Search Results (18)

While gaining increasing attention, plant–microbiome–environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron—elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology. Full article

The main purpose of this study is to set up a biogeochemistry model for the Ria de Aveiro ecosystem and evaluate the relative importance of the main parameters and the processes occurring at the interface between the water column and the upper layer of the bottom sediment. It addresses a gap in modeling the interactions between the biogeochemical status of the water column and the upper sediment layer in the Ria de Aveiro lagoon ecosystem. Traditional modeling studies treated the bottom sediment as a rigid boundary, ignoring significant biogeochemical interactions at the interface between the water column and the upper layer of the bottom sediment. Therefore, the model integrates, besides the main biogeochemical processes within the water column, those occurring at the upper benthic layer, focusing on nitrogen (N) and phosphorus (P) cycles. This approach aims to enhance the accuracy of model predictions and understanding of the Ria de Aveiro lagoon’s biogeochemical dynamics. The study will be focused on the following coupled state variables: TN/IN and TP/IP, for total and inorganic nitrogen (N) and total and inorganic phosphorus (P), respectively, where total stands for the sum of organic and inorganic components of those elements. The model was set up and validated for some water quality stations of the Ria de Aveiro. Analysis has identified key parameters influencing TN and TP, such as nitrification, denitrification rates, and oxygen penetration. TN was found sensitive to nitrate and ammonium diffusion coefficients, while TP was influenced by iron–phosphate interactions and phosphorus mineralization. Concerning the model validation, the results demonstrated that the RMSE and MAPE values for the main variables fall within an acceptable range, given the uncertainty related to data. The model was applied to assess the impact of the following physical forcing: river flow, water temperature, and salinity on N and P status of the water column. The results clearly demonstrate that bottom layer and water column interactions play an important role in the N and P status of the water column and contribute to the N and P concentration changes of the water. The influence of river flows alone led to contrasting behaviors among the lagoon stations, with significant increases in TP levels, which may be attributed to sediment release from the sediment layer. Nevertheless, the combination of high river flows and elevated nutrient levels at the river boundaries has led to significantly increased nitrogen (N) and phosphorus (P) levels, underscoring the influence of river flow on the interaction between bottom layer sediment and the water column. High water temperatures typically lead to an increase in total phosphorus (TP) levels, indicating a possible release from the sediment layer. Meanwhile, TN levels remained stable. Salinity changes had a minor impact compared to river flow and temperature. The study emphasizes the importance of understanding interactions between the water column and sediment, particularly in shallow intertidal areas. Overall, the inclusion of biogeochemical interactions between the benthic and pelagic layers represents progress in ecosystem modeling of the Ria de Aveiro. Full article

Although mangrove forests occupy only 0.5% of the global coastal area, they account for 10–15% of coastal organic carbon (OC) storage, and 49–98% of OC is stored in sediments. The biogeochemistry of iron minerals and OC in marine sediments is closely related. To better reveal the role of iron minerals in OC preservation in mangrove sediments, an established dithionite–citrate–bicarbonate (DCB) extraction method was used to extract iron-bound OC (Fe-OC), and then the parameters of OC, Fe-OC, iron content, carbon isotopes, infrared spectroscopy, and XRD diffractions of sediments at a 1 m depth in four typical mangrove communities in the Gaoqiao Mangrove Reserve, Guangdong, China, were systematically measured. XRD diffractograms showed that the iron minerals in mangrove sediments may mainly exist in the form of goethite, which is consistent with the predominant types of iron minerals in marine sediments. About 10% of OC is directly bound to iron, and it is further estimated that about 2.4 × 10¹²–3.8 × 10¹² g OC is preserved in global mangrove forests each year based on the high burial rate of OC in mangrove sediments. Lower Fe-OC/OC molar ratios indicated that iron mainly binds to OC via adsorption mechanisms. More depleted δ¹³C_Fe-OC relative to δ13C_bulk indicated that iron minerals are mainly associated with terrigenous OM, and the infrared spectra also revealed that iron minerals preferentially bind to terrigenous aromatic carbon. This work supports the “giant rusty sponge” view, elucidating that iron plays an important role in the preservation of OC in mangrove sediments. Full article

