Tropical forest soil microbial communities couple iron and carbon biogeochemistry

Contrasting organic carbon respiration pathways in coastal wetlands undergoing accelerated sea level changes

Carbon cycling in coastal wetland soil is controlled by a complex interplay between microbial processes and porewater chemistry that are often influenced by various external forcings like wind, river discharge, and sea-level changes, where most of the organic carbon is mineralized to its inorganic form by various aerobic and anaerobic respiration pathways. The export of this inorganic carbon (DIC) from coastal wetlands has long been recognized as a significant component of the global carbon cycle. The major objective of this work is to determine the relative contribution of various respiration pathways to seasonal DIC production in two contrasting marshes (brackish and salt). The DIC fluxes estimates for the brackish and salt marshes were found to range between 36.52 ± 5.81 and 33.98 ± 2.21 mmol m-2 d-1 in winter and 133.10 ± 102.60 and 82.37 ± 30.87 mmol m-2 d-1 during summer of 2020. For the brackish marsh, aerobic respiration and iron reduction were found to be the primary contributors to DIC production representing 17.91-35.21 % and 61.13-81.97 % of total measured organic matter (OM) respiration respectively. On the other hand, aerobic respiration and sulfate reduction were the primary contributors to DIC production in the salt marsh, accounting for 37.91-83.93 % and 15.87-62.04 % of the total measured OM respiration respectively. The Mississippi River Deltaic Plain experiences high relative sea level rise and expected to undergo rapid change in salinity regime in near future from additional changes in river discharge, proposed sediment diversion plans, and storm surge intensities. The current study represents the first attempt to concurrently estimate various respiration pathways in this region and more studies are needed to understand the trajectories of soil OM respiration pathways and its impact on coastal carbon cycling.

Geobatteries in environmental biogeochemistry: Electron transfer and utilization

The efficiency of direct electron flow from electron donors to electron acceptors in redox reactions is significantly influenced by the spatial separation of these components. Geobatteries, a class of redox-active substances naturally present in soil-water systems, act as electron reservoirs, reversibly donating, storing, and accepting electrons. This capability allows the temporal and spatial decoupling of redox half-reactions, providing a flexible electron transfer mechanism. In this review, we systematically examine the critical role of geobatteries in influencing electron transfer and utilization in environmental biogeochemical processes. Typical redox-active centers within geobatteries, such as quinone-like moieties, nitrogen- and sulfur-containing groups, and variable-valent metals, possess the potential to repeatedly charge and discharge. Various characterization techniques, ranging from qualitative methods like elemental analysis, imaging, and spectroscopy, to quantitative techniques such as chemical, spectroscopic, and electrochemical methods, have been developed to evaluate this reversible electron transfer capacity. Additionally, current research on the ecological and environmental significance of geobatteries extends beyond natural soil-water systems (e.g., soil carbon cycle) to engineered systems such as water treatment (e.g., nitrogen removal) and waste management (e.g., anaerobic digestion). Despite these advancements, challenges such as the complexity of environmental systems, difficulties in accurately quantifying electron exchange capacity, and scaling-up issues must be addressed to fully unlock their potential. This review underscores both the promise and challenges associated with geobatteries in responding to environmental issues, such as climate change and pollutant transformation.

Fe oxides simultaneously improve stability of Cd and carbon in paddy soil：The underlying influence at aggregate level

Iron (Fe) oxides have a strong adsorption affinity for Cd and organic carbon (SOC). However, under alternate wet-dry (IF) condition,the influences of Fe oxides on the speciation and disrtribution of Cd and SOC in soil aggregates are unkown. In the present study, soils untreated (S), removed (S-Fe) or added (S+Fe) Fe oxide soils were blended with cadmium chloride solution and cultivated for 56 days under different moisture management practices. Compared with the S-Fe soil, the IF treatment increased the contents of Fe oxide-bound SOC (Fe-OC) and Fe/Mn oxide-bound Cd (Fe/Mn-Cd) by 18.5-29.8-fold and 1.45-2.45-fold, repectively, in the S and S+Fe soils, corresponding to a 36 %-42 % increase in the recalcitrant C pool (RCP) and a 53 %-87 % decrease in the exchangeable Cd content. These results could be attributed to soil particle aggregation and Fe redistribution. Fe addition promoted the transfer of Cd/SOC accumulated in microaggregates to macroaggregates and increased the variable negative charge content in macroaggregates and the adsorption capacity of macroaggregates for Cd/SOC. More Cd/SOC accumulated in macroaggregates in Fe oxide-bound form, which reduced the risk of Cd migration and Cd availability and increased the physical protection of SOC. Therefore, Fe oxide has great potential to simultaneously reduce carbon emissions and cadmium toxicity in paddy soil.

Diversity of soil fungi and entomopathogenic fungi in subtropical mountain forest in southwest China

Till now, the diversity of entomopathogenic fungi in subtropical mountain forest was less studied. Here, the vertical distribution of forest soil fungi, entomopathogenic fungi, and their environmental influencing factors in a subtropical mountain in western China were investigated. Soil samples were collected from four elevations in a subtropical forest in Shaanxi. The results indicated a greater richness of soil fungi at middle elevations and soil fungi were more even at low elevation. Soil pH, available iron, available potassium, total potassium, and available zinc were the most important influencing factors affecting this vertical distribution of fungi. Interestingly, the Isaria genus was predominant while Metarhizium and Beauveria showed decreasing abundance. The presence of Isaria showed a significant positive correlation with both total phosphorus and available iron, while, available zinc was negatively correlated. Metarhizium was influenced by elevation, pH, available phosphorus, and available copper and Beauveria was influenced by soil organic carbon, total nitrogen, total potassium, available potassium, and available zinc. Overall, as environmental factors affecting soil fungi, elevation, and plant species diversity were less important than soil physical and chemical properties. The virulence of isolated entomopathogenic fungi were tested against larvae of Tenebrio molitor, with mortality ranging from 31.11% to 100%. The above findings provide valuable data to deepen our understanding of the diversity of entomopathogenic fungi in subtropical mountain forests.

Metallic micronutrients are associated with the structure and function of the soil microbiome

The relationship between metallic micronutrients and soil microorganisms, and thereby soil functioning, has been little explored. Here, we investigate the relationship between metallic micronutrients (Fe, Mn, Cu, Zn, Mo and Ni) and the abundance, diversity and function of soil microbiomes. In a survey across 180 sites in China, covering a wide range of soil conditions the structure and function of the soil microbiome are highly correlated with metallic micronutrients, especially Fe, followed by Mn, Cu and Zn. These results are robust to controlling for soil pH, which is often reported as the most important predictor of the soil microbiome. An incubation experiment with Fe and Zn additions for five different soil types also shows that increased micronutrient concentration affects microbial community composition and functional genes. In addition, structural equation models indicate that micronutrients positively contribute to the ecosystem productivity, both directly (micronutrient availability to plants) and, to a lesser extent, indirectly (via affecting the microbiome). Our findings highlight the importance of micronutrients in explaining soil microbiome structure and ecosystem functioning.

Promotion of Humic Acid Transformation by Abiotic and Biotic Fe Redox Cycling in Nontronite

The redox activity of Fe-bearing minerals is coupled with the transformation of organic matter (OM) in redox dynamic environments, but the underlying mechanism remains unclear. In this work, a Fe redox cycling experiment of nontronite (NAu-2), an Fe-rich smectite, was performed via combined abiotic and biotic methods, and the accompanying transformation of humic acid (HA) as a representative OM was investigated. Chemical reduction and subsequent abiotic reoxidation of NAu-2 produced abundant hydroxyl radicals (thereafter termed as ·OH) that effectively transformed the chemical and molecular composition of HA. More importantly, transformed HA served as a more premium electron donor/carbon source to couple with subsequent biological reduction of Fe(III) in reoxidized NAu-2 by Geobacter sulfurreducens, a model Fe-reducing bacterium. Destruction of aromatic structures and formation of carboxylates were mechanisms responsible for transforming HA into an energetically more bioavailable substrate. Relative to unaltered HA, transformed HA increased the extent of the bioreduction by 105%, and Fe(III) reduction was coupled with oxidation and even mineralization of transformed HA, resulting in bleached HA and formation of microbial products and cell debris. ·OH transformation slightly decreased the electron shuttling capacity of HA in bioreduction. Our results provide a mechanistic explanation for rapid OM mineralization driven by Fe redox cycling in redox-fluctuating environments.

