased while protein-like components increased with enriched stable water isotope δ2H-H2O, indicating that DOM aromaticity declined while autochthonous production increased along the flow paths. Glacier meltwater contributed to elevated relative abundances of aliphatic and protein-like compounds in headwater streams, while increased relative abundances of aromatics and humic-like DOM were found in glacier-fed lakes than downstream lakes. We conclude that changes in hydrological conditions, including glacier melt driven by a warming climate, will significantly alter DOM composition and potentially their biogeochemical function in surface waters on the Tibetan Plateau.

Microclimate stability on the critical zone of a karst hillslope in southwest China: Insights from continuous temperature observations at the air–soil–epikarst interface

Temperature is an important near-surface microclimate parameter that plays a key role in hydrological, ecological, and biogeochemical functions. However, the spatio-temporal distribution of temperature on the invisible and inaccessible soil–weathered bedrock continuum, wherein hydrothermal processes are most active, remains poorly understood. Temperature dynamics were monitored at 5 min intervals in the air–soil–epikarst (∼3 m) system at different topographical positions of the karst peak-cluster depression in southwest China. The weathering intensity was characterized based on the physicochemical properties of samples collected through drilling. No significant difference was observed in air temperature across slope positions, which was related to the limited distance and elevation resulting in roughly consistent energy input. The control effect of air temperature on the soil–epikarst was weakened with the decrease in elevation (±0.36 to ±0.25 °C). It is attributed to the enhanced temperature regulation capacity of vegetation cover from the up slope (shrub dominant) to down slope (tree dominant) in a relatively uniform energy environment. Temperature stability is clearly distinguished in two adjacent hillslopes that were differentiated by weathering intensity. For every 1 °C change in the ambient temperature, the amplitude of soil-epikasrt temperature variation on the strongly and weakly weathered hillslopes were ±0.28 and ± 0.32 °C, respectively. The response of soil-epikarst temperature to ambient temperature was more sensitive in the wet season (±0.40 °C) than in the dry season (±0.20 °C), which was related to the cooling effect caused by abundant rainfall. The cooling effect was particularly prominent in the preferential flow development area composed of pipeline cracks, which appear in the hillslope with relatively weak weathering intensity. These demonstrate that soil–epikarst temperature responds more gently to the variability of rainfall and ambient temperature on a relatively strong weathered hillslope. Accordingly, this study highlights that the sensitivity of soil–epikarst temperature to climate change is regulated by vegetation and weathering intensity on karst hillslopes in southwest China.

Thermal Selection of Microbial Communities and Preservation of Microbial Function in Guaymas Basin Hydrothermal Sediments.

The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, hydrothermal activity, and organic matter accumulation on the seafloor due to high sedimentation rates. In the hydrothermal sediments of Guaymas Basin, microbial community compositions and coexistence patterns change across steep gradients of temperature, potential carbon sources, and electron acceptors. Nonmetric multidimensional scaling and guanine-cytosine percentage analyses reveal that the bacterial and archaeal communities adjust compositionally to their local temperature regime. Functional inference using PICRUSt shows that microbial communities consistently maintain their predicted biogeochemical functions in different sediments. Phylogenetic profiling shows that microbial communities retain distinct sulfate-reducing, methane-oxidizing, or heterotrophic lineages within specific temperature windows. The preservation of similar biogeochemical functions across microbial lineages with different temperature adaptations stabilizes the hydrothermal microbial community in a highly dynamic environment. IMPORTANCE Hydrothermal vent sites have been widely studied to investigate novel bacteria and archaea that are adapted to these extreme environments. However, community-level analyses of hydrothermal microbial ecosystems look beyond the presence and activity of particular types of microbes and examine to what extent the entire community of bacteria and archaea is adapted to hydrothermal conditions; these include elevated temperatures, hydrothermally generated carbon sources, and inorganic electron donors and acceptors that are characteristic for hydrothermal environments. In our case study of bacterial and archaeal communities in hydrothermal sediments of Guaymas Basin, we found that sequence-inferred microbial function was maintained in differently structured bacterial and archaeal communities across different samples and thermal regimes. The resulting preservation of biogeochemical functions across thermal gradients is an important factor in explaining the consistency of the microbial core community in the dynamic sedimentary environment of Guaymas Basin.

