Effects of tomato straw fermentation on nutrients and bacterial community structure.

Unsustainable straw treatment methods detrimentally affect the environment and ecology. Aerobic fermentation (AE) and anaerobic fermentation (AN) are environmentally friendly treatments that better utilise straw resources. In this study, high-throughput sequencing was used to investigate the effects of AE and AN on nutrient content and microbial community structure during tomato straw fermentation. Nitrate nitrogen, available phosphorus, available potassium, and fulvic acid contents following AE were 1250.04 mg/kg, 80.34 %, 161.39 %, and 49.31 %, respectively, which were higher than those following AN. Ammonium nitrogen, humic acid, and humic substance levels following AN were 309.07 %, 31.18 %, and 17.38 %, respectively, which were higher than those following AE. Firmicutes (24.76 %) and Actinobacteria (12.93 %) were more abundant following AE, whereas Proteobacteria (33.82 %) and Bacteroidetes (33.82 %) exhibited higher abundance following AN. AE more effectively eliminated pathogenic bacteria (22.01%-0.26 %) and encouraged stronger interactions between dominant bacterial genera. Redundancy and Mantel test analyses revealed that electrical conductivity and temperature were the most important environmental factors affecting bacterial communities in AE and AN, respectively. AE had a stronger effect on effective nutrient release from tomato straw, implying its greater application potential as a fertiliser. Overall, our study provides a theoretical basis for the optimisation of fermentation methods and processes.

Long-term contamination of decabromodiphenyl ether reduces sediment multifunctionality: Insights from nutrient cycling, microbial ecological clusters, and microbial co-occurrence patterns.

Despite the widespread detection of polybrominated diphenyl ethers in aquatic ecosystems, their long-term effects on sediment multifunctionality remain unclear. Herein, a 360-day microcosm experiment was conducted to investigate how decabromodiphenyl ether (BDE-209) contamination at different levels (0.2, 2, and 20 mg/kg dry weight) affects sediment multifunctionality, focusing on carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling. Results showed that BDE-209 significantly increased sediment total organic carbon, nitrate, ammonium, available phosphorus, and sulfide concentrations, but decreased sulfate. Additionally, BDE-209 significantly altered key enzyme activities related to nutrient cycling. Bacterial community dissimilarity was positively correlated with nutrient variability. Long-term BDE-209 exposure inhibited C degradation, P transport and regulation, and most N metabolic pathways, but enhanced C fixation, methanogenesis, organic P mineralization, inorganic P solubilization, and dissimilatory sulfate reduction pathways. These changes were mainly regulated by microbial ecological clusters and keystone taxa. Overall, sediment multifunctionality declined under BDE-209 stress, primarily related to microbial co-occurrence network complexity and ecological cluster diversity. Interestingly, sediment C and N cycling had greater impacts on multifunctionality than P and S cycling. This study provides crucial insights into the key factors altering multifunctionality in contaminated sediments, which will aid pollution control and mitigation in aquatic ecosystems.

Cryptogam biomass estimation using taxonomic and life form models for accurate assessment.

Accurate estimation of cryptogam biomass, encompassing bryophytes and lichens, is crucial for understanding their ecological significance. This estimation is conducted based on the strong correlations between mass and volume of cryptogams. However, mass-volume correlations vary among cryptogams because of their morphological differences. This problem can be solved using models that consider life forms that classify cryptogams based on morphological similarities. In this study, we investigated whether life form models improve cryptogam biomass estimation accuracy. The cryptogam mass-volume correlation of each life form was estimated using Bayesian linear models. The coefficients and intercepts of linear models differed between life forms, which was attributed to the morphological characteristics of each life form. Therefore, life form models can improve the accuracy of estimation models by incorporating morphological differences. However, taxonomic models that consider only the taxonomic difference (bryophytes vs lichens) demonstrated better overall estimation than the life form models, probably because of the ability of taxonomic models to capture systematic differences between bryophytes and lichens. Furthermore, these models may mitigate estimation errors related to morphological variations that cannot be adequately represented by life form types. Based on these results, we propose the appropriate use of estimation models.

Impact of seasonality and forest stand age on ion deposition in rehabilitated forests.