Deep-sea hydrothermal vents have been extensively explored around the globe in the past decades, and the diversity of microbial communities and their ecological functions related to hydrothermal vents have become hotspots in the study of microbial biogeochemistry. However, knowledge of dominant microbial communities and their unique metabolic characteristics adapting to hydrothermal vents is still limited. In our study, the sediment sample near the Tangyin hydrothermal vent in the southern part of the Okinawa Trough was collected, and the most abundant phyla are Proteobacteria and Desulfobacterota based on the 16S rRNA genes and metagenome sequencing. Metagenomic analysis revealed that methane metabolism, sulfur reduction, and Fe²⁺ uptake were abundantly distributed in hydrothermal sediment. In addition, most of the metagenomic assembly genomes (MAGs), belonging to Chloroflexota, Desulfobacterota, and Gammaproteobacteria, were found to be involved in methanogenesis, sulfur oxidation/reduction, and ferrous/ferric iron metabolisms. Among these MAGs, the two representative groups (Bathyarchaeia and Thioglobaceae) also showed distinct metabolic characteristics related to carbon, sulfur, and iron to adapt to hydrothermal environments. Our results reveal the dominant microbial populations and their metabolic features in the sediment near the Tangyin hydrothermal fields, providing a better understanding of microbial survival strategies in the extreme environment. Full article

Nitrate is globally the most widespread and widely studied groundwater contaminant. However, few studies have been conducted in sub-Saharan Africa, where the leaching potential is enhanced during the rainy monsoon phase. The few monitoring studies found concentrations over drinking water standards of 10 mg N-NO₃⁻ L⁻¹ in the groundwater, the primary water supply in rural communities. Studies on nitrate movement are limited to the volcanic Ethiopian highlands. Therefore, this study aimed to evaluate the transport and fate of nitrate in groundwater and identify processes that control the concentrations. Water table height, nitrate, chloride, ammonium, reduced iron, and three other groundwater constituents were determined monthly in the groundwater in over 30 wells in two contrasting volcanic watersheds over two years in the Ethiopian highlands. The first watershed was Dangishta, with lava intrusion dikes that blocked the subsurface flow in the valley bottom. The water table remained within 3 m of the surface. The second watershed without volcanic barriers was Robit Bata. The water table dropped rapidly within three months of the end of the rain phase and disappeared except near faults. The average nitrate concentration in both watersheds was between 4 and 5 mg N-NO₃⁻ L⁻¹. Hydrogeology influenced the transport and fate of nitrogen. In Dangishta, water was blocked by volcanic lava intrusion dikes, and residence time in the aquifer was larger than in Robit Bata. Consequently, nitrate remained high (in several wells, 10 mg N-NO₃⁻ L⁻¹) and decreased slowly due to denitrification. In Robit Bata, the water residence time was lower, and peak concentrations were only observed in the month after fertilizer application; otherwise, it was near an average of 4 mg N-NO₃⁻ L⁻¹. Nitrate concentrations were predicted using a multiple linear regression model. Hydrology explained the nitrate concentrations in Robit Bata. In Dangishta, biogeochemistry was also significant. Full article