Temperature, species identity and morphological traits predict carbonate excretion and mineralogy in tropical reef fishes

Anthropogenic pressures are restructuring coral reefs globally. Sound predictions of the expected changes in key reef functions require adequate knowledge of their drivers. Here we investigate the determinants of a poorly-studied yet relevant biogeochemical function sustained by marine bony fishes: the excretion of intestinal carbonates. Compiling carbonate excretion rates and mineralogical composition from 382 individual coral reef fishes (85 species and 35 families), we identify the environmental factors and fish traits that predict them. We find that body mass and relative intestinal length (RIL) are the strongest predictors of carbonate excretion. Larger fishes and those with longer intestines excrete disproportionately less carbonate per unit mass than smaller fishes and those with shorter intestines. The mineralogical composition of excreted carbonates is highly conserved within families, but also controlled by RIL and temperature. These results fundamentally advance our understanding of the role of fishes in inorganic carbon cycling and how this contribution will change as community composition shifts under increasing anthropogenic pressures.

Impact of an exceptional winter flood on benthic oxygen and nutrient fluxes in a temperate macrotidal estuary: Potential consequences on summer deoxygenation

Despite 20 years of control on eutrophication, episodes of summer hypoxia still occur in the Loire estuary, impacting water quality and posing a key scientific and management challenge. This work aimed to quantify the contribution of the benthic compartment to hypoxia in the Loire estuary by direct measurement of water–sediment fluxes and an in-depth understanding of the seasonal variations of oxides and phosphorus stocks. During the summer’s low-discharge period, results show that the iron oxide-rich deposit is stable under hypoxic conditions, limiting the release of dissolved phosphorus into the overlying water column. The high nitrate content of the water column appears to be an important oxidizer of iron during hypoxic periods, limiting dissolved phosphorus leakage and aggravation of hypoxia. During the exceptional winter flood, significant sediment erosion associated with bubbling phenomena (attributed to methane efflux) created severe fractures in the sediment and stimulated water–sediment exchange. During the following months, these fractures were progressively filled, which decreased the intensity of benthic fluxes. However, due to the high residence time in the water during the summer period, a simple model demonstrated that benthic contributions were sufficient to directly (by direct oxygen consumption) or indirectly (by promoting ammonia oxidation) affect the oxygen stock in the water column during the low-discharge period. Our study demonstrates the importance of the benthic compartment in the occurrence of hypoxia and the obvious lack of knowledge to illustrate and model the biogeochemical functioning of the estuary.

Simulating fish farm enrichment and fallowing impacts reveals unequal biogeochemical recovery of benthic variables

Finfish aquaculture is playing an increasing role in global food provision, with accompanying increases in benthic impacts under intensive pen production systems. Deposited faeces under and near fish pens affect the seafloor environment and biogeochemical functioning. To maintain healthy coastal environments, many fish farms operate by alternating input and fallowing periods to allow benthic coastal receiving environments to recover from excess organic matter inputs. Here, we used flow-through annular flume mesocosms to simulate sustained organic matter inputs to the benthos with a subsequent fallowing period of no inputs. To quantify the effects of excess organic matter loading on benthic receiving environments, we carried out repeated closed-system flux studies to quantify the benthic carbon mineralisation processes, with a focus on benthic oxygen, inorganic and organic carbon, nitrogen, phosphate, and sulphide fluxes, along with the redox state throughout the input and recovery period. We found that recovery periods were input-dependent, with parameters requiring longer fallowing periods to recover following larger inputs. While some benthic parameter fluxes such as dissolved organic carbon, sulphide, and ammonium returned to their pre-input state relatively rapidly (1-2 mo) following cessation of inputs, others such as sediment oxygen demand, ammonium, and redox required longer (>7 mo) to recover. Our results suggest that in situations where the benthic macrofaunal community has been severely impaired, extended fallowing periods may be required in order to permit the biogeochemical composition of the seabed to return to a more natural state, with implications for farm-consenting permits and planning as well as operational fallowing practices.