This study examines the critical interaction between seasonal precipitation variability and forest maturity in determining ion deposition patterns in rehabilitated forest ecosystems. This research was conducted in rehabilitated forest sites in Bintulu, Sarawak, Malaysia that had ecologically similar plant distribution, species, and age in each planting area. This facilitated the standardization of rainfall deposition in the different study plots which streamlined the study of these specific facets of ecosystem dynamics. The goal is to understand how seasonal changes and the age of the forest influence the chemical composition of the flux that relates to the movement and deposition of nutrients through the forest ecosystem. This flux is a key factor in the health of the forest ecosystem and nutrient cycling. Using ion exchange resin (IER) samplers, we accurately measured and compared the deposition of different ions (Ca2+, Na+, Fe2+, Cu2+, NO3 -, NH4 + and SO4 2-) across different seasons and forest ages. The deposition of Ca2+ and NH4+ was significantly lower in the low-precipitation season than in the high-precipitation season in all forest stands, regardless of the year they were established (1996, 1999, 2002, 2005, and 2009). In contrast, ions such as Na+, Fe2+, Cu2+, NO3 - and SO4 2- showed no clear seasonal fluctuations. In addition, the study shows that through-fall in forest stands from 2002, 2005 and 2009 had higher concentrations of Ca2+ in both seasons than in 1996 and 1999. Interestingly, forest stands from 2009 and 2002 had elevated levels of Na+ and SO42- in seasons with low precipitation, while stands from 1996 had higher levels in seasons with high precipitation. Our results emphasize the crucial role of precipitation amount and canopy age in determining ion deposition in forest ecosystems. By demonstrating the significant influence of precipitation seasonality and forest maturity on the chemical composition of throughfall, this study contributes to a deeper understanding of nutrient dynamics in developing forest landscapes and provides valuable insights for ecological restoration measures.

Safe Circular Food Systems: A Transdisciplinary Approach to Identify Emergent Risks in Food Waste Nutrient Cycling.

With growing awareness of the environmental, economic, and social costs associated with food waste, there is a concerted effort on multiple scales to recover the nutrient value of discarded food. These developments are positive, but the rapid movement toward alternatives and the complexity of solving problems located at the intersection of economic, social, and environmental systems also have the potential to produce unanticipated risks. This paper draws upon long-term stakeholder-engaged research throughout New England, with a focus on Maine, to develop a transdisciplinary, systems-based model of the potential social, economic, and environmental risks of food waste nutrient cycling. Our effort is intended to help inform the creation of safe, functional, and environmentally benign circular food systems.

Core Bacterial Taxa Determine Formation of Forage Yield in Fertilized Soil.

Understanding the roles of core bacterial taxa in forage production is crucial for developing sustainable fertilization practices that enhance the soil bacteria and forage yield. This study aims to investigate the impact of different fertilization regimes on soil bacterial community structure and function, with a particular focus on the role of core bacterial taxa in contributing to soil nutrient content and enhancing forage yield. Field experiments and high-throughput sequencing techniques were used to analyze the soil bacterial community structure and function under various fertilization regimes, including six treatments, control with no amendment (CK), double the standard rate of organic manure (T01), the standard rate of organic manure with nitrogen input equal to T04 (T02), half the standard rate of inorganic fertilizer plus half the standard rate of organic manure (T03), the standard rate of inorganic fertilizer reflecting local practice (T04), and double the standard rate of inorganic fertilizer (T05). The results demonstrated that organic manure treatments, particularly T01, significantly increased the forage yield and the diversity of core bacterial taxa. Core taxa from the Actinomycetota, Alphaproteobacteria, and Gammaproteobacteria classes were crucial in enhancing the soil nutrient content, directly correlating with forage yield. Fertilization significantly influenced functions relating to carbon and nitrogen cycling, with core taxa playing central roles. The diversity of core microbiota and soil nutrient levels were key determinants of forage yield variations across treatments. These findings underscore the critical role of core bacterial taxa in agroecosystem productivity and advocate for their consideration in fertilization strategies to optimize forage yield, supporting the shift towards sustainable agricultural practices.

Plant economics spectrum governs leaf nitrogen and phosphorus resorption in subtropical transitional forests.