Dissimilatory iron reduction contributes to anaerobic mineralization of sediment in a shallow transboundary lake

Dissimilatory iron reduction (DIR) coupled with carbon cycling is increasingly being recognized as an influential process in freshwater wetland soils and sediments. The role of DIR in organic matter (OM) mineralization, however, is still largely unknown in lake sediment environments. In this study, we clarified rates and pathways of OM mineralization in two shallow lakes with seasonal hydrological connectivity and different eutrophic situations. We found that in comparison with the domination of DIR (55%) for OM mineralization in Lake Xiaoxingkai, the contribution of methanogenesis was much higher (68%) in its connected lake (Lake Xingkai). The differences in rates and pathways of sediment OM mineralization between the two lakes were attributed to higher concentrations of carbonate associated iron oxides (Fecarb) in Lake Xiaoxingkai compared to Lake Xingkai (P = 0.002), due to better deposition mixing, more contributions of terrigenous detrital materials, and higher OM content in Lake Xiaoxingkai. Results of structural equation modeling showed that Fecarb and total iron content (TFe) regulated 25% of DIR in Lake Xiaoxingkai and 76% in Lake Xingkai, accompanied by a negative effect of TFe on methanogenesis in Lake Xingkai. The relative abundance and diversity of Fe-reducing bacteria were significantly different between the two lakes, and showed a weak effect on sediment OM mineralization. Our findings emphasize the role of iron minerals and geochemical characterizations in regulating rates and pathways of OM mineralization, and deepen the understanding of carbon cycling in lake sediments.

Coprecipitation with Ferrihydrite Inhibits Mineralization of Glucuronic Acid in Anoxic Soils

It is known that the association of soil organic matter (SOM) with iron minerals limits carbon mobilization and degradation in aerobic soils and sediments. However, the efficacy of iron mineral protection mechanisms under reducing soil conditions, where Fe(III)-bearing minerals may be used as terminal electron acceptors, is poorly understood. Here, we quantified the extent to which iron mineral protection inhibits mineralization of organic carbon in reduced soils by adding dissolved ¹³C-glucuronic acid, a ⁵⁷Fe-ferrihydrite-¹³C-glucuronic acid coprecipitate, or pure ⁵⁷Fe-ferrihydrite to anoxic soil slurries. In tracking the re-partitioning and transformation of ¹³C-glucuronic acid and native SOM, we find that coprecipitation suppresses mineralization of ¹³C-glucuronic acid by 56% after 2 weeks (at 25 °C) and decreases to 27% after 6 weeks, owing to ongoing reductive dissolution of the coprecipitated ⁵⁷Fe-ferrihydrite. Addition of both dissolved and coprecipitated ¹³C-glucuronic acid resulted in increased native SOM mineralization, but the reduced bioavailability of the coprecipitated versus dissolved ¹³C-glucuronic acid decreased the priming effect by 35%. In contrast, the addition of pure ⁵⁷Fe-ferrihydrite resulted in negligible changes in native SOM mineralization. Our results show that iron mineral protection mechanisms are relevant for understanding the mobilization and degradation of SOM under reducing soil conditions.

Shower thoughts: why scientists should spend more time in the rain

Stormwater is a vital resource and dynamic driver of terrestrial ecosystem processes. However, processes controlling interactions during and shortly after storms are often poorly seen and poorly sensed when direct observations are substituted with technological ones. We discuss how human observations complement technological ones and the benefits of scientists spending more time in the storm. Human observation can reveal ephemeral storm-related phenomena such as biogeochemical hot moments, organismal responses, and sedimentary processes that can then be explored in greater resolution using sensors and virtual experiments. Storm-related phenomena trigger lasting, oversized impacts on hydrologic and biogeochemical processes, organismal traits or functions, and ecosystem services at all scales. We provide examples of phenomena in forests, across disciplines and scales, that have been overlooked in past research to inspire mindful, holistic observation of ecosystems during storms. We conclude that technological observations alone are insufficient to trace the process complexity and unpredictability of fleeting biogeochemical or ecological events without the shower thoughts produced by scientists' human sensory and cognitive systems during storms.

Fe(III) stabilizing soil organic matter and reducing methane emissions in paddy fields under varying flooding conditions

The role of iron (Fe) in soil organic matter (SOM) stabilization and decomposition in paddy soils has recently gained attention, but the underlying mechanisms during flooding and drying periods remain elusive. As the depth water layer is maintained in the fallow season, there will be more soluble Fe than during the wet and drainage seasons and the availability of oxygen (O₂) will be different. To assess the influence of soluble Fe on SOM mineralization during flooding, an incubation experiment was designed under oxic and anoxic flooding conditions, with and without Fe(III) addition. The results showed that Fe(III) addition significantly (p < 0.05) decreased SOM mineralization by 14.4 % under oxic flooding conditions over 16 days. Under anoxic flooding incubation, Fe(III) addition significantly (p < 0.05) decreased 10.8 % SOM decomposition, mainly by 43.6 % methane (CH₄) emission, while no difference in carbon dioxide (CO₂) emission was noticed. These findings suggest that implementing appropriate water management strategies in paddy soils, considering the roles of Fe under both oxic and anoxic flooding conditions, can contribute to SOM preservation and mitigation of CH₄ emissions.

Performance of pilot-scale membrane aerated biofilm reactors integrated with anoxic nano-biotechnological reactor for domestic wastewater treatment

Membrane-aerated biofilm reactors (MABRs) have aroused increasing attention due to their excellent performance in treating wastewater, where the membranes behave as bio-carriers for microorganisms and bubbleless air diffusers. The MABR technology has not been fully commercialized due to reactor design and low total nitrogen (TN) removal efficiency at short hydraulic retention times (HRT). In this study, a hybrid system of MABR 1 integrated with an anoxic nano-biotechnological reactor filled with Granulated Nanoscale Oxyhydroxides of Fe (GNOF) media was evaluated to assess the improvement in nitrogen removal performance at 12, 10, and 4 h of HRTs. At the same time, another MABR (MABR 2) was operated individually at 12, 10, 8, 6, 4, and 2 h of HRTs to assess the influence of HRT on nitrogen removal performance. An enhancement in removal performance was reported in the hybrid MABR-GNOF, achieving the highest removal efficiencies of 74.3 ± 3.1% for ammonium nitrogen (NH₄⁺-N), 69.8 ± 2.1% for total nitrogen (TN), and 90.9 ± 1.7% for chemical oxygen demand (COD), at 12 h HRT. The hybrid MABR-GNOF system attained 18% higher nitrogen removal than the MABR-only system at 12 h of HRT. A simultaneous anoxic nitrification-denitrification and COD oxidation might be developed for the removal of COD, NH₄⁺-N, and TN from domestic wastewater by using GNOF as an electron acceptor in the hybrid MABR-GNOF unit. The findings in this study confirmed the possibility of integration of GNOF and MABR on a pilot scale and are promising for the application of this hybrid system on a full scale.

Characteristics of soil carbon emissions and bacterial community composition in peatlands at different stages of vegetation succession

Microorganisms are important components of soil ecosystems and play an important role in material cycles. Northern peatlands are important ecosystems in middle-high latitude regions. In peatlands, different vegetation successions occur with changes in groundwater levels. The overall carbon emission of peat bogs is related to the carbon stability of the surrounding environment. Unraveling the assembly and distribution of bacterial communities at different succession stages in peatland is essential to understanding the soil nutrient cycle. In this study, we investigated the characteristics of soil carbon emissions and the composition of subsurface microorganisms under six different succession stages. The highest carbon emission was observed in mossy peatlands, and their soil enzyme activity was closely related to the aboveground vegetation cover type. The succession pattern of ground vegetation was the main driver of soil microorganisms. The abundance of the dominant Proteobacteria decreased with increasing soil depth, while the opposite trend was observed for Chloroflexi. Furthermore, the community structure of microorganisms became progressively simpler and looser as soil water content decreased. The bacterial alpha diversity was driven by soil dissolved organic carbon and Fe, and the beta diversity was driven mainly by soil water content. The bacteria presented a random distribution in a nutrient-rich soil environment and shifted to deterministic distribution with decreasing water and nutrient contents. The balance between taxonomic diversity and dispersal limitation mediates species coexistence in the soil microbiome. This study provides new insights into the soil environment at different stages of succession in peatlands.