Reproductive and vegetative phenology of the micro endemic Stachytarpheta cassiae (Verbenaceae)

Abstract The flora of the Brazilian rupestrian grasslands represents a hotspot of species richness and endemisms. Stachytarpheta cassiae (Verbenaceae), is a micro endemic species, from which nothing is known. Here, we quantified the activity and intensity of vegetative and reproductive phenophases throughout 12 months and tested for their seasonality and their relationship with local climatic variables. Both vegetative and reproductive phenophases were continuous. No seasonality was observed in the vegetative phenophases and none of them was influenced by climatic variables. Only flower buds and mature fruits’ intensities showed seasonality in February (rainy season) and July (dry season), respectively. Accordingly, increased temperature and humidity combined explained increased production of flower buds whereas decreased rainfall explained increased mature fruits. Higher intensity in flower buds may respond to similar climatic conditions as other species in the community. However, S. cassiae is much different as it continues producing flowers continuously. Higher intensity of mature fruits in the dry season is expected as their seeds are abiotically dispersed. Due to constant flower and leaf production, S. cassia may be a key species for the conservation of many vertebrate and invertebrate species and for maintaining the biogeochemical functioning of the impoverished soils of the rupestrian grasslands.

Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments.

Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.

Impacts of humic-based products on the microbial community structure and functions toward sustainable agriculture

Humic-based products (HPs) are carbon-rich organic amendments in the forms of extracted humic substances from manure, compost, and raw and extracted forms of lignites, coals and peats. HPs are widely used in agriculture and have beneficial effects on plants. While the agronomic benefits of HPs have been widely reported, information on their impact on the soil microbial community composition and functions is lacking, despite claims made by companies of humic substances as biostimulants. In this review, we explored published research on microbial responses with HPs application in an agronomic context. Although research data are sparse, current results suggest indirect impacts of HPs on microbial community composition and activities. HPs application changes the physico-chemical properties of the soil and influence root exudation, which in turn impact the microbial structure and function of the soil and rhizosphere. Application of HPs to the soil as biostimulants seemed to favor plant/soil beneficial bacterial community composition. HPs impacts on microbial activities that influence soil biogeochemical functioning remain unclear; existing data are also inconsistent and contradictory. The structural properties of HPs caused inconsistencies in their reported impacts on soil properties and plants. The sources of HPs and forms (whether extracted or raw), soil type, geographic location, crop species, and management strategies, among others, affect microbial communities affecting HPs efficacy as biostimulants. A more holistic approach to research encompassing multiple influential factors and leveraging the next-generation sequencing technology is needed to unravel the impacts of HPs on the soil microbiome. Addressing these knowledge gaps facilitates sustainable and efficient use of HPs as organic agricultural amendments reducing the use of chemical fertilizers.

Matrix-associated microbial communities in a nitrogen-removing on-site wastewater treatment system are largely structured by niche processes.

On-site wastewater treatment systems (OWTSs) can be designed to promote microbial communities with naturally occurring metabolic functions desirable to wastewater treatment. Among such OWTSs are nitrogen-removing biofilters (NRBs), comprising a sand layer overlying a sand-lignocellulose (sand-lc) layer and intended to promote sequential nitrification and denitrification. The design of NRBs is based on the hypothesis that niche processes like environmental selection strongly structure the microbial communities, which predicts that immigrating wastewater communities and matrix-associated communities will be distinct and that the matrix communities in the two layers will be distinct. We characterized NRB microbial communities by 16S ribosomal RNA amplicon sequencing. Selection of the matrix-associated communities was indicated by clear differences from the immigrating community. For matrix-associated communities, alpha and beta diversity differed between the matrix layers, as did the relative abundances of many functional groups and genera. Functional groups with strict metabolisms were nearly exclusively detected in either the sand (ammonia and nitrite oxidizers) or sand-lc layer (methanogens), consistent with the niche hypothesis. Contrary to expectations, denitrifiers as a functional group were not present at greater relative abundance in the sand-lc than sand matrix because of a portfolio effect: some denitrifying genera were more abundant in the sand layer, whereas others were more abundant in the sand-lc layer. This study reveals niche processes acting at different levels of community organization for different biogeochemical functions, a crucial consideration in designing effective and reliable OWTSs to mitigate nitrogen pollution.