BACKGROUND: Leaf nitrogen (N) and phosphorus (P) resorption is a fundamental adaptation strategy for plant nutrient conservation. However, the relative roles that environmental factors and plant functional traits play in regulating N and P resorption remain largely unclear, and little is known about the underlying mechanism of plant functional traits affecting nutrient resorption. Here, we measured leaf N and P resorption and 13 plant functional traits of leaf, petiole, and twig for 101 representative broad-leaved tree species in our target subtropical transitional forests. We integrated these multiple functional traits into the plant economics spectrum (PES). We further explored whether and how elevation-related environmental factors and these functional traits collectively control leaf N and P resorption. RESULTS: We found that deciduous and evergreen trees exhibited highly diversified PES strategies, tending to be acquisitive and conservative, respectively. The effects of PES, rather than of environmental factors, dominated leaf N and P resorption patterns along the elevational gradient. Specifically, the photosynthesis and nutrient recourse utilization axis positively affected N and P resorption for both deciduous and evergreen trees, whereas the structural and functional investment axis positively affected leaf N and P resorption for evergreen species only. Specific leaf area and green leaf nutrient concentrations were the most influential traits driving leaf N and P resorption. CONCLUSIONS: Our study simultaneously elucidated the relative contributions of environmental factors and plant functional traits to leaf N and P resorption by including more representative tree species than previous studies, expanding our understanding beyond the relatively well-studied tropical and temperate forests. We highlight that prioritizing the fundamental role of traits related to leaf resource capture and defense contributes to the monitoring and modeling of leaf nutrient resorption. Therefore, we need to integrate PES effects on leaf nutrient resorption into the current nutrient cycling model framework to better advance our general understanding of the consequences of shifting tree species composition for nutrient cycles across diverse forests.

Plant growth promoting endophyte modulates soil ecological characteristics during the enhancement process of cadmium phytoremediation.

Endophyte assisted phytoremediation of cadmium (Cd) contaminated soil represents a promising strategy. However, the precise soil ecological regulatory mechanisms by which endophyte enhance the Cd phytoextraction remain unclear. Here, we employed the plant growth promoting endophyte (PGPE) Pseudomonas sp. E3, which has been validated to effectively enhance Cd extraction in Solanum nigrum L., to investigate its regulatory mechanism on soil ecology. The results demonstrated that while PGPE inoculation resulted in minimal alterations to the physicochemical properties of the bulk soil, it led to a notable increase in acid phosphatase activity by 17.86% and urease activity by 24.85% in the rhizosphere soil. This, in turn, significantly raised the available nitrogen and phosphorus contents by 16.93% and 21.27%, respectively, in the rhizosphere soil. Additionally, PGPE inoculation effectively replenished the bioavailable fractions of Fe and Cd, which had been depleted due to root uptake. Importantly, the inoculation specifically augmented the abundance of biomarkers p_Patescibacteria, f_Saccharimonadales, and g_Saccharimonadales in the rhizosphere soil. These biomarkers exhibited a significant positive correlation with the available nutrient and metal element contents. Moreover, the co-occurrence network analysis demonstrated that the inoculation resulted in a simplified bacterial community network, which may have facilitated community synergism by displacing bacteria with a negative association. This regulation appears to occur independently of PGPE colonization. Overall, our findings suggested that PGPE also exerts a regulatory influence on soil ecological features, significantly aiding hyperaccumulators in nutrient acquisition and heavy metal accumulation.

Increased anaerobic conditions promote the denitrifying nitrogen removal potential and limit anammox substrate acquisition within paddy irrigation and drainage units.