The formation of thin mineral films or encrustations floating on the water surface of low-flow or stagnant zones of acid mine drainage (AMD)-affected streams is probably among the most exotic features that can be found in mining areas. However, most fundamental questions about their origin (biotic vs. abiotic), structure, mineralogy, physical stability and metal-retention capacity remain unanswered. This study aims to reveal the factors promoting their formation and to clarify their composition in detail. With this purpose, the major mineral phases were studied with XRD in surface film samples found in different mine sites of the Iberian Pyrite Belt mining district (SW Spain), and the major oxide and trace metal concentrations were measured with XRF and/or ICP-MS. Fe(III) minerals dominated these formations, with mineralogy controlled by the pH (jarosite at pH~2.0, schwertmannite at pH 2.5–3.5, ferrihydrite at pH > 6.0). Other minerals have also been identified in minor proportions, such as brushite or khademite. These mineral formations show an astounding capacity to concentrate, by orders of magnitude (×10² to ×10⁵), many different trace metals present in the underlying aqueous solutions, either as anionic complexes (e.g., U, Th, As, Cr, V, Sb, P) or as divalent metal cations (e.g., Cu, Zn, Cd, Pb). These floating mineral films are usually formed in Fe(II)-rich acidic waters, so their formation necessarily implies the oxidation of Fe(II) to Fe(III) phases. The potential involvement of Fe(II)-oxidizing microorganisms was investigated through 16S rRNA gene amplicon sequencing of water underneath the Fe(III)-rich floating mineral films. The sequenced reads were dominated by Ferrovum (51.7 ± 0.3%), Acidithiobacillus (18.5 ± 0.9%) and Leptospirillum (3.3 ± 0.1%), three well-known Fe(II)-oxidizing genera. These microorganisms are major contributors to the formation of the ferric mineral films, although other genera most likely also play a role in aspects such as Fe(III) sequestration, nucleation or mineral growth. The floating mineral films found in stagnant acidic mine waters represent hotspots of biosphere/hydrosphere/atmosphere interactions of great value for the study of iron biogeochemistry in redox boundaries. Full article

Primary production in the Southern Ocean highly depends on phytoplankton and has been reported to be limited by the availability of the micronutrient iron. The aim of this review is to summarize the past and current knowledge on iron limitation in the Southern Ocean, and specifically how it affects primary producers, thus influencing the whole Southern Ocean community structure, carbon cycling, and large-scale ocean biogeochemistry. In this region, extensive variability exists between different areas regarding iron availability, but also between seasons. Moreover, co-limitations with other abiotic environmental factors exist, further complicating the assessment of the role of iron as limiting factor for phytoplankton productivity. Currently, climate change is altering the Southern Ocean environment. How these changes will affect resident phytoplankton is still not clear, possibly modifying the iron supply mechanisms. Existing projections point towards a possible partial relief of iron stress on phytoplankton, but the interactions between different environmental changes, and the cascade effects they will have, are still poorly understood, and some aspects understudied. Here we try to synthetize the available predictions and uncertainties concerning this topic. Full article

Iron (Fe) is one of the most biochemically active and widely distributed elements and one of the most important elements for biota and human activities. Fe plays important roles in biological and chemical processes. Fe redox reactions in groundwater have been attracting increasing attention in the geochemistry and biogeochemistry fields. This study reviews recent research into Fe redox reactions and biogeochemical Fe enrichment processes, including reduction, biotic and abiotic oxidation, adsorption, and precipitation in groundwater. Fe biogeochemistry in groundwater and the water-bearing medium (aquifer) often involves transformation between Fe(II) and Fe(III) caused by the biochemical conditions of the groundwater system. Human activities and anthropogenic pollutants strongly affect these conditions. Generally speaking, acidification, anoxia and warming of groundwater environments, as well as the inputs of reducing pollutants, are beneficial to the migration of Fe into groundwater (Fe(III)→Fe(II)); conversely, it is beneficial to the migration of it into the media (Fe(II)→Fe(III)). This study describes recent progress and breakthroughs and assesses the biogeochemistry of Fe enrichment in groundwater, factors controlling Fe reactivity, and Fe biogeochemistry effects on the environment. This study also describes the implications of Fe biogeochemistry for managing Fe in groundwater, including the importance of Fe in groundwater monitoring and evaluation, and early groundwater pollution warnings. Full article