The Effect of the Artificial Reef on the Structure and Function of Sediment Bacterial Community

The bacterial community in sediment is sensitive to artificial disturbance, and they respond differently to human disturbance, such as changing the nutrient cycling and energy flow in marine ecosystems. However, little is known about the dynamics and distribution of bacterial community structures in marine sediments and potential biogeochemical functions during the long-time succession in marine ranching. In the present study, we compared the dynamics of the bacterial composition and potential biogeochemical functions of sediment to ten years (TR) and one-year new artificial reef (NR) areas using metagenomic next-generation sequencing technology. Results revealed that NR reduces the Pielou’s evenness and Shannon index. Similarly, nonmetric multidimensional scaling showed that the beta diversity of sediment bacterial communities in NR significantly differed between TR and non-artificial reef areas. Previously, TR biomarkers were frequently associated with organic matter decomposing and assimilating in the organically enriched sediments (i.e., Acinetobacter). The soluble reactive phosphate (SRP) and total phosphorus (TP) concentrations were thought to be the primary driving forces in shaping the microbial community in sediment. Pseudomonas, Lactobacillus, and Ralstonia have a significant positive correlation with SRP, TP, nitrate, and TN, but a negative association with pH, Salinity, Hg, and depth. NR was found to have more negative correlation nodes, indicating that taxa face more competition or predation press. Vibrio served as the module-hubs in the network in all areas. In addition, chemoheterotrophy, aerobic chemoheterotrophy, and fermentation were the three most prominent functions of the three areas, accounting for 59.96% of the relative abundance of the functional annotation. Different bacteria in sediments may change the amount of biogeochemical cycle in the marine ranching ecosystem. These findings can increase our understanding of the succession of the microecosystem for the marine ranching sedimentary environment by revealing how artificial reefs affect the indigenous sediment bacterial community and their responses to environmental variation.

Hillslope Geodiversity Impact on Biocrusts’ Biogeochemical Functions

Geodiversity integrates physical parameters such as geological, geomorphological, and pedological components. It represents the abiotic diversity of the earth surface layer. It incorporates geological (bedrocks and mineral sediments), geomorphological (geography, land surface formations, physical processes), pedological (soils), and hydrological characteristics. Biological soil crusts (biocrusts) play an essential role in regulating the biogeochemical cycles of carbon and nitrogen. Their ability is dependent on habitat conditions, composition, and cover percentage of the ground surface, all of which are affected by geodiversity. This study’s objective was to assess the effects of geodiversity on the biogeochemical functions of biocrusts by regulating the soil water dynamics and the subsequent impact on readily available nitrogen and carbon. Hillslope geodiversity is determined by the geodiversity found in the stone cover on the ground surface and in the stone content throughout the soil profile, as well as by the soil profile thickness of the underlying bedrock. We hypothesized that in dry environments, the physical conditions in high-geodiversity hillslopes, compared to low-geodiversity hillslopes, positively affect the soil water budget, which would affect the biocrusts and their readily available nitrogen and carbon. The results showed higher soil moisture content in the heterogeneous hillslopes. The ammonium and labile organic carbon in the biocrusts were more substantial in the heterogeneous than in the homogeneous hillslopes, while soil protein, nitrite, and soil organic matter were similar. We suggest that the comparatively high soil moisture content in the heterogeneous hillslopes stimulates biocrust community activities and increases the readily available nitrogen and carbon, thus improving the survival of shrubs in these ecosystems under long-term drought conditions.