Ecohydrology 2.0

This paper aims at a definition of the domain of ecohydrology, a relatively new discipline borne out of an intrusion-as advertised by this Topical Collection of the Rendiconti Lincei-of hydrology and geomorphology into ecology (or vice-versa, depending on the reader's background). The study of hydrologic controls on the biota proves, in our view, significantly broader than envisioned by its original focus that was centered on the critical zone where much of the action of soil, climate and vegetation interactions takes place. In this review of related topics and contributions, we propose a reasoned broadening of perspective, in particular by firmly centering ecohydrology on the fluvial catchment as its fundamental control volume. A substantial unity of materials and methods suggests that our advocacy may be considered legitimate.

Hydroxyl radicals induced mineralization of organic carbon during oxygenation of ferrous mineral-organic matter associations: Adsorption versus coprecipitation

The iron (Fe) phases have been widely proposed to preserve organic carbon (OC) via adsorption or coprecipitation pathways, however, such role of Fe phases might be largely reversed under redox-fluctuation conditions, especially for Fe(II) minerals-protected OC. In this study, we synthesized the Fe(II)-OC associations via adsorption and coprecipitation using FeCO₃ and three types of low-molecular-weight organic compounds (LMWOCs) at different C/Fe molar ratios, and investigated the OC mineralization induced by hydroxyl radicals (OH) during oxygenation processes. Abundant OH can be produced upon oxygenation of FeCO₃-LMWOCs associations within 96 h, giving values of 28.49-151.36 μM in adsorption and 12.63-76.41 μM in coprecipitation treatments depended on types of LMWOCs and C/Fe molar ratios. Fe(II) species in coprecipitates with hydroquinone (HQ) mainly transformed into Goethite-like phases after oxygenation, while adsorption samples induced more formation of lower-crystalline Fe phase (e.g., ferrihydrite). The surface-Fe(II) was the primary electron donors to O₂, which further induced hydrogen peroxide (H₂O₂) formation via one- and two-electron transfer pathways. Finally, the produced OH removed 0.55-9.65 and 0.16-85.54 mg L^-1 total OC in adsorption and coprecipitation treatments after oxygenation. Collectively, this study highlights that OC associated with Fe(II) minerals might be labile due to the oxidation of formed OH, and the role of Fe phases in OC sequestration may be further re-evaluated under redox fluctuation conditions.

Methanogen Productivity and Microbial Community Composition Varies With Iron Oxide Mineralogy

Quantifying the flux of methane from terrestrial environments remains challenging, owing to considerable spatial and temporal variability in emissions. Amongst a myriad of factors, variation in the composition of electron acceptors, including metal (oxyhydr)oxides, may impart controls on methane emission. The purpose of this research is to understand how iron (oxyhydr)oxide minerals with varied physicochemical properties influence microbial methane production and subsequent microbial community development. Incubation experiments, using lake sediment as an inoculum and acetate as a carbon source, were used to understand the influence of one poorly crystalline iron oxide mineral, ferrihydrite, and two well-crystalline minerals, hematite and goethite, on methane production. Iron speciation, headspace methane, and 16S-rRNA sequencing microbial community data were measured over time. Substantial iron reduction only occurred in the presence of ferrihydrite while hematite and goethite had little effect on methane production throughout the incubations. In ferrihydrite experiments the time taken to reach the maximum methane production rate was slower than under other conditions, but methane production, eventually occurred in the presence of ferrihydrite. We suggest that this is due to ferrihydrite transformation into more stable minerals like magnetite and goethite or surface passivation by Fe(II). While all experimental conditions enriched for Methanosarcina, only the presence of ferrihydrite enriched for iron reducing bacteria Geobacter. Additionally, the presence of ferrihydrite continued to influence microbial community development after the onset of methanogenesis, with the dissimilarity between communities growing in ferrihydrite compared to no-Fe-added controls increasing over time. This work improves our understanding of how the presence of different iron oxides influences microbial community composition and methane production in soils and sediments.

Micronutrients in Food Production: What Can We Learn from Natural Ecosystems?

Soil micronutrients limit crop productivity in many regions worldwide, and micronutrient deficiencies affect over two billion people globally. Microbial biofertilizers could combat these issues by inoculating arable soils with microorganisms that mobilize micronutrients, increasing their availability to crop plants in an environmentally sustainable and cost-effective manner. However, the widespread application of biofertilizers is limited by complex micronutrient–microbe–plant interactions, which reduce their effectiveness under field conditions. Here, we review the current state of seven micronutrients in food production. We examine the mechanisms underpinning microbial micronutrient mobilization in natural ecosystems and synthesize the state-of-knowledge to improve our overall understanding of biofertilizers in food crop production. We demonstrate that, although soil micronutrient concentrations are strongly influenced by soil conditions, land management practices can also substantially affect micronutrient availability and uptake by plants. The effectiveness of biofertilizers varies, but several lines of evidence indicate substantial benefits in co-applying biofertilizers with conventional inorganic or organic fertilizers. Studies of micronutrient cycling in natural ecosystems provide examples of microbial taxa capable of mobilizing multiple micronutrients whilst withstanding harsh environmental conditions. Research into the mechanisms of microbial nutrient mobilization in natural ecosystems could, therefore, yield effective biofertilizers to improve crop nutrition under global changes.

Carbon Materials Advancing Microorganisms in Driving Soil Organic Carbon Regulation

Carbon emission from soil is not only one of the major sources of greenhouse gases but also threatens biological diversity, agricultural productivity, and food security. Regulation and control of the soil carbon pool are political practices in many countries around the globe. Carbon pool management in engineering sense is much bigger and beyond laws and monitoring, as it has to contain proactive elements to restore active carbon. Biogeochemistry teaches us that soil microorganisms are crucial to manage the carbon content effectively. Adding carbon materials to soil is thereby not directly sequestration, as interaction of appropriately designed materials with the soil microbiome can result in both: metabolization and thereby nonsustainable use of the added carbon, or-more favorably-a biological amplification of human efforts and sequestration of extra CO₂ by microbial growth. We review here potential approaches to govern soil carbon, with a special focus set on the emerging practice of adding manufactured carbon materials to control soil carbon and its biological dynamics. Notably, research on so-called "biochar" is already relatively mature, while the role of artificial humic substance (A-HS) in microbial carbon sequestration is still in the developing stage. However, it is shown that the preparation and application of A-HS are large biological levers, as they directly interact with the environment and community building of the biological soil system. We believe that A-HS can play a central role in stabilizing carbon pools in soil.

Redox Heterogeneity Entangles Soil and Climate Interactions

Interactions between soils and climate impact wider environmental sustainability. Soil heterogeneity intricately regulates these interactions over short spatiotemporal scales and therefore needs to be more finely examined. This paper examines how redox heterogeneity at the level of minerals, microbial cells, organic matter, and the rhizosphere entangles biogeochemical cycles in soil with climate change. Redox heterogeneity is used to develop a conceptual framework that encompasses soil microsites (anaerobic and aerobic) and cryptic biogeochemical cycling, helping to explain poorly understood processes such as methanogenesis in oxygenated soils. This framework is further shown to disentangle global carbon (C) and nitrogen (N) pathways that include CO2, CH4, and N2O. Climate-driven redox perturbations are discussed using wetlands and tropical forests as model systems. Powerful analytical methods are proposed to be combined and used more extensively to study coupled abiotic and biotic reactions that are affected by redox heterogeneity. A core view is that emerging and future research will benefit substantially from developing multifaceted analyses of redox heterogeneity over short spatiotemporal scales in soil. Taking a leap in our understanding of soil and climate interactions and their evolving influence on environmental sustainability then depends on greater collaborative efforts to comprehensively investigate redox heterogeneity spanning the domain of microscopic soil interfaces.