Microbial nitrogen (N) removal is crucial for purifying surface water quality in paddy irrigation and drainage units (IDUs). However, the spatiotemporal microbial N removal potential characteristics within these IDUs and the effects of changing anaerobic conditions on this potential remain insufficiently studied. In this study, we investigated the microbial N removal potential of conventional rice-wheat rotation and anaerobically enhanced rice-crayfish rotation IDUs using field measurements, isotope tracing techniques, and quantitative PCR. Our findings reveal that paddy fields were identified as hotspots for anammox activity, contributing to 76.0 %-97.4 % of the total anammox N removal potential in the IDU, while denitrification processes in ditches accounted for 43.5 %-77.4 % of the IDU's denitrification potential. During the rice transplanting period, the anammox N removal potential peaked, representing 35.8 % and 71.8 % of the total anammox N removal potential of the paddy fields in rice-wheat and rice-crayfish IDUs, respectively. An increase in anaerobic conditions diminished the anammox N removal potential while amplifying denitrification capabilities. The N removal potential in paddy fields decreased with increasing depth, contrasting with the relative stability in ditches. Spatiotemporal fluctuations in N removal potentials within these units are influenced by Fe2+ concentration, carbon and N content, WFPS, and pH levels. This study provides a scientific basis for improving nitrogen removal and water quality treatment in IDUs.

Unveiling the impacts of microplastic pollution on soil health: A comprehensive review.

Soil contamination by microplastics (MPs) has emerged as a significant global concern. Although traditionally associated with crop production, contemporary understanding of soil health has expanded to include a broader range of factors, including animal safety, microbial diversity, ecological functions, and human health protection. This paradigm shifts underscores the imperative need for a comprehensive assessment of the effects of MPs on soil health. Through an investigation of various soil health indicators, this review endeavors to fill existing knowledge gaps, drawing insights from recent studies conducted between 2021 and 2024, to elucidate how MPs may disrupt soil ecosystems and compromise their crucial functions. This review provides a thorough analysis of the processes leading to MP contamination in soil environments and highlights film residues as major contributors to agricultural soils. MPs entering the soil detrimentally affect crop productivity by hindering growth and other physiological processes. Moreover, MPs hinder the survival, growth, and reproductive rates of the soil fauna, posing potential health risks. Additionally, a systematic evaluation of the impact of MPs on soil microbes and nutrient cycling highlights the diverse repercussions of MP contamination. Moreover, within soil-plant systems, MPs interact with other pollutants, resulting in combined pollution. For example, MPs contain oxygen-containing functional groups on their surfaces that form high-affinity hydrogen bonds with other pollutants, leading to prolonged persistence in the soil environment thereby increasing the risk to soil health. In conclusion, we succinctly summarize the current research challenges related to the mediating effects of MPs on soil health and suggest promising directions for future studies. Addressing these challenges and adopting interdisciplinary approaches will advance our understanding of the intricate interplay between MPs and soil ecosystems, thereby providing evidence-based strategies for mitigating their adverse effects.

Do Tasmanian devil declines impact ecosystem function?

Tasmanian eucalypt forests are among the most carbon-dense in the world, but projected climate change could destabilize this critical carbon sink. While the impact of abiotic factors on forest ecosystem carbon dynamics have received considerable attention, biotic factors such as the input of animal scat are less understood. Tasmanian devils (Sarcophilus harrisii)-an osteophageous scavenger that can ingest and solubilize nutrients locked in bone material-may subsidize plant and microbial productivity by concentrating bioavailable nutrients (e.g., nitrogen and phosphorus) in scat latrines. However, dramatic declines in devil population densities, driven by the spread of a transmissible cancer, may have underappreciated consequences for soil organic carbon (SOC) storage and forest productivity by altering nutrient cycling. Here, we fuse experimental data and modeling to quantify and predict future changes to forest productivity and SOC under various climate and scat-quality futures. We find that devil scat significantly increases concentrations of nitrogen, ammonium, phosphorus, and phosphate in the soil and shifts soil microbial communities toward those dominated by r-selected (e.g., fast-growing) phyla. Further, under expected increases in temperature and changes in precipitation, devil scat inputs are projected to increase above- and below-ground net primary productivity and microbial biomass carbon through 2100. In contrast, when devil scat is replaced by lower-quality scat (e.g., from non-osteophageous scavengers and herbivores), forest carbon pools are likely to increase more slowly, or in some cases, decline. Together, our results suggest often overlooked biotic factors will interact with climate change to drive current and future carbon pool dynamics in Tasmanian forests.

Small Interfering RNAs (siRNAs) Negatively Impact Growth and Gene Expression of Environmentally Relevant Bacteria in In Vitro Conditions.