Biogeochemical buffers in a eutrophic coastal lagoon along an oxic-hypoxic transition

The effects of bottom water oxic-hypoxic transition on estuarine benthic ecosystems have been extensively studied as oxygen (O2) depletion leads to the accumulation of toxic sulphides impacting sediment biogeochemical functioning. The role of benthic macrofauna in modulating such effects is understudied. Macrofauna may increase the resilience of sediments to critical O2 transitions via direct and indirect mechanisms acting upon organic matter (OM) and solid-phase metal pools that represent internal geochemical buffers for sediments. In this study we analysed whether and how the macrofaunal community may facilitate sediment resilience against short-term hypoxic events. Thus, net fluxes of reduced metals and inorganic nutrients were measured under oxic conditions and induced hypoxia in intact cores representing most of the sedimentary environments of the eutrophic Curonian Lagoon. Afterwards, distance-based linear models (distLM) were applied to explore the relationship between the dominant macrofauna taxa, sediment properties and the net fluxes. The results show a mosaic of sedimentary environments including OM poor (0.3%) sandy areas, OM rich (23%) muddy areas and variable combinations of these extremes. The variability of the macrofauna community was comparatively much lower, with oligochaetes and chironomids representing the most abundant taxa at most sampling sites. Along with the induced oxic-hypoxic transition metal fluxes tended to increase, together with dissolved inorganic phosphorus release, whereas dissolved inorganic nitrogen and silica tended to decrease. The distLM model evidenced that sediment properties accounted for 84.2% of the total flux variability whereas Chironomidae, Gammaridae and Gastropoda cumulatively accounted for 15.8% of the total explained variation in fluxes under oxic conditions. Under hypoxic conditions macrofauna explained a measurable but minor fraction of flux variability whereas OM and granulometry were best predictors. In the Curonian Lagoon macrofauna has a minor role in regulating fluxes and in providing biogeochemical services as compared to sediment features. As such, the benthic system appears vulnerable to short-term events of O2 shortage.

Climax forest has a higher soil bacterial diversity but lower soil nutrient contents than degraded forests in temperate northern China.

Bacteria are a crucial component of forest soil biodiversity and play an important role in numerous ecosystem processes. Here, we studied the patterns of soil bacterial community diversity and structure in a climax forest (Larix gmelinii; LG) compared with those in degraded forest ecosystems of four forest vegetation types (BD, Betula dahurica; BP, Betula platyphylla; QM, Quercus mongolica; and LGQM, a mixed coniferous-broadleaved forest composed of Larix gmelinii and Quercus mongolica) in the Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve in northern China, using Illumina MiSeq sequencing of 16 S rRNA genes. Soil physicochemical properties (pH, soil organic carbon=SOC, total nitrogen=TN, carbon/nitrogen=C/N, total phosphorous=TP, available nitrogen=AN, available phosphorous=AP) differed significantly (p < .05) among the five forests. SOC, C/N, TP, AN, and AP were highest in QM, whereas SOC was lowest in LGQM. Soil pH was lowest in BD and highest in LGQM. α diversity was highest in LG and lowest in QM. The soil bacterial community composition in the climax forest was significantly different from that in the four degraded forests (p < .05). The dominant bacterial phyla were Acidobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Firmicutes, Chloroflexi, and Rokubacteria. The highest relative abundances of these phyla were: 30.7% for Acidobacteria in LGQM, 42.6% for Proteobacteria in LG, 17.6% for Verrucomicrobia in BD, 5.5% for Firmicutes in BP, and 6.9% for Actinobacteria in QM. The dominant bacterial genera across the five forest vegetation types were Bryobacter and some poorly characterized taxa (e.g., Candidatus_Udaeobacter and Candidatus_Solibacter). Redundancy analysis indicated that SOC, C/N, TP, AN, and AP were the main soil physicochemical properties that shaped the bacterial communities. Our study revealed distinct bacterial diversity and composition in the climax forest compared with values in degraded forests, suggesting that the biotic and abiotic factors associated with climax ecosystems play an important role in shaping soil bacterial community structure and thus biogeochemical functions. The results of this study contribute to a deeper understanding and better predictions of the network among belowground systems and of the functions and services of degraded forests compared with climax ecosystems.