Iron and total organic carbon shape the spatial distribution pattern of sediment Fe(III) reducing bacteria in a volcanic lake, NE China

Fe(III) reducing bacteria (FeRB) play a vital role in the biogeochemical cycle of Fe, C and N in nature. The volcanic lake can be considered as an ideal habitat for FeRB. Here, we investigated the diversity and spatial distribution of FeRB in sediments of Wenbo lake in Wudalianchi volcano based on culture-dependent and independent methods. A total of 28 isolates affiliated with the genera of Enterobacter, Bacillus, Pseudomonas and Clostridium were obtained from 18 sediment samples. We detected 783 operational taxonomic units (OTUs) belonged to FeRB using high high-throughput sequencing, and the dominant phyla were Proteobacteria (3.65%), Acidobacteria (0.29%), Firmicutes (10.78%). The representative FeRB genera such as Geobacter, Pseudomonas, Thiobacillus and Acinetobacter distributed widely in Wenbo lake. Results showed that the diversity and abundance of FeRB declined along the water-flow direction from Libo to Jingbo. In contrast, the FeRB diversity decreased and the FeRB abundance increased along with depth transect of sediments. It was found that the dominant phylum changed from Firmicutes to Proteobacteria along the water-flow direction, while changed from Proteobacteria to Firmicutes along with the depth of sediments. RDA indicated that the FeRB distribution were driven by soluble total iron, total organic carbon, Fe(II) and Fe(III). These will provide information for understanding the role of FeRB in the elements geochemical cycles in the volcanic environment.

Geographical Distribution of Iron Redox Cycling Bacterial Community in Peatlands: Distinct Assemble Mechanism Across Environmental Gradient

Microbial-mediated iron (Fe) oxidation and reduction greatly contribute to the biogeochemistry and mineralogy of ecosystems. However, knowledge regarding the composition and distribution patterns of iron redox cycling bacteria in peatlands remains limited. Here, using high-throughput sequencing, we compared biogeographic patterns and assemblies of the iron redox cycling bacterial community between soil and water samples obtained from different types of peatland across four regions in Northeast China. A total of 48 phylotypes were identified as potential iron redox bacteria, which had greater than 97% similarity with Fe(II)-oxidizing bacteria (FeOB) and Fe(III)-reducing bacteria (FeRB). Among them, Rhodoferax, Clostridium, Geothrix, Sideroxydans, Geobacter, Desulfovibrio, and Leptothrix could be used as bioindicators in peatlands for characterizing different hydrological conditions and nutrient demands. Across all samples, bacterial communities associated with iron redox cycling were mainly affected by pH, dissolved organic carbon (DOC), and Fe²⁺. Distance-decay relationship (DDR) analysis indicated that iron redox cycling bacterial communities in soil, but not in water, were highly correlated with geographic distance. Additionally, null model analysis revealed that stochastic processes substituted deterministic processes from minerotrophic fens to ombrotrophic bogs in soils, whereas deterministic processes were dominant in water. Overall, these observations suggest that bacteria involved in iron redox cycling are widespread in diverse habitats and exhibit distinct patterns of distribution and community assembly mechanisms between soil and water in peatlands.

Contribution of the Fenton reaction and ligninolytic enzymes to soil organic matter mineralisation under anoxic conditions

Mechanisms of carbon dioxide (CO₂) release from soil in the absence of oxygen were studied considering the Fenton process, which encompasses the reaction of H₂O₂ with Fe(II) yielding a hydroxyl radical (OH), in combination with manganese peroxidase (MnP) and lignin peroxidase (LiP). This study aimed to explain the high rate of soil organic matter (SOM) mineralisation and CO₂ release from humid temperate rainforest soils under oxygen-limited conditions. The investigated mechanisms challenge the traditional view that SOM mineralisation in rainforest is slow due to anaerobic (micro)environments under high precipitation and explain intensive CO₂ release even under oxygen limitation. We hypothesised that the Fenton reaction (FR) greatly contributes to the CO₂ released from SOM mineralised under anaerobic conditions especially in the presence of ligninolytic enzymes. We used a novel technique that combines labelled H₂¹⁸O₂ and Fe(II) to induce the FR and measured CO¹⁸O, Fe(II) solubilisation, and peroxide consumption in a closed gas circulation system for 6 h. Maximal CO₂ amount was released when the FR was induced in combination with LiP addition. The CO₂ efflux with LiP was 10-fold that of abiotic FR reactions without enzymes, or in soils amended with MnP. This was consistent with i) the contribution of ¹⁸O from peroxide to CO₂ release, ii) peroxide consumption, and iii) Fe(II) solubilisation by FR. The amount of consumed peroxide was closely correlated with the CO¹⁸O derived from soil without enzyme addition or with LiP addition. Concluding, abiotic Fenton Reaction coupled with oxidative enzymes, such as LiP, are crucial for SOM oxidation under anaerobic conditions, e.g. in temperate rainforest soils.

Interaction between hexavalent chromium and biologically formed iron mineral-biochar composites: Kinetics, products and mechanisms

Biogenic Fe(II) is a dominant natural reductant to convert carcinogenic Cr(VI) to less toxic Cr(III). Field-applied biochar could promote microbial production of Fe(II) and form iron-biochar composites. Although there have been mounting research on the interactions of biochar or Fe(II) with Cr(VI), their coupling effects on Cr(VI) immobilization have been largely neglected. Here, iron mineral-biochar composite (IMBC) was prepared via biochar-mediated dissimilatory reduction of ferrihydrite or goethite by Shewanella oneidensis MR-1, and its reaction with Cr(VI) was investigated. IMBC was able to effectively remove aqueous Cr(VI) via reductive transformation by adsorbed Fe(II). The removal process nicely followed pseudo-second-order kinetics and Langmuir isotherm model. The removal ability of IMBC decreased with increasing pH (5.5-8.0) but was independent of ionic strength changes (0-100 mM). After reaction, the Fe-Cr coprecipitates formed on IMBC exhibited slightly higher Fe/Cr ratios (0.93-0.96) than those on corresponding iron mineral controls (0.88-0.94). For IMBC, while the presence of biochar decreased the reactivity of adsorbed Fe(II), their removal capacities were ~30% higher than those of iron minerals alone, due to the enhanced yields of adsorbed Fe(II). These findings improved our knowledge of interactions among biochar, iron mineral and iron-reducing bacteria and their contribution to chromium immobilization.

Complete Genome Sequence of Geobacter sp. Strain FeAm09, a Moderately Acidophilic Soil Bacterium

A moderately acidophilic Geobacter sp. strain, strain FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp, with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

A moderately acidophilic Geobacter sp. strain, FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

Large seasonal variation of soil respiration in a secondary tropical moist forest in Puerto Rico

Tropical forests are the largest contributors to global emissions of carbon dioxide (CO2) to the atmosphere via soil respiration (R s). As such, identifying the main controls on R s in tropical forests is essential for accurately projecting the consequences of ongoing and future global environmental changes to the global C cycle. We measured hourly R s in a secondary tropical moist forest in Puerto Rico over a 3-year period to (a) quantify the magnitude of R s and (b) identify the role of climatic, substrate, and nutrient controls on the seasonality of R s. Across 3 years of measurements, mean R s was 7.16 ± 0.02 μmol CO2 m-2 s-1 (or 2,710 g C m-2 year-1) and showed significant seasonal variation. Despite small month-to-month variation in temperature (~4°C), we found significant positive relationships between daily and monthly R s with both air and soil temperature, highlighting the importance of temperature as a driver of R s even in warm ecosystems, such as tropical forests. We also found a significant parabolic relationship between mean daily volumetric soil moisture and mean daily R s, with an optimal moisture value of 0.34 m3 m-3. Given the relatively consistent climate at this site, the large range in mean monthly R s (~7 μmol CO2 m-2 s-1) was surprising and suggests that even small changes in climate can have large implications for ecosystem respiration. The strong positive relationship of R s with temperature at monthly timescales particularly stands out, as moisture is usually considered a stronger control of R s in tropical forests that already experience warm temperatures year-round. Moreover, our results revealed the strong seasonality of R s in tropical moist forests, which given its high magnitude, can represent a significant contribution to the seasonal patterns of atmospheric (CO2) globally.

From pools to flow: The PROMISE framework for new insights on soil carbon cycling in a changing world

Soils represent the largest terrestrial reservoir of organic carbon, and the balance between soil organic carbon (SOC) formation and loss will drive powerful carbon-climate feedbacks over the coming century. To date, efforts to predict SOC dynamics have rested on pool-based models, which assume classes of SOC with internally homogenous physicochemical properties. However, emerging evidence suggests that soil carbon turnover is not dominantly controlled by the chemistry of carbon inputs, but rather by restrictions on microbial access to organic matter in the spatially heterogeneous soil environment. The dynamic processes that control the physicochemical protection of carbon translate poorly to pool-based SOC models; as a result, we are challenged to mechanistically predict how environmental change will impact movement of carbon between soils and the atmosphere. Here, we propose a novel conceptual framework to explore controls on belowground carbon cycling: Probabilistic Representation of Organic Matter Interactions within the Soil Environment (PROMISE). In contrast to traditional model frameworks, PROMISE does not attempt to define carbon pools united by common thermodynamic or functional attributes. Rather, the PROMISE concept considers how SOC cycling rates are governed by the stochastic processes that influence the proximity between microbial decomposers and organic matter, with emphasis on their physical location in the soil matrix. We illustrate the applications of this framework with a new biogeochemical simulation model that traces the fate of individual carbon atoms as they interact with their environment, undergoing biochemical transformations and moving through the soil pore space. We also discuss how the PROMISE framework reshapes dialogue around issues related to SOC management in a changing world. We intend the PROMISE framework to spur the development of new hypotheses, analytical tools, and model structures across disciplines that will illuminate mechanistic controls on the flow of carbon between plant, soil, and atmospheric pools.

Mutual Interactions between Reduced Fe-Bearing Clay Minerals and Humic Acids under Dark, Oxygenated Conditions: Hydroxyl Radical Generation and Humic Acid Transformation

Hydroxyl radicals (·OH) exert a strong impact on the carbon cycle due to their nonselective and highly oxidizing nature. Reduced iron-containing clay minerals (RIC) are one of the major contributors to the formation of ·OH in dark environments, but their interactions with humic acids (HA) are poorly known. Here, we investigate the mutual interactions between RIC and HA under dark and oxygenated conditions. HA decreased the oxidation rate of structural Fe(II) in RIC but significantly promoted the ·OH yield. HA dissolved a fraction of Fe(II) from RIC to form an aqueous Fe(II)-HA complex. ·OH were generated through both heterogeneous (through oxidation of structural Fe(II)) and homogeneous pathways (through oxidation of aqueous Fe(II)-HA species). RIC-mediated ·OH production by providing H₂O₂ to react with Fe(II)-HA and electrons to regenerate Fe(II)-HA. This highly efficient homogeneous pathway was responsible for increased ·OH yield. Abundant ·OH significantly decreased the molecular size, bleached chromophores, and increased the oxygen-containing functional groups of HA. These molecular changes of HA resembled photochemical transformation of HA. The mutual interaction between RIC and HA in dark and redox-fluctuating environments provides a new pathway for fast turnover of recalcitrant organic matters in clay- and HA-rich ecosystems such as tropical forest soils and tidal marsh sediments.

Mineralogical associations with soil carbon in managed wetland soils

Carbon (C)-rich wetland soils are often drained for agriculture due to their capacity to support high net primary productivity. Increased drainage is expected this century to meet the agricultural demands of a growing population. Wetland drainage can result in large soil C losses and the concentration of residual soil minerals such as iron (Fe) and aluminum (Al). In upland soils, reactive Fe and Al minerals can contribute to soil C accumulation through sorption to poorly crystalline minerals and coprecipitation of organo-metal complexes, as well as C loss via anaerobic respiration by Fe-reducing bacteria. The role of these minerals in soil C dynamics is often overlooked in managed wetland soils and may be particularly important in both drained and reflooded systems with elevated mineral concentrations. Reflooding drained soils have been proposed as a means to sequester C for climate change mitigation, yet little is known about how reactive Fe and Al minerals affect C cycling in restored wetlands. We explored the interactions among soil C and reactive Fe and Al minerals in drained and reflooded wetland soils. In reflooded soils, soil C was negatively associated with reactive Fe and reduced Fe(II), a proxy for anaerobic conditions (reactive Fe: R²  = .54-.79; Fe(II): R²  = .59-.89). In drained soils, organo-Al complexes were positively associated with soil C and Fe(II) (Al R²  = .91; Fe(II): R²  = .54-.60). Soil moisture, organo-Al, and reactive Fe explained most of the variation observed in soil C concentrations across all sites (p < .01). Reactive Fe was negatively correlated to soil C concentrations across sites, suggesting these Fe pools may drive additional C losses in drained soils and limit C sequestration with reflooding. In contrast, reactive organo-Al in drained soils facilitates C storage via aggregation and/or formation of anaerobic (micro)sites that protect residual soil C from oxidation and may at least partially offset C losses.

Resolving a paradox-high mercury deposition, but low bioaccumulation in northeastern Puerto Rico

At a "clean air" trade winds site in northeastern Puerto Rico, we found an apparent paradox: atmospheric total mercury (THg) deposition was highest of any site in the USA Mercury Deposition Network, but assimilation into the local food web was quite low. Avian blood THg concentrations (n = 31, from eight species in five foraging guilds) ranged widely from 0.2 to 32 ng g^-1 (median of 4.3 ng g^-1). Within this population, THg was significantly greater at a low-elevation site near a wetland compared to an upland montane site, even when the comparison was limited to a single species. Overall, however, THg concentrations were approximately an order of magnitude lower than comparable populations in the continental U.S. In surface soil and sediment, potential rates of demethylation were 3 to 9-fold greater than those for Hg(II)-methylation (based on six radiotracer amendment incubations), but rates of change of ambient MeHg pools showed a slight net positive Hg(II)-methylation. Thus, the resolution of the paradox is that MeHg degradation approximately keeps pace with MeHg production in this landscape. Further, any net production of MeHg is subject to frequent flushing by high rainfall on chronically wet soils. The interplay of these microbial processes and hydrology appears to shield the local food web from adverse effects of high atmospheric mercury loading. This scenario may play out in other humid tropical ecosystems as well, but it is difficult to evaluate because coordinated studies of Hg deposition, methylation, and trophic uptake have not been conducted at other tropical sites.

Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.

Iron-mediated organic matter decomposition in humid soils can counteract protection

Soil organic matter (SOM) is correlated with reactive iron (Fe) in humid soils, but Fe also promotes SOM decomposition when oxygen (O₂) becomes limited. Here we quantify Fe-mediated OM protection vs. decomposition by adding ¹³C dissolved organic matter (DOM) and ⁵⁷Fe^II to soil slurries incubated under static or fluctuating O₂. We find Fe uniformly protects OM only under static oxic conditions, and only when Fe and DOM are added together: de novo reactive Fe^III phases suppress DOM and SOM mineralization by 35 and 47%, respectively. Conversely, adding ⁵⁷Fe^II alone increases SOM mineralization by 8% following oxidation to ⁵⁷Fe^III. Under O₂ limitation, de novo reactive ⁵⁷Fe^III phases are preferentially reduced, increasing anaerobic mineralization of DOM and SOM by 74% and 32‒41%, respectively. Periodic O₂ limitation is common in humid soils, so Fe does not intrinsically protect OM; rather reactive Fe phases require their own physiochemical protection to contribute to OM persistence.

Reactive iron minerals protect vast amounts of terrestrial carbon from decomposition and release as CO₂. Here the authors show that reactive iron alone does not provide sufficient protection except under strict oxic conditions—instead, iron itself promotes carbon decomposition.

Phenazine-1-Carboxylic Acid-Producing Bacteria Enhance the Reactivity of Iron Minerals in Dryland and Irrigated Wheat Rhizospheres

Phenazine-1-carboxylic acid (PCA) is a broad-spectrum antibiotic produced by rhizobacteria in the dryland wheat fields of the Columbia Plateau. PCA and other phenazines reductively dissolve Fe and Mn oxyhydroxides in bacterial culture systems, but the impact of PCA upon Fe and Mn cycling in the rhizosphere is unknown. Here, concentrations of dithionite-extractable and poorly crystalline Fe were approximately 10% and 30-40% higher, respectively, in dryland and irrigated rhizospheres inoculated with the PCA-producing (PCA⁺) strain Pseudomonas synxantha 2-79 than in rhizospheres inoculated with a PCA-deficient mutant. However, rhizosphere concentrations of Fe(II) and Mn did not differ significantly, indicating that PCA-mediated redox transformations of Fe and Mn were transient or were masked by competing processes. Total Fe and Mn uptake into wheat biomass also did not differ significantly, but the PCA⁺ strain significantly altered Fe translocation into shoots. X-ray absorption near edge spectroscopy revealed an abundance of Fe-bearing oxyhydroxides and phyllosilicates in all rhizospheres. These results indicate that the PCA⁺ strain enhanced the reactivity and mobility of Fe derived from soil minerals without producing parallel changes in plant Fe uptake. This is the first report that directly links significant alterations of Fe-bearing minerals in the rhizosphere to a single bacterial trait.

Long-Term Mineral Fertilization Improved the Grain Yield and Phosphorus Use Efficiency by Changing Soil P Fractions in Ferralic Cambisol

Elevated mineral fertilization may change the composition and increase the availability of soil phosphorus (P) in subtropical paddy soils and thus affect long-term plant growth. However, an understanding of the response of soil P fractions to long-term nitrogen, phosphorus and potassium (NPK) additions remains elusive. This study aimed to explore the responses of soil P-fractions and their mobility to different long-term chemical fertilization rates under a double rice cropping system. The rates of nitrogen (N), phosphorus (P), and potassium (K) in the low NPK treatment (LNPK) were 90, 45, and 75 kg ha−1 year−1, respectively, and in the high NPK treatment (HNPK), they were 180, 90, and 150 kg ha−1 year−1, respectively. The results showed that the concentrations of soil organic matter (SOM), total P, Olsen P, total N, and mineral N were remarkably increased under HNPK by 17.46%, 162.66%, 721.16%, 104.42%, and 414.46%, respectively, compared with those under control (CT). Compared to the CT P fractions, HNPK increased the labile P fractions (i.e., NaHCO3-Pi and NaHCO3-Po) by 322.25% and 83.53% and the moderately labile P fractions (i.e., NaOH-Pi, NaOH-Po and HCl. dil. Pi) by 163.54%, 183.78%, and 3167.25% respectively, while the non-labile P was decreased by the HNPK addition. P uptake and grain yield were increased by LNPK and HNPK by 10.02% and 35.20%, respectively, compared with CT. P use efficiency indices were also higher under HNPK than under LNPK. There was a strong positive relationship between grain yield and P use efficiency (R2 = 0.97). A redundancy analysis (RDA) showed a strong correlation between soil chemical properties and the labile and moderately labile P pools. Structural equation modeling (SEM) revealed that SOM, mineral N, and available P strongly control the labile P pool. In conclusion, NPK additions under the paddy soils significantly influences the soil P fractions. The soil P dynamics and the mechanisms governing the interactions between plants and soil nutrients are clearly explained in this study.

Iron Redox Reactions Can Drive Microtopographic Variation in Upland Soil Carbon Dioxide and Nitrous Oxide Emissions

Topographic depressions in upland soils experience anaerobic conditions conducive for iron (Fe) reduction following heavy rainfall. These depressional areas can also accumulate reactive Fe compounds, carbon (C), and nitrate, creating potential hot spots of Fe-mediated carbon dioxide (CO2) and nitrous oxide (N2O) production. While there are multiple mechanisms by which Fe redox reactions can facilitate CO2 and N2O production, it is unclear what their cumulative effect is on CO2 and N2O emissions in depressional soils under dynamic redox. We hypothesized that Fe reduction and oxidation facilitate greater CO2 and N2O emissions in depressional compared to upslope soils in response to flooding. To test this, we amended upslope and depressional soils with Fe(II), Fe(III), or labile C and measured CO2 and N2O emissions in response to flooding. We found that depressional soils have greater Fe reduction potential, which can contribute to soil CO2 emissions during flooded conditions when C is not limiting. Additionally, Fe(II) addition stimulated N2O production, suggesting that chemodenitrification may be an important pathway of N2O production in depressions that accumulate Fe(II). As rainfall intensification results in more frequent flooding of depressional upland soils, Fe-mediated CO2 and N2O production may become increasingly important pathways of soil greenhouse gas emissions.

Enrichment of Lignin-Derived Carbon in Mineral-Associated Soil Organic Matter

A modern paradigm of soil organic matter proposes that persistent carbon (C) derives primarily from microbial residues interacting with minerals, challenging older ideas that lignin moieties contribute to soil C because of inherent recalcitrance. We proposed that aspects of these old and new paradigms can be partially reconciled by considering interactions between lignin decomposition products and redox-sensitive iron (Fe) minerals. An Fe-rich tropical soil (with C₄ litter and either ¹³C-labeled or unlabeled lignin) was pretreated with different durations of anaerobiosis (0-12 days) and incubated aerobically for 317 days. Only 5.7 ± 0.2% of lignin ¹³C was mineralized to CO₂ versus 51.2 ± 0.4% of litter C. More added lignin-derived C (48.2 ± 0.9%) than bulk litter-derived C (30.6 ± 0.7%) was retained in mineral-associated organic matter (MAOM; density >1.8 g cm^-3), and 12.2 ± 0.3% of lignin-derived C vs 6.4 ± 0.1% of litter C accrued in clay-sized (<2 μm) MAOM. Longer anaerobic pretreatments increased added lignin-derived C associated with Fe, according to extractions and nanoscale secondary ion mass spectrometry (NanoSIMS). Microbial residues are important, but lignin-derived C may also contribute disproportionately to MAOM relative to bulk litter-derived C, especially following redox-sensitive biogeochemical interactions.

Underlying lithology controls trace metal mobilization during redox fluctuations

Redox state fluctuations are a primary mechanism controlling the mobilization of trace metals in soils. However, underlying lithology may modulate the effect that redox fluctuations have on trace metal mobility by influencing soil particle size and mineral composition. To investigate the relationships among trace metal behavior, lithology, and redox state, we subjected surface soils from two intensely weathered soil profiles formed on contrasting lithologies to consecutive, 8-day redox cycles. A suite of metals (Al, Mn, Fe, Ti, Rb, Zr, Nb, Mo, REEs, Pb, Th, U) were quantified in the aqueous phase (<10 nm) and solution (<415 nm, including colloids) from soil slurries. In soil formed on volcaniclastic bedrock with high clay content and a high abundance of short-range-ordered Fe-(oxyhydr)oxides phases (e.g. nano-goethite; quantified by Mössbauer spectroscopy), reducing events and colloidal dynamics drove trace metal mobilization. In contrast, in soil formed on granite bedrock with lower clay content and a low abundance of short-range-ordered Fe-(oxyhydr)oxides phases (nano-goethite and lepidocrocite), overall trace metal mobilization was lower, and mobilization was not predictable from redox state. Molybdenum isotopes were also measured through redox cycles but did not exhibit redox-dependent behavior. This study provides direct evidence that lithology remains an overarching factor governing the characteristics of metal mobility in soils, even after extended and intense chemical weathering and soil development processes.

Redox Fluctuations Control the Coupled Cycling of Iron and Carbon in Tropical Forest Soils

Oscillating redox conditions are a common feature of humid tropical forest soils, driven by an ample supply and dynamics of reductants, high moisture, microbial oxygen consumption, and finely textured clays that limit diffusion. However, the net result of variable soil redox regimes on iron (Fe) mineral dynamics and associated carbon (C) forms and fluxes is poorly understood in tropical soils. Using a 44-day redox incubation experiment with humid tropical forest soils from Puerto Rico, we examined patterns in Fe and C transformations under four redox regimes: static anoxic, "flux 4-day" (4d oxic, 4d anoxic), "flux 8-day" (8d oxic, 4d anoxic) and static oxic. Prolonged anoxia promoted reductive dissolution of Fe-oxides, and led to an increase in soluble Fe(II) and amorphous Fe oxide pools. Preferential dissolution of the less-crystalline Fe pool was evident immediately following a shift in bulk redox status (oxic to anoxic), and coincided with increased dissolved organic C, presumably due to acidification or direct release of organic matter (OM) from dissolving Fe(III) mineral phases. The average nominal oxidation state of water-soluble C was lowest under persistent anoxic conditions, suggesting that more reduced organic compounds were metabolically unavailable for microbial consumption under reducing conditions. Anoxic soil compounds had high H/C values (and were similar to lignin-like compounds) whereas oxic soil compounds had higher O/C values, akin to tannin- and cellulose-like components. Cumulative respiration derived from native soil organic C was highest in static oxic soils. These results show how Fe minerals and Fe-OM interactions in tropical soils are highly sensitive to variable redox effects. Shifting soil oxygen availability rapidly impacted exchanges between mineral-sorbed and aqueous C pools, increased the dissolved organic C pool under anoxic conditions implying that the periodicity of low-redox events may control the fate of C in wet tropical soils.

Transient O2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome

BACKGROUND

Many environments contain redox transition zones, where transient oxygenation events can modulate anaerobic reactions that influence the cycling of iron (Fe) and carbon (C) on a global scale. In predominantly anoxic soils, this biogeochemical cycling depends on Fe mineral composition and the activity of mixed Fe(III)-reducer populations that may be altered by periodic pulses of molecular oxygen (O₂).

METHODS

We repeatedly exposed anoxic (4% H₂:96% N₂) suspensions of soil from the Luquillo Critical Zone Observatory to 1.05 × 10², 1.05 × 10³, and 1.05 × 10⁴ mmol O₂ kg^-1 soil h^-1 during pulsed oxygenation treatments. Metatranscriptomic analysis and ⁵⁷Fe Mössbauer spectroscopy were used to investigate changes in Fe(III)-reducer gene expression and Fe(III) crystallinity, respectively.

RESULTS

Slow oxygenation resulted in soil Fe-(oxyhydr)oxides of higher crystallinity (38.1 ± 1.1% of total Fe) compared to fast oxygenation (30.6 ± 1.5%, P < 0.001). Transcripts binning to the genomes of Fe(III)-reducers Anaeromyxobacter, Geobacter, and Pelosinus indicated significant differences in extracellular electron transport (e.g., multiheme cytochrome c, multicopper oxidase, and type-IV pilin gene expression), adhesion/contact (e.g., S-layer, adhesin, and flagellin gene expression), and selective microbial competition (e.g., bacteriocin gene expression) between the slow and fast oxygenation treatments during microbial Fe(III) reduction. These data also suggest that diverse Fe(III)-reducer functions, including cytochrome-dependent extracellular electron transport, are associated with type-III fibronectin domains. Additionally, the metatranscriptomic data indicate that Methanobacterium was significantly more active in the reduction of CO₂ to CH₄ and in the expression of class(III) signal peptide/type-IV pilin genes following repeated fast oxygenation compared to slow oxygenation.

CONCLUSIONS

This study demonstrates that specific Fe(III)-reduction mechanisms in mixed Fe(III)-reducer populations are uniquely sensitive to the rate of O₂ influx, likely mediated by shifts in soil Fe(III)-(oxyhydr)oxide crystallinity. Overall, we provide evidence that transient oxygenation events play an important role in directing anaerobic pathways within soil microbiomes, which is expected to alter Fe and C cycling in redox-dynamic environments.

Abundance and diversity of iron reducing bacteria communities in the sediments of a heavily polluted freshwater lake

Iron reduction mediated by Fe(III)-reducing bacteria (FeRB) occurs in aqueous environments and plays an essential role in removing contaminates in polluted freshwater lakes. Two model FeRB species, Shewanella and Geobacter, have been intensively studied because of their functions in bioremediation, iron reduction, and bioelectricity production. However, the abundance and community diversity of Shewanella and Geobacter in eutrophic freshwater lakes remain largely unknown. In this work, the distribution, abundance and biodiversity of Shewanella, Geobacter and other FeRB in the sediments of a heavily polluted lake, Chaohu Lake, China, across four successive seasons were investigated. Shewanella, Geobacter, and other FeRB were found to be widely distributed in the sediment of this heavily eutrophic lake. Geobacter was abundant with at least one order of magnitude more than Shewanella in cold seasons. Three Shewanella-related operational taxonomic units were detected and sixty one Geobacter-related operational taxonomic units were grouped into three phylogenetic clades. Thiobacillus, Desulfuromonas and Geobacter were identified as the main members of FeRB in the lake sediments. Interestingly, nutrients like carbon, nitrogen, and phosphorus were found to be the key factors governing the abundance and diversity of FeRB. Total FeRB, as well as Geobacter and Shewanella, were more abundant in the heavily eutrophic zone than those in the lightly eutrophic zone. The abundance and diversity of FeRB in the sediments of freshwater lakes were highly related with the degree of eutrophication, which imply that FeRB might have a great potential in alleviating the eutrophication and contamination in aqueous environments.

Soil properties and sediment accretion modulate methane fluxes from restored wetlands

Wetlands are the largest source of methane (CH₄ ) globally, yet our understanding of how process-level controls scale to ecosystem fluxes remains limited. It is particularly uncertain how variable soil properties influence ecosystem CH₄ emissions on annual time scales. We measured ecosystem carbon dioxide (CO₂ ) and CH₄ fluxes by eddy covariance from two wetlands recently restored on peat and alluvium soils within the Sacramento-San Joaquin Delta of California. Annual CH₄ fluxes from the alluvium wetland were significantly lower than the peat site for multiple years following restoration, but these differences were not explained by variation in dominant climate drivers or productivity across wetlands. Soil iron (Fe) concentrations were significantly higher in alluvium soils, and alluvium CH₄ fluxes were decoupled from plant processes compared with the peat site, as expected when Fe reduction inhibits CH₄ production in the rhizosphere. Soil carbon content and CO₂ uptake rates did not vary across wetlands and, thus, could also be ruled out as drivers of initial CH₄ flux differences. Differences in wetland CH₄ fluxes across soil types were transient; alluvium wetland fluxes were similar to peat wetland fluxes 3 years after restoration. Changing alluvium CH₄ emissions with time could not be explained by an empirical model based on dominant CH₄ flux biophysical drivers, suggesting that other factors, not measured by our eddy covariance towers, were responsible for these changes. Recently accreted alluvium soils were less acidic and contained more reduced Fe compared with the pre-restoration parent soils, suggesting that CH₄ emissions increased as conditions became more favorable to methanogenesis within wetland sediments. This study suggests that alluvium soil properties, likely Fe content, are capable of inhibiting ecosystem-scale wetland CH₄ flux, but these effects appear to be transient without continued input of alluvium to wetland sediments.

Influence of pO2 on Iron Redox Cycling and Anaerobic Organic Carbon Mineralization in a Humid Tropical Forest Soil

Ferrous iron (Fe^II) oxidation is an important pathway for generating reactive Fe^III phases in soils, which can affect organic carbon (OC) persistence/decomposition. We explored how pO₂ concentration influences Fe^II oxidation rates and Fe^III mineral composition, and how this impacts the subsequent Fe^III reduction and anaerobic OC mineralization following a transition from oxic to anoxic conditions. We conducted batch soil slurry experiments within a humid tropical forest soil amended with isotopically labeled ⁵⁷Fe^II. The slurries were oxidized with either 21% or 1% pO₂ for 9 days and then incubated for 20 days under anoxic conditions. Exposure to 21% pO₂ led to faster Fe^II oxidation rates and greater partitioning of the amended ⁵⁷Fe into low-crystallinity Fe^III-(oxyhydr)oxides (based on Mössbauer analysis) than exposure to 1% pO₂. During the subsequent anoxic period, low-crystallinity Fe^III-(oxyhydr)oxides were preferentially reduced relative to more crystalline forms with higher net rates of anoxic Fe^II and CO₂ production-which were well correlated-following exposure to 21% pO₂ than to 1% pO₂. This study illustrates that in redox-dynamic systems, the magnitude of O₂ fluctuations can influence the coupled iron and organic carbon cycling in soils and more broadly, that reaction rates during periods of anoxia depend on the characteristics of prior oxidation events.

Composition and Diversity of Soil Fungi in Dipterocarpaceae-Dominated Seasonal Tropical Forests in Thailand

Although fungi play essential roles in nutrient cycles and plant growth in forest ecosystems, limited information is currently available on the community compositions of soil fungi in tropical forests. Few studies have examined fungal community structures in seasonal tropical forests, in which forest fires potentially have a large impact on above- and belowground community processes. Based on high-throughput sequencing technologies, we herein examined the diversity and community structures of soil fungi in dry seasonal tropical forests in Sakaerat, northeast Thailand. We found that fungal community compositions diverged among dry evergreen, dry deciduous, and fire-protected dry deciduous forests within the region. Although tree species diversity did not positively correlate with soil fungal diversity, the coverage of an understory bamboo species (Vietnamosasa pusilla) showed a strong relationship with fungal community structures. Our community ecological analysis also yielded a list of fungi showing habitat preferences for either of the neighboring evergreen and deciduous forests in Sakaerat. The present results provide a basis for managing soil fungal communities and aboveground plant communities in seasonal tropical forests in Southeast Asia.

Yeasts dominate soil fungal communities in three lowland Neotropical rainforests

Forest soils typically harbour a vast diversity of fungi, but are usually dominated by filamentous (hyphae-forming) taxa. Compared to temperate and boreal forests, though, we have limited knowledge about the fungal diversity in tropical rainforest soils. Here we show, by environmental metabarcoding of soil samples collected in three Neotropical rainforests, that Yeasts dominate the fungal communities in terms of the number of sequencing reads and OTUs. These unicellular forms are commonly found in aquatic environments, and their hyperdiversity may be the result of frequent inundation combined with numerous aquatic microenvironments in these rainforests. Other fungi that are frequent in aquatic environments, such as the abundant Chytridiomycotina, were also detected. While there was low similarity in OTU composition within and between the three rainforests, the fungal communities in Central America were more similar to each other than the communities in South America, reflecting a general biogeographic pattern also seen in animals, plants and protists.

Rapid Iron Reduction Rates Are Stimulated by High-Amplitude Redox Fluctuations in a Tropical Forest Soil

Iron oxides are important structural and biogeochemical components of soils that can be strongly altered by redox-driven processes. This study examined the influence of temporal oxygen variations on Fe speciation in soils from the Luquillo Critical Zone Observatory (Puerto Rico). We incubated soils under cycles of oxic-anoxic conditions (τ_oxic:τ_anoxic = 1:6) at three frequencies with and without phosphate addition. Fe(II) production, P availability, and Fe mineral composition were monitored using batch analytical and spectroscopic techniques. The rate of soil Fe(II) production increased from ∼3 to >45 mmol Fe(II) kg^-1 d^-1 over the experiment with a concomitant increase of an Fe(II) concentration plateau within each anoxic period. The apparent maximum in Fe(II) produced is similar in all treatments, but was hastened by P-amendment. Numerical modeling suggests the Fe(II) dynamics can be explained by the formation of a rapidly reducible Fe(III) phases derived from the progressive dissolution and re-oxidation of native Fe(III) oxides accompanied by minor increases in Fe reducer populations. The shift in Fe(III) reactivity is evident from Fe-reducibility assays using Shewanella sp., however was undetectable by chemical extractions, Mössbauer or X-ray Absorption spectroscopies. More broadly, our findings suggest Fe reduction rates are strongly coupled to redox dynamics of the recent past, and that frequent shifts in redox conditions can prime a soil for rapid Fe-reduction.

Shifts in indigenous microbial communities during the anaerobic degradation of pentachlorophenol in upland and paddy soils from southern China

Pentachlorophenol (PCP) is a common persistent pesticide in soil that has generated a significant environmental problem worldwide. Therefore, anaerobic degradation of PCP by the soil indigenous microbial community has gained increasing attention. However, little information is available concerning the functional microorganisms and the potential shifts in the microbial community associated with PCP degradation. In this study, we conducted a set of experiments to determine which components of the indigenous microbial community were capable of degrading PCP in soils of two land use types (upland and paddy soils) in southern China. Our results showed that the PCP degradation rate was significantly higher in paddy soils than that in upland soils. 16S ribosomal RNA (rRNA) high-throughput sequencing revealed significant differences in microbial taxonomic composition between the soil with PCP and blank (soil without PCP) with Acinetobacter, Clostridium, Coprococcus, Oxobacter, and Sedimentibacter dominating the PCP-affected communities. Acinetobacter was also apparently enriched in the paddy soils with PCP (up to 52.2 %) indicated this genus is likely to play an important role in PCP degradation. Additionally, the Fe(III)-reducing bacteria Clostridium may also be involved in PCP degradation. Our data further revealed hitherto unknown metabolisms of potential PCP degradation by microorganisms including Coprococcus, Oxobacter, and Ruminiclostridium. Overall, these findings indicated that land use types may affect the PCP anaerobic degradation rate via the activities of indigenous bacterial populations and extend our knowledge of the bacterial populations responsible for PCP degradation.

Enhancement of sediment phosphorus release during a tunnel construction across an urban lake (Lake Donghu, China)

Tunnel construction in watershed area of urban lakes would accelerate eutrophication by inputting nutrients into them, while mechanisms underlying the internal phosphorus cycling as affected by construction events are scarcely studied. Focusing on two main pathways of phosphorus releasing from sediment (enzymatic mineralization and anaerobic desorption), spatial and temporal variations in phosphorus fractionation, and activities of extracellular enzymes (alkaline phosphatase, β-1,4-glucosidase, leucine aminopeptidase, dehydrogenase, lipase) in sediment were examined, together with relevant parameters in interstitial and surface waters in a Chinese urban lake (Lake Donghu) where a subaqueous tunnel was constructed across it from October 2013 to July 2014. Higher alkaline phosphatase activity (APA) indicated phosphorus deficiency for phytoplankton, as illustrated by a significantly negative relationship between APA and concentration of dissolved total phosphorus (DTP). Noticeably, in the construction area, APAs in both sediment and surface water were significantly lower than those in other relevant basins, suggesting a phosphorus supply from some sources in this area. In parallel, its sediment gave the significantly lower iron-bound phosphorus (Fe(OOH)∼P) content, coupled with significantly higher ratio of iron (II) to total iron content (Fe(2+)/TFe) and dehydrogenase activities (DHA). Contrastingly, difference in the activities of sediment hydrolases was not significant between the construction area and other basins studied. Thus, in the construction area, subsidy of bioavailable phosphorus from sediment to surface water was attributable to the anaerobic desorption of Fe(OOH)∼P rather than enzymatic mineralization. Finally, there existed a significantly positive relationship between chlorophyll a concentration in surface water and Fe(OOH)∼P content in sediment. In short, construction activities within lakes may interrupt cycling patterns of phosphorus across sediment-water interface by enhancing release of redox-sensitive phosphate, and thereby facilitating phytoplankton growth in water column.

Relative contribution of iron reduction to sediments organic matter mineralization in contrasting habitats of a shallow eutrophic freshwater lake

Iron reduction is one of the important organic matter (OM) mineralization pathway in sediments. Here we investigated the rates and the relative contribution of iron reduction to OM mineralization in Zhushan bay (ZSB, cyanobacterial bloom biomass (CBB)-dominated habitats) and East Taihu Lake (ETL, submerged macrophypes (SM)-dominated habitats) of Lake Taihu, China. Anaerobic microcosm incubation revealed that the rate of iron reduction at ZSB (4.42 μmol cm(-3) d(-1)) in summer was almost 1.5 times higher than at ETL (3.13 μmol cm(-3) d(-1)). Iron reduction accounted for 66.5% (ZSB) and 31.8% (ETL) of total anaerobic carbon mineralization, respectively. No detectable methanogenesis was found at ZSB, while methanogenesis was responsible for 16.7% of total anaerobic respiration in sediments of ETL. Geochemical analysis of solid phase constituents indicated that ZSB surface sediments experienced highly oxidizing conditions with much higher amorphous Fe(III) (71 mmol m(-2)) than ETL (11 mmol m(-2)). Conversely, AVS inventories at ETL (38 mmol m(-2)) were up to 30 times higher than at ZSB (1.27 mmol m(-2)), indicating significant sulfate reduction in sediments of ETL. Overall results suggested that varying carbon sources and distinct geochemical characterizations of the sediments in contrasting habitats significantly influenced the rate of iron reduction and the pathway of C mineralization in a large freshwater lake.

Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism

Global climate models predict a future of increased severity of drought in many tropical forests. Soil microbes are central to the balance of these systems as sources or sinks of atmospheric carbon (C), yet how they respond metabolically to drought is not well-understood. We simulated drought in the typically aseasonal Luquillo Experimental Forest, Puerto Rico, by intercepting precipitation falling through the forest canopy. This approach reduced soil moisture by 13% and water potential by 0.14 MPa (from -0.2 to -0.34). Previous results from this experiment have demonstrated that the diversity and composition of these soil microbial communities are sensitive to even small changes in soil water. Here, we show prolonged drought significantly alters the functional potential of the community and provokes a clear osmotic stress response, including the production of compatible solutes that increase intracellular C demand. Subsequently, a microbial population emerges with a greater capacity for extracellular enzyme production targeting macromolecular carbon. Significantly, some of these drought-induced functional shifts in the soil microbiota are attenuated by prior exposure to a short-term drought suggesting that acclimation may occur despite a lack of longer-term drought history.