Rising global populations have amplified food scarcity and ushered in the development of genetically modified (GM) crops containing small interference RNAs (siRNAs) that control gene expression to overcome these challenges. The use of RNA interference (RNAi) in agriculture remains controversial due to uncertainty regarding the unintended release of genetic material and downstream nontarget effects, which have not been assessed in environmental bacteria to date. To evaluate the impacts of siRNAs used in agriculture on environmental bacteria, this study assessed microbial growth and viability as well as transcription activity with and without the presence of environmental stressors. Results showed a statistically significant reduction in growth capacity and maximum biomass achieved when bacteria are exposed to siRNAs alone and with additional external stress (p < 0.05). Further transcriptomic analysis demonstrated that nutrient cycling gene activities were found to be consistently and significantly altered following siRNA exposure, particularly among carbon (xylA, FBPase, limEH, Chitinase, rgl, rgh, rgaE, mannanase, ara) and nitrogen (ureC, nasA, narB, narG, nirK) cycling genes (p < 0.05). Decreases in carbon cycling gene transcription profiles were generally significantly enhanced when siRNA exposure was coupled with nutrient or antimicrobial stress. Collectively, findings suggest that certain conditions facilitate the uptake of siRNAs from their surrounding environments that can negatively affect bacterial growth and gene expression activity, with uncertain downstream impacts on ecosystem homeostasis.

Scavenging in two mountain ecosystems: Distinctive contribution of ants in grassland and non-ant invertebrates in forest.

Scavenging is a key process for the cycling of nutrients in ecosystems, yet it is still neglected in the ecological literature. Apart from the importance of specific groups of animals in scavenging, there have been few ecological studies that compare them. Furthermore, the ecological studies on scavenging have mainly focused on vertebrates despite the crucial importance of invertebrates in this process. Here, we performed a large-scale ant suppression and vertebrate exclusion experiment to quantify the relative contribution of ants, non-ant invertebrates and vertebrates in scavenging nitrogen-rich (insect carcasses) and carbon-rich (seeds) baits in two contrasting mountainous habitats in Brazil (grasslands and forests). Overall, bait removal was 23.2% higher in forests than in grasslands. Ants were the primary scavengers in grasslands, responsible for more than 57% of dead insect larvae and seed removal, while, in forests, non-ant invertebrates dominated, removing nearly 65% of all baits. Vertebrates had a minor role in scavenging dead insect larvae and seeds in both habitats, with <4% of removals. Furthermore, our results show that animal-based baits were more consumed in forests than seeds, and both resources were equally consumed in grasslands. Therefore, we demonstrate the superiority of invertebrates in this process, with a particular emphasis on the irreplaceable role of ants, especially in this grassland ecosystem. As such, we further advance our knowledge of a key ecosystem process, showing the relative importance of three major groups in scavenging and the differences in ecosystems functioning between two contrasting tropical habitats.

Synthetic Microbial Community Promotes Bacterial Communities Leading to Soil Multifunctionality in Desertified Land.

Soil desertification is an important challenge in global soil management, and effectively and stably restoring soil function is an urgent problem. Using synthetic microbial communities (SynComs) is a burgeoning microbial strategy aimed at enhancing soil nutrients through functional synergies among diverse microorganisms; nevertheless, their effectiveness in restoring desertified soils remains unknown. In this study, we conducted a two-year field experiment using a SynCom constructed by in situ probiotic bacteria and set up control, chemical fertilizer, and combined SynCom-chemical fertilizer (combined fertilizer) treatments to investigate the linkage between microbial communities and soil multifunctionality in the soil surface layer (0-10 cm). Both the bacterial and fungal communities differed the most under the combined fertilizer treatment compared to the control. The bacterial communities differed more under treatments of the SynCom than the chemical fertilizer, while the fungal communities differed more under the chemical fertilizer treatment than the SynCom treatment. Regarding soil function, the SynCom strengthened the correlation between enzyme activities and both bacterial communities and functional properties. pH and available potassium were the main influencing factors under the chemical fertilizer and combined fertilizer treatments. The beta-diversity of the bacterial communities was significantly correlated with soil multifunctionality. Random forest analyses showed that the SynCom significantly enhanced the bacterial communities, driving soil multifunctionality, and that some potential microbial taxa drove multiple nutrient cycles simultaneously. In summary, the SynCom effectively increased the abundance of most carbon, nitrogen, and phosphorus functional genes as well as soil enzyme activities. The bacterial community composition contributed significantly to soil multifunctionality. Hence, the development of novel microbial agents holds significant potential for improving soil functionality and managing desertification.

Postfire Phosphorus Enrichment Mitigates Nitrogen Loss in Boreal Forests.

Net nitrogen mineralization (Nmin) and nitrification regulate soil N availability and loss after severe wildfires in boreal forests experiencing slow vegetation recovery. Yet, how microorganisms respond to postfire phosphorus (P) enrichment to alter soil N transformations remains unclear in N-limited boreal forests. Here, we investigated postfire N-P interactions using an intensive regional-scale sampling of 17 boreal forests in the Greater Khingan Mountains (Inner Mongolia-China), a laboratory P-addition incubation, and a continental-scale meta-analysis. We found that postfire soils had an increased risk of N loss by accelerated Nmin and nitrification along with low plant N demand, especially during the early vegetation recovery period. The postfire N/P imbalance created by P enrichment acts as a "N retention" strategy by inhibiting Nmin but not nitrification in boreal forests. This strategy is attributed to enhanced microbial N-use efficiency and N immobilization. Importantly, our meta-analysis found that there was a greater risk of N loss in boreal forest soils after fires than in other climatic zones, which was consistent with our results from the 17 soils in the Greater Khingan Mountains. These findings demonstrate that postfire N-P interactions play an essential role in mitigating N limitation and maintaining nutrient balance in boreal forests.

Reservoir regulation-induced variations in water level impacts cyanobacterial bloom by the changing physiochemical conditions.

Gaining insight into the impact of reservoir regulation on algal blooms is essential for comprehending the dynamic changes and response mechanisms in the reservoir ecosystem. In this study, we conducted a comprehensive field investigation linking physiochemical parameters, and phytoplankton community to different water regimes in the Three Gorges Reservoir. Our aim was to explore the effects of reservoir regulation on the extinction of cyanobacterial blooms. The results showed that during the four regulatory events, the water levels decreased by 2.02-4.33 m, and the average water velocity increased 68 % compared to before. The average total phosphorus and total nitrogen concentrations reduced by up to 20 %, and the cyanobacterial biomass correspondingly declined dramatically, between 66.94 % and 75.17 %. As the change of water level decline increasing, there was a significant increase of algal diversity and a notable decrease of algal cell density. Additionally, a shift in the dominant phytoplankton community from Cyanobacteria to Chlorophyceae was observed. Our analysis indicated that water level fluctuations had a pronounced effect on cyanobacterial extinction, with hydrodynamic changes resulting in a reduction of cyanobacterial biomass. This research underlined the potential for employing hydrodynamic management as a viable strategy to mitigate the adverse ecological impacts of cyanobacterial blooms, providing a solution for reservoir's eco-environmental management.

Do Added Microplastics, Native Soil Properties, and Prevailing Climatic Conditions Have Consequences for Carbon and Nitrogen Contents in Soil? A Global Data Synthesis of Pot and Greenhouse Studies.

Microplastics threaten soil ecosystems, strongly influencing carbon (C) and nitrogen (N) contents. Interactions between microplastic properties and climatic and edaphic factors are poorly understood. We conducted a meta-analysis to assess the interactive effects of microplastic properties (type, shape, size, and content), native soil properties (texture, pH, and dissolved organic carbon (DOC)) and climatic factors (precipitation and temperature) on C and N contents in soil. We found that low-density polyethylene reduced total nitrogen (TN) content, whereas biodegradable polylactic acid led to a decrease in soil organic carbon (SOC). Microplastic fragments especially depleted TN, reducing aggregate stability, increasing N-mineralization and leaching, and consequently increasing the soil C/N ratio. Microplastic size affected outcomes; those <200 µm reduced both TN and SOC contents. Mineralization-induced nutrient losses were greatest at microplastic contents between 1 and 2.5% of soil weight. Sandy soils suffered the highest microplastic contamination-induced nutrient depletion. Alkaline soils showed the greatest SOC depletion, suggesting high SOC degradability. In low-DOC soils, microplastic contamination caused 2-fold greater TN depletion than in soils with high DOC. Sites with high precipitation and temperature had greatest decrease in TN and SOC contents. In conclusion, there are complex interactions determining microplastic impacts on soil health. Microplastic contamination always risks soil C and N depletion, but the severity depends on microplastic characteristics, native soil properties, and climatic conditions, with potential exacerbation by greenhouse emission-induced climate change.