Assessing the water quality of the Seine land-to-sea continuum for three agro-food system scenarios

Three scenarios for the future of the French agro-food system were specified for the territory draining into the Seine Bight, comprising Paris megacity and the Seine watershed. The first scenario assumes the pursuit of the current trend of opening and specialization of agriculture, as well as of concentration of population within the Paris agglomeration. The second scenario assesses the generalization of agro-ecological practices and a healthier human diet. A third, hybrid, scenario was elaborated assuming that agro-ecological practices were implemented in some protected areas (namely Regional Natural Parks and drinking water protection areas, making up about one-third of the total watershed area), while the rest of the territory will follow the trends of the first scenario. We use a unique modelling chain (GRAFS-Riverstrahler-ECOMARS3D) that couples the biogeochemical functioning of the river basin, the estuary and the adjacent bay. It allows exploring the implications of changes in terrestrial activities throughout the aquatic continuum in a consistent way and assessing to what extent changes in population, agricultural practices, food consumption, and sanitation may sustain the current trend of recovery in the Seine River or either increase stress on the system. Results show that only the full agro-ecological scenario would be able to restore good water quality everywhere in the river network, as well as decrease significantly the risks of toxic algal blooms in the coastal zone. Intermediate situations, such as the protection of specific areas, however attractive as a solution, are not enough to offset the impacts of intensive human activities unless the protected areas dedicated to compensating for damage are sufficiently large.

A photographic transect method for field measurement of vegetation cover along an ecotone gradient in a desert environment

Vegetation cover is essential to the ecologic and biogeochemical functioning of drylands. These systems are marked by spatiotemporal variation in vegetation cover and biomass. Regular monitoring of vegetation cover in drylands is critical for their conservation and management. This study examines the effectiveness of photo-based grid point intercept field survey for quantifying vegetation characteristics in drylands. The field data provides ground truth data for space borne remote sensing to analyze changes in vegetation cover. The study integrates rapid field photo sampling, GPS, and GIS to maximize raw data collection in the field and allow for subsequent sampling in the laboratory setting. Paired T-tests and simple linear regression were employed to assess sample size. Quantification of vegetation cover using minimum distance (MD), spectral angle mapper (SAM), and support vector machine (SVM) automated classification were assessed using visual sampling as a reference. Fifty sampling points are sufficient for quantifying vegetation cover of steppe, but are less adequate for desert steppe. The assessment of automated classifications of photo plots revealed that SAM outperformed both MD and SVM. Photo-based Grid-point Intercept provides a cost- and time-effective technique for data collection to support satellite and air platform remote sensing analysis of vegetation dynamics.

Dissolved organic matter concentration and composition discontinuity at the peat–pool interface in a boreal peatland

Abstract. Pools are common features of peatlands and can represent from 5 % to 50 % of the peatland ecosystem's surface area. Pools play an important role in the peatland carbon cycle by releasing carbon dioxide and methane to the atmosphere. However, the origin of this carbon is not well constrained. A hypothesis is that the majority of the carbon emitted from pools predominantly originates from mineralized allochthonous (i.e., plant-derived) dissolved organic matter (DOM) from peat rather than in situ primary production. To test this hypothesis, this study examined the origin, composition, and degradability of DOM in peat porewater and pools of an ombrotrophic boreal peatland in northeastern Quebec (Canada) for 2 years over the growing season. The temporal evolution of dissolved organic carbon (DOC) concentration, the optical properties, molecular composition (THM-GC-MS), stable isotopic signature (δ13C-DOC), and degradability of DOM were determined. This study demonstrates that DOM, in both peat porewater and pools, presents a diverse composition and constitutes highly dynamic components of peatland ecosystems. The molecular and isotopic analyses showed that DOM in pools was derived from plants. However, DOM compositions in the two environments were markedly different. Peat porewater DOM was more aromatic, with a higher molecular weight and DOC : DON (dissolved organic nitrogen) ratio compared to pools. The temporal dynamics of DOC concentration and DOM composition also differed. In peat porewater, the DOC concentration followed a strong seasonal increase, starting from 9 mg L−1 and reaching a plateau above 20 mg L−1 in summer and autumn. This was explained by seasonal peatland vegetation productivity, which is greater than microbial DOM degradation. In pools, DOC concentration also increased but remained 2 times lower than in the peat porewaters at the end of the growing season (∼ 10 mg L−1). Those differences might be explained by a combination of physical, chemical, and biological factors. The limited hydraulic conductivity in deeper peat horizons and associated DOM residence time might have favored both DOM microbial transformation within the peat and the interaction of DOM aromatic compounds with the peat matrix, explaining part of the shift of DOM compositions between peat porewater and pools. This study did not report any photolability of DOM and only limited microbial degradability. Thus, it is likely that the DOM might have been microbially transformed at the interface between peat and pools. The combination of DOM quantitative and qualitative analyses presented in this study demonstrates that most of the carbon present within and released from the pools originates from peat vegetation. These results demonstrate that pools represent a key component of the peatland ecosystem ecological and biogeochemical functioning.