Greater knowledge concerning the interspecific diversity of the plant leaf ionome is required to effectively understand the spatiotemporal dynamics of biogeochemistry, but Micronesia has been ignored in this literature. The objectives of this study were to quantify the leaf ionome, resorption efficiency, and stoichiometry of leaves from 25 plant species representing Guam’s coastal karst forests. Carbon and nitrogen were quantified by dry combustion, and other minerals and metals were quantified by spectrometry. Nitrogen and calcium concentrations in Guam’s green leaves exceeded the published global means, but manganese and copper concentrations were less than the global means. The remainder of the elements were within the expected ranges. Nutrient resorption rates exhibited a decreasing order of potassium > phosphorus > nitrogen > zinc > copper. The term “accretion efficiency” is introduced to describe the accumulation of an element throughout leaf aging and senescence, and calcium and iron exhibited substantial accretion efficiency in this study. Stoichiometry relations indicated that Guam’s karst forest is most limited by phosphorus and then secondarily limited by nitrogen, although several individual taxa exhibited co-limitation by potassium. Five of the species are officially listed on extinction threat lists. Of these, the Malvaceae tree Heriteria longipetiolata exhibited leaf traits depicting the most recalcitrant litter characteristics, and the Fabaceae tree Serianthes nelsonii exhibited leaf traits depicting the most labile litter characteristics. The contributions of these two tree species to spatiotemporal diversity in biogeochemistry appear to be profound, indicating species recovery efforts are of paramount importance for maintaining ecosystem function and soil heterotroph biodiversity in northern Guam. Full article

In the Gulf of California; mineral deposits have contributed to high metal contents in coastal environments. This study examined cadmium; lead; copper; zinc; and iron contents in three fish species; Kyphosus vaigiensis (herbivore), Stegastes rectifraenum (omnivore), and Balistes polylepis (carnivore) at two mining sites. Metal concentrations were analyzed by atomic absorption spectrophotometry and stable nitrogen and carbon isotopes were estimated using mass spectrophotometry. Also, we assessed the risk to human health from the consumption of these three species based on permissible limits; although only two of them (Kyphosus and Balistes) are consumed as food. Metal concentrations differed among fish species; except for iron. The highest concentrations of metals were not always recorded in the species at the highest trophic level; i.e., Balistes. The highest concentrations (dry weight) recorded were cadmium (0.21 ± 0.03 µg g⁻¹) and lead (1.67 ± 0.26 µg g⁻¹), in S. rectifraenum; copper (1.60 ± 0.49 µg g⁻¹) and zinc (67.30 ± 8.79 µg g⁻¹), in B. polylepis; and iron (27.06 ± 2.58 µg g⁻¹), in K. vaigiensis. Our findings show that each element accumulates differently in particular marine organisms; depending on the physiology of the species and the biogeochemistry of its habitat; which in turn is affected by the anthropogenic activities in adjacent areas. No risk of heavy metals toxicity is expected from the human consumption of the species and sites studied Full article

Phosphorus (P) is an essential limiting nutrient in marine and terrestrial ecosystems. Understanding the natural and anthropogenic influence on P concentration in soils is critical for predicting how its distribution in soils may shift as climate changes. While it is known that P is sourced from bedrock weathering, relationships between weathering, P, and other soil-forming factors have not been quantified at continental scales, limiting our ability to predict large-scale changes in P concentrations. Additionally, while we know that Fe oxide-associated P is an important P phase in terrestrial environments, the range in and controls on soil Fe concentrations and species (e.g., Fe in oxides, labile Fe) are poorly constrained. Here, we explore the relationships between soil P and Fe concentrations, soil order, climate, and vegetation in over 5000 soils, and Fe speciation in ca. 400 soils. Weathering intensity has a nuanced control on P concentrations in soils, with P concentrations peaking at intermediate weathering intensities (Chemical Index of Alteration, CIA~60). The presence of vegetation (but not plant functional types) affected soils’ ability to accumulate P. Contrary to expectations, P was not more strongly associated with Fe in oxides than other Fe phases. These results are useful both for predicting changes in potential P fluxes from soils to rivers under climate change and for reconstructing changes in terrestrial nutrient limitations in Earth’s past. In particular, soils’ tendency to accumulate more P with the presence of vegetation suggests that biogeochemical models invoking the evolution and spread of land plants as a driver for increased P fluxes in the geological record may need to be revisited. Full article

Organic ligands such as exopolymeric substances (EPS) are known to form complexes with iron (Fe) and modulate phytoplankton growth. However, the effect of organic ligands on bacterial and viral communities remains largely unknown. Here, we assessed how Fe associated with organic ligands influences phytoplankton, microbial, and viral abundances and their diversity in the Southern Ocean. While the particulate organic carbon (POC) was modulated by Fe chemistry and bioavailability in the Drake Passage, the abundance and diversity of microbes and viruses were not governed by Fe bioavailability. Only following amendments with bacterial EPS did bacterial abundances increase, while phenotypic alpha diversity of bacterial and viral communities decreased. The latter was accompanied by significantly enhanced POC, pointing toward the relief of C limitation or other drivers of the microbial loop. Based on the literature and our findings, we propose a conceptual framework by which EPS may affect phytoplankton, bacteria, and viruses. Given the importance of the Southern Ocean for Earth’s climate as well as the prevalence of viruses and their increasingly recognized impact on marine biogeochemistry and C cycling; the role of microbe–virus interactions on primary productivity in the Southern Ocean needs urgent attention. Full article

Cyanobacteria have high iron requirements due to iron-rich photosynthetic machineries. Despite the high concentrations of iron in the Earth’s crust, iron is limiting in many marine environments due to iron’s low solubility. Oxic conditions leave a large portion of the ocean’s iron pool unavailable for biotic uptake, and so the physiochemical properties of iron are hugely important for iron’s bioavailability. Our study is the first to investigate the effect of iron source on iron internalization and extracellular reduction by Synechococcus sp. PCC 7002. The results indicated that the amorphous iron hydrolysis species produced by FeCl₃ better support growth in Synechococcus through more efficient iron internalization and a larger degree of extracellular reduction of iron than the crystalline FeO(OH). An analysis of dissolved iron (II) indicated that biogenic reduction took place in cultures of Synechococcus grown on both FeCl₃ and FeO(OH). Full article

Iron is an essential, yet scarce, nutrient in marine environments. Phytoplankton, and especially cyanobacteria, have developed a wide range of mechanisms to acquire iron and maintain their iron-rich photosynthetic machinery. Iron limitation studies often utilize either oceanographic methods to understand large scale processes, or laboratory-based, molecular experiments to identify underlying molecular mechanisms on a cellular level. Here, we aim to highlight the benefits of both approaches to encourage interdisciplinary understanding of the effects of iron limitation on cyanobacteria with a focus on avoiding pitfalls in the initial phases of collaboration. In particular, we discuss the use of trace metal clean methods in combination with sterile techniques, and the challenges faced when a new collaboration is set up to combine interdisciplinary techniques. Methods necessary for producing reliable data, such as High Resolution Inductively Coupled Plasma Mass Spectrometry (HR-ICP-MS), Flow Injection Analysis Chemiluminescence (FIA-CL), and 77K fluorescence emission spectroscopy are discussed and evaluated and a technical manual, including the preparation of the artificial seawater medium Aquil, cleaning procedures, and a sampling scheme for an iron limitation experiment is included. This paper provides a reference point for researchers to implement different techniques into interdisciplinary iron studies that span cyanobacteria physiology, molecular biology, and biogeochemistry. Full article

Abandoned mine lands continue to serve as non-point sources of acid and metal contamination to water bodies long after mining operations have ended. Although soils formed from abandoned mine spoil can support forest vegetation, as observed throughout the Appalachian coal basin, the effects of vegetation on metal cycling in these regions remain poorly characterized. Iron (Fe) and manganese (Mn) biogeochemistry were examined at a former coal mine where deciduous trees grow on mine spoil deposited nearly a century ago. Forest vegetation growing on mine spoil effectively removed dissolved Mn from pore water; however, mineral weathering at a reaction front below the rooting zone resulted in high quantities of leached Mn. Iron was taken up in relatively low quantities by vegetation but was more readily mobilized by dissolved organic carbon produced in the surface soil. Dissolved Fe was low below the reaction front, suggesting that iron oxyhydroxide precipitation retains Fe within the system. These results indicate that mine spoil continues to produce Mn contamination, but vegetation can accumulate Mn and mitigate its leaching from shallow soils, potentially also decreasing Mn leaching from deeper soils by reducing infiltration. Vegetation had less impact on Fe mobility, which was retained as Fe oxides following oxidative weathering. Full article