General reversal of N-decomposition relationship during long-term decomposition in boreal and temperate forests.

Decomposition of dead organic matter is fundamental to carbon (C) and nutrient cycling in terrestrial ecosystems, influencing C fluxes from the biosphere to the atmosphere. Theory predicts and evidence strongly supports that the availability of nitrogen (N) limits litter decomposition. Positive relationships between substrate N concentrations and decomposition have been embedded into ecosystem models. This decomposition paradigm, however, relies on data mostly from short-term studies analyzing controls on early-stage decomposition. We present evidence from three independent long-term decomposition investigations demonstrating that the positive N-decomposition relationship is reversed and becomes negative during later stages of decomposition. First, in a 10-y decomposition experiment across 62 woody species in a temperate forest, leaf litter with higher N concentrations exhibited faster initial decomposition rates but ended up a larger recalcitrant fraction decomposing at a near-zero rate. Second, in a 5-y N-enrichment experiment of two tree species, leaves with experimentally enriched N concentrations had faster decomposition initial rates but ultimately accumulated large slowly decomposing fractions. Measures of amino sugars on harvested litter in two experiments indicated that greater accumulation of microbial residues in N-rich substrates likely contributed to larger slowly decomposing fractions. Finally, a database of 437 measurements from 120 species in 45 boreal and temperate forest sites confirmed that higher N concentrations were associated with a larger slowly decomposing fraction. These results challenge the current treatment of interactions between N and decomposition in many ecosystems and Earth system models and suggest that even the best-supported short-term controls of biogeochemical processes might not predict long-term controls.

Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater.

Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signal and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.

Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments.

The Okinawa Trough (OT) is a back-arc basin with a wide distribution of active cold seep systems. However, our understanding of the metabolic function of microbial communities in the cold seep sediments of the OT remains limited. In this study, we investigated the vertical profiles of functional genes involved in methane, nitrogen, and sulphur cycling in the cold seep sediments of the OT. Furthermore, we explored the possible coupling mechanisms between these biogeochemical cycles. The study revealed that the majority of genes associated with the nitrogen and sulphur cycles were most abundant in the surface sediment layers. However, only the key genes responsible for sulphur disproportionation (sor), nitrogen fixation (nifDKH), and methane metabolism (mcrABG) were more prevalent within sulfate-methane transition zone (SMTZ). Significant positive correlations (P < 0.05) were observed between functional genes involved in sulphur oxidation, thiosulphate disproportionation with denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), as well as between AOM/methanogenesis and nitrogen fixation, and between sulphur disproportionation and AOM. A genome of Filomicrobium (class Alphaproteobacteria) has demonstrated potential in chemoautotrophic activities, particularly in coupling DNRA and denitrification with sulphur oxidation. Additionally, the characterized sulfate reducers such as Syntrophobacterales have been found to be capable of utilizing nitrate as an electron acceptor. The predominant methanogenic/methanotrophic groups in the OT sediments were identified as H2-dependent methylotrophic methanogens (Methanomassiliicoccales and Methanofastidiosales) and ANME-1a. This study offered a thorough understanding of microbial ecosystems in the OT cold seep sediments, emphasizing their contribution to nutrient cycling.IMPORTANCEThe Okinawa Trough (OT) is a back-arc basin formed by extension within the continental lithosphere behind the Ryukyu Trench arc system. Cold seeps are widespread in the OT. While some studies have explored microbial communities in OT cold seep sediments, their metabolic potential remains largely unknown. In this study, we used metagenomic analysis to enhance comprehension of the microbial community's role in nutrient cycling and proposed hypotheses on the coupling process and mechanisms involved in biogeochemical cycles. It was revealed that multiple metabolic pathways can be performed by a single organism or microbes that interact with each other to carry out various biogeochemical cycling. This data set provided a genomic road map on microbial nutrient cycling in OT sediment microbial communities.