Grazing, egg production and carbon budgets for Calanus finmarchicus across the Fram Strait

Calanoid copepods comprise around 90% of Arctic zooplankton biomass and are fundamental to the ecological and biogeochemical functioning of high-latitude pelagic ecosystems. They accumulate lipid reserves during the productive months and represent an energy-rich food source for higher trophic levels. Rapidly changing climate in the Arctic may alter the quantity and composition of the food environment for one of the key copepod species, Calanus finmarchicus, with as yet unquantified effects on its production. Here we present rates of feeding and egg production in female C. finmarchicus exposed to the range of feeding conditions encountered across the Fram Strait in May/June 2018. Carbon (C) budgets were constructed and used to examine the relationship between feeding and growth (= egg production) in these animals. C-specific ingestion rates (mean ± standard deviation) were highly variable, ranging from 0.015 ± 0.004 to 0.645 ± 0.017 day-1 (mean = 0.295 ± 0.223 day-1), and were positively correlated with food availability. C-specific egg production rates ranged from 0.00 to 0.049 day-1 (mean = 0.012 ± 0.011) and were not correlated with either food availability or ingestion rate. Calculated gross growth efficiencies (GGE: growth/ingestion) were low, 0.12 ± 0.13 (range = 0.01 to 0.39). The assembled C budgets indicate that the average fraction of ingested food that was surplus to the requirements for egg production, respiration and losses to faecal pellets was 0.17 ± 0.42. We suggest that this excess occurred, at least in part, because many of the incubated females were still undergoing the energetically (C-) expensive process of gonad maturation at the time of sampling, an assertion that is supported by the relatively high C:N (nitrogen) ratios of the incubated females, the typically low egg production rates, and gonad maturation status. Ontogenetic development may thus explain the large variability seen in the relationship between egg production and ingestion. The apparently excessive ingestion rates may additionally indicate that recently moulted females must acquire additional N via ingestion to complete the maturation process and begin spawning. Our results highlight the need for improved fundamental understanding of the physiology of high-latitude copepods and its response to environmental change.

Trace metal complexation with dissolved organic matter stresses microbial metabolisms and triggers community shifts: The intercorrelations

The response of microorganisms to heavy metal-dissolved organic matter (Me-DOM) complexation is critical for the microbial-mediated coupled biogeochemical cycling of metals and DOM. This study investigated the impact of typical metals [As, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn (at an environmentally-relevant concentration of 200 ppb)], model DOM substrates [humic acids (HA) and bovine serum albumin (BSA)], and their complexation on riverine microbial DOM metabolisms. DOM biodegradability decreased after the metal complexation (especially Co, Cr, and Mn for HA and Ni for BSA). While microbial transformation of humics and proteins was observed, components with lower aromaticity and hydrophobicity were accumulated during the cultivation. The substrate difference and metal speciation changed community compositions and resulted in distinctive community member networks, which accounted for the varied metabolic DOM patterns. The correlations indicated that rather than metal uptakes, Me-DOM complexation and community shifts controlled microbial DOM metabolisms. Microbial BSA metabolisms were less correlated to the key genera identified by network analysis or community diversity. Instead, they were sensitive to metal speciation, which may be attributed to the complicated utilization and production of proteins and their essential roles in detoxification. The constructed correlations among metals (Me-DOM complexes), DOM metabolisms, and community shifts provide strong implications for the biogeochemical function of Me-DOM complexes and highlight the effect of metal speciation on microbial protein metabolisms even at trace concentrations.