Using metacommunity ecology to understand environmental metabolomes

Skyglow increases cyanobacteria abundance and organic matter cycling in lakes

Artificial light propagating towards the night sky can be scattered back to Earth and reach ecosystems tens of kilometres away from the original light source. This phenomenon is known as artificial skyglow. Its consequences on freshwaters are largely unknown. In a large-scale lake enclosure experiment, we found that skyglow at levels of 0.06 and 6 lux increased the abundance of anoxygenic aerobic phototrophs and cyanobacteria by 32 (±22) times. An ecosystem metabolome analysis revealed that skyglow increased the production of algal-derived metabolites, which appeared to stimulate heterotrophic activities as well. Furthermore, we found evidence that skyglow decreased the number of bacteria-bacteria interactions. Effects of skyglow were more pronounced at night, suggesting that responses to skyglow can occur on short time scales. Overall, our results call for considering skyglow as a reality of increasing importance for microbial communities and carbon cycling in lake ecosystems.

Sex-induced alterations in rumen microbial communities and metabolite profiles: implications for lamb body weight

BACKGROUND

Microbiota-metabolome interactions play a crucial role in host physiological regulation and metabolic homeostasis. The aim of this study was to investigate that sex induces alterations in rumen microbial community composition and metabolite profiles in lambs and the influence on body weight. This study aimed to demonstrate that sex- induced alterations in rumen microbial community and metabolite profiles and blood indices and their linkage to growth performance in lambs.

RESULTS

This study examined (growth indices, serum indices, rumen fermentation parameters, rumen fluid microbiota community and metabolome profiles) in 180 Hu lambs (90 males, and 90 females) with the same age and diet. At six months, male lambs showed significantly greater body weight, serum indices (glutamic pyruvic transaminase, glutamic oxalacetic transaminase, growth hormone, glucagon-like peptide 1, and ghrelin), and molar percentage of propionic acid, isobutyric acid, butyric acid, isovaleric acid and valeric acid compared to female. However, male had lower VFA molar concentrations (acetic acid, propionic acid, butyric acid, and TVFAs), acetic acid/propionic acid, and VFA molar percentage (acetic acid) than female. Significant sex-related differences were observed in rumen microbiota and metabolic enrichment between genders. Moreover, compared with the females lambs, the relative abundance of Succiniclasticum, uncultured_rumen_bacterium, NK4 A214_group, Veillonellaceae_UCG_001 and Butyrivibrio in the male lambs has been significantly increased, while the relative abundance of Prevotella has been significantly decreased (P < 0.05). Notably, there were significant rumen microbiota-metabolite interactions, especially Firmicutes and Bacteroidota as dominant phyla in the sheep rumen with significant differences in correlation with rumen metabolic modules. Additionally, there are pronounced correlations among the microbiota, particularly within the Firmicutes phylum. Furthermore, the up-regulated metabolites in the rumen fluid of male lambs were predominantly enriched in the amino acid metabolite pathway, and these metabolites exhibited a significant positive correlation with body weight. However, the metabolites that were up-regulated in ewe lambs were predominantly enriched in the lipid metabolic pathway, and these metabolites exhibited a significant negative correlation with body weight. Moreover, lamb rumen microbial markers (Lachnospiraceae_UCG_008, Saccharofermentans, unclassified_Clostridia, Christensenellaceae_R_7_group, Anaerovorax, Mogibacterium, and unclassified_Erysipelotrichaceae) and metabolic markers (C75, 4-Coumarate, Flibanserin,3-Amino-5-mercapto-1,2,4-triazole, 1,3-Propane sultone, Fingolimod phosphate ester, S-,) were significantly positively correlated with body weight, but lamb rumen microbial markers (Anaeroplasma, unclassified_Acholeplasmataceae, uncultured_rumen_bacterum_4c28 d_15) and metabolic markers (Mozenavir, Reduced riboflavin, PG(18:2(9Z,12Z)/0:0), Cowanin) were significantly negatively correlated body weight.

CONCLUSIONS

This study shows that sex-induced alterations in rumen microbial communities and metabolite profiles, adapting to the growth and development of lambs. The findings may help develop targeted strategies to optimize sheep rumen microbiota and improve productivity.

Decomposing the molecular complexity and transformation of dissolved organic matter for innovative anaerobic bioprocessing

The sustainable transformation and management of dissolved organic matter (DOM) are crucial for advancing organic waste treatment towards resource-oriented processes. However, the intricate molecular complexity of DOM poses significant challenges, impeding a comprehensive understanding of the underlying biochemical processes. Here, we focus on the chemical "dark matter" mining using ultra-high resolution mass spectrometry technologies to elucidate the molecular diversity and transformation in anaerobic bioprocessing of food waste. We developed an analytical framework that reveals the persistence of DOM in the final effluent is mainly determined by its molecular properties, such as carbon chain length, aromaticity, unsaturation, and redox states. Our in-depth characterization and quantitative analysis of key biochemical reactions unveils the evolution of DOM composition, providing valuable insights into the targeted conversion of persistent molecules toward full utilization. Additionally, we establish a correlation between the redox state and energy density of a broad range of DOM molecules, enabling us to comprehend and evaluate their biodegradability. These insights enhance the mechanistic understanding of DOM transformation, guiding the rational design and regulation of sustainable organic waste treatment strategies.

Interactive effects of soil dissolved organic matter (DOM) and Per- and polyfluoroalkyl substances on contaminated soil site: DOM molecular-level perspective

Dissolved organic matter (DOM), as the most active soil component, plays a crucial role in regulating the transport of contaminants. Per- and polyfluoroalkyl substances (PFAS) have been found to be widespread contaminants in the soil environment, and their migration would be also affected by DOM. Herein, the surface and subsurface soil samples collected from two PFAS manufacturing factories were studied for the variation characteristics of DOM under PFAS contamination, and the interaction between DOM and PFAS in soil was further explored. The results showed that PFAS contamination significantly reduced the richness of surface soil DOM. For the specific DOM components, the potential transformation of DOM in subsurface soil indicates that the presence of PFAS promotes the transformation of other DOM components to PA compounds. Moreover, a strong positive relationship was observed between the concentration of most perfluoroalkyl sulfonic acids (PFSAs) and the average unsaturation (DBE) and aromaticity index (AImod) of DOM, while no such relationship for perfluoroalkyl carboxylic acids (PFCAs), suggesting DBE and AImod may be a potential contributor influencing the distribution and transport of PFSAs. These findings highlight the interaction between DOM and the PFAS in the soil environment, which may enhance our understanding of the release and fate of PFAS in the soil environment.

Quantifying assembly processes of dissolved organic matter pools in eutrophication using high-resolution mass spectrometry and ecological models

Dissolved organic matter (DOM) represents a large, dynamic pool of carbon, playing a crucial role in eutrophic aquatic ecosystems through its continuous transport and transformation. However, the assembly mechanisms of DOM under different eutrophic conditions remain elusive, hindering the understanding of carbon dynamics and the prediction of carbon fate. Here we collected 72 lake water samples during two sampling events in Chaohu Lake, the fifth largest freshwater lake in China, and performed high-resolution mass spectrometry (HRMS) and ecological null modeling to quantify the assembly processes of DOM in eutrophication. We found that as eutrophic levels increased, the relative contribution of homogeneous selection rose, while the contributions of variable selection and dispersal limitation decreased. The influence of different assembly processes on the DOM pool across sites, although estimated solely from HRMS data, exhibited reasonable consistency with the spatiotemporal variations. Several environmental parameters, including total phosphorus, Secchi disk depth, trophic state index, pH, temperature, and fluorescence index, were significantly correlated with one or more DOM assembly processes (p < 0.05), and assembly mechanisms also shaped the compound composition of DOM. Our findings reveal a shift in DOM assembly from variable selection to homogeneous selection in eutrophication, highlighting the importance of DOM dynamics and environmental homogenization in the management and restoration of eutrophic lakes.

Organic molecular network analysis reveals transformation signatures of dissolved organic matter during anaerobic digestion process

Identifying the transformation types, i.e., syntheses or decompositions, of organic molecules in complex environmental systems remains a significant challenge. To address this, we propose a new analytical framework, Transformation-based Organic Molecular Ecological Network Analysis (TOMENA) for the systematic recognition and analysis of molecular transformations according to the measurement of high-resolution mass spectrometry (FT-ICR MS) through time-series data. Applying the TOMENA framework, we systematically investigated transformation signatures of dissolved organic matter (DOM) during anaerobic digestion processes. We found a close relationship between molecular transformation and molecular weight in the biodegradation system. A total of 129 transformations were identified, involving carbon numbers ranging from 0 to 24, with 59 of these transformations concentrated in small molecular weight changes involving 1-3 carbons. As the molecular weight corresponding to transformations increased, the proportion of bio-transformations used for decomposition decreased linearly. Simultaneously, large molecules were decomposed and small molecules synthesized, indicating a system tendency to transform molecules towards a medium mass range. Topological analysis of the transformation network further expanded our understanding. We discovered that molecular transformations did not follow the shortest path, as the path distance was significantly longer than in random networks (2.558 vs. 2.383). We identified that N-containing transformations were centrally located in the system through edge analysis. However, the transformations' position did not coincide with functional importance. A comprehensive indicator of irreplaceability and usage frequency revealed that C(+1)H(+3)O(+2)N(-1), C(+1)H(+2), O(+1), C(+3)H(+4)O(+2), and H(-2)O(+1) are critical transformation pathways in the system, showing the top 5 efficiency contributions. Our developed TOMENA workflow provides novel insights and robust methodological support for future research, advancing our understanding of molecular transformations in complex biodegradation system.

Carbon Isotopic Signatures of Aquifer Organic Molecules along Anthropogenic Recharge Gradients

The property of groundwater dissolved organic matter (DOM) subjected to anthropogenic groundwater recharge (AGR) might be affected by the water quality disparity between surface water and natural groundwater. However, the diverse molecular scenarios of groundwater DOM under uneven recharging levels remain largely unexplored. We combined molecular characteristics, carbon isotopic signatures of organic molecules, and end-member mixing analysis to explore the sensitivity and potential tracking capabilities of DOM to AGR along with recharging gradients. Our findings suggested that AGR enriched groundwater with diverse, saturated, labile, and sulfur-rich molecules, amplifying DOM abundance and intensity, which intensified with recharge gradients. Additionally, S-containing molecules and their indicators like CHOS% (with threshold values of 7.82%) exhibited high sensitivity and predictive power for AGR recognition. The major signatures (diversity, saturated degree, and stability) indicated by 13C-containing molecules were similar to the whole molecular pool. Notably, specific molecules (C12H10O5S and C15H16O12), although not detected in all groundwater samples, exhibit robust stability or favorable solubility, rendering them potential candidates as AGR-sensitive molecules. The R13C/12C ratio of 13C-containing C19H24O5 emerged as the most robust tracer, exhibiting a strong correlation with the recharge ratio and the smallest deviation from the theoretical mixing line, signifying its optimal suitability for precise groundwater DOM source apportionment. This study offers novel insights into AGR impacts and contributes to fostering a harmonious balance between human activities and water resource sustainability.

Enhanced Release and Reactivity of Soil Water-Extractable Organic Matter Following Wildfire in a Subtropical Forest

Climate-driven increases in wildfire frequency may disrupt soil carbon dynamics, potentially creating positive feedback within global carbon cycle. However, the release and lability of soil carbon following wildfire remain unclear, limiting our ability to predict fire impacts on carbon cycling. Here, we investigated chemical alterations in soil water-extractable organic matter (WEOM) following a subtropical forest wildfire by comparing burned soils to an adjacent unburned site. The consensus is that fire-altered DOM is aromatic and less reactive. However, we found that 10 months postfire, burned soils contained nearly three times more water-extractable organic carbon (WEOC) than the control site. Reactomics analysis further revealed an overall 8-fold increase in potential reactivity of this carbon, identified by higher abundances of molecular formulas involved in identified microbial reaction pathways. Specifically, burned soils exhibited elevated potential oxidative enzyme reactions, linked to a higher nominal oxidation state of carbon (NOSC) in WEOM. Metagenomic analysis revealed an enrichment of microbial taxa specialized in degrading aromatic compounds in burned areas, supporting the occurrence of potential microbial reaction pathways acting on WEOM in postfire soils. These findings highlight that wildfires may accelerate soil carbon loss through reactive WEOM mobilization and microbial response, with implications for long-term carbon-climate projections.

Ecosystem ecology needs an ecology of molecules

Ecosystem ecology needs a framework that explicitly considers the roles of organic compounds. The ecology of molecules integrates compound identity, diversity, and interactions to understand ecosystem processes, such as nutrient and carbon cycling. This approach leverages advances in analytical chemistry and molecular biology to unravel the complex chemical interplay within ecosystems.

Marine Recalcitrant Dissolved Organic Matter Gained by Processing at Sandy Subterranean Estuaries

The sandy subterranean estuary (STE) connecting fresh groundwater to saline sea water is characterized by strong geochemical (salinity, redox, and pH) gradients, with evidence emerging for its role as a hot spot for consumption of labile substrates. This inspired us to conduct a study to evaluate whether this holds true for dissolved organic matter (DOM), especially given the still mysterious origin of marine recalcitrant DOM. Here, characterization of DOM of 21 groundwater samples (depth 1-13 m, salinity 3.9‰ to 32.4‰) across a 65 m transect of an STE located in coastal Guangdong, China, has found systematic biotransformation toward "recalcitrant" carboxyl-rich alicyclic molecules (CRAM). The fraction of CRAM (%CRAM) increases from 33.1% to 76.7% with an increasing degree of DOM degradation and increasing salinity. Further, processing of DOM, including the more "biolabile" DOM with lower %CRAM released from aquitard, is more active under oxic conditions than under reducing conditions. Given the large quantities of sea water that recirculates through the sandy STEs globally, the amount of "recalcitrant" DOM (RDOM) entering the ocean after processing is likely to be considerable. While more studies are needed, the ocean can gain "recalcitrant" CRAM-like compounds in this way.

Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear

Dissolved organic matter (DOM) is vital to ecosystem functions, influencing nutrient cycles and water quality. Understanding the processes driving DOM chemistry variation remains a challenge. By examining these processes through a community ecology perspective, we aim to understand the balance between stochastic forces (e.g., random mixing of DOM) and deterministic forces (e.g., systematic loss of certain types of DOM molecules) shaping DOM chemistry. Previous research on stochastic and deterministic influences over DOM chemistry applied null models to aquatic environments and subsurface pore water. Our study extends this to variably inundated riverbed sediments, which are widespread globally. We studied 38 river reaches across biomes, finding that DOM chemistry within most sites was governed by deterministic processes that were highly localized and led to spatial divergence in DOM chemistry within each reach. The degree of determinism varied substantially across reaches and we hypothesized this was related to differences in sediment moisture. Our findings partially supported this, showing that the upper limit of determinism decreased with increasing sediment moisture. We integrated our results with previous studies to develop a post-hoc conceptual model proposing that DOM assemblages become more deterministic along the continuum from river water to saturated sediment pore spaces to drier sediments or soils. This conceptual model aligns with previous work linking DOM chemistry to the Damköhler number and hydrologic connectivity, suggesting generalizable patterns and processes that can be further revealed by quantifying the stochastic-deterministic balance through space, time, and across scales.

Tire Wear Particles Exposure Enhances Denitrification in Soil by Enriching Labile DOM and Shaping the Microbial Community

Tire wear particles (TWP) are emerging contaminants in the soil environment due to their widespread occurrence and potential threat to soil health. However, their impacts on soil biogeochemical processes remain unclear. Here, we investigated the effects of TWP at various doses and their leachate on soil respiration and denitrification using a robotized continuous-flow incubation system in upland soil. Fourier transform ion cyclotron resonance mass spectrometry and high-throughput sequencing were employed to elucidate the mechanisms underpinning the TWP effects. We show that TWP increased soil CO2, N2, and N2O emissions, which were attributed to the changes in content and composition of soil dissolved organic matter (DOM) induced by TWP and their leachate. Specifically, the labile DOM components (H/C ≥ 1.5 and transformation >10), which were crucial in shaping the denitrifying community, were significantly enriched by TWP exposure. Furthermore, the abundances of denitrification genes (nirK/S and nosZ-I) and the specific denitrifying genera Pseudomonas were increased following TWP exposure. Our findings provide new insights into impacts of TWP on carbon and nitrogen cycling in soil, highlighting that TWP exposure may exacerbate greenhouse gas emissions and fertilizer N loss, posing adverse effects on soil fertility in peri-urban areas and climate change mitigation.

Broad Microbial Community Functions in a Conventional Activated Sludge System Exhibit Temporal Stability

Wastewater microbial communities within conventional activated sludge (CAS) systems can perform hundreds of biotransformations whose relative importance, frequency, and temporal stability remain largely unexplored. To improve our understanding of biotransformations in CAS systems, we collected 24 h composite samples from the influent and effluent of a CAS system over 14 days, analyzed samples using high-resolution mass spectrometry (HRMS), and conducted a nontarget analysis of our HRMS acquisitions. We found that over 50% of the chemical features in the influent were completely removed, and the daily number of detected features exhibited low variability with a coefficient of variation of 0.07. Additionally, we found 352 Core chemical features present in every sample at both locations. We used chemical features to search for evidence of 19 potential biotransformations and detected 9 of these biotransformations at a frequency of over 80 times per day, where evidence for dehydrogenations, hydroxylations, and acetylations was most frequently detected. The daily number of detections for the 9 biotransformations exhibited coefficients of variation ranging from 0.13-0.20, revealing the broad temporal stability for these wastewater microbial community functions. This stability contrasts with the previously observed temporal variability for micropollutant biotransformations, suggesting that micropollutant biotransformations are linked to specialized microbial community functions.

Long-term straw return enhanced the chlorine reactivity of soil DOM: Highlighting the molecular-level activity and transformation trade-offs

Chemical properties and molecular diversity of dissolved organic matter (DOM) in agricultural soils are important for soil carbon dynamics and chlorine activity. Yet the chlorine reactivity of soil DOM at the molecular level under agricultural management practices remains unidentified. Here, we investigated the chlorine reactivity of soil DOM under long-term straw return and the molecular activities and transformations during chlorination. The 9-year straw return enhanced the chlorine reactivity of soil DOM, leading to increases in the production of traditional disinfection byproducts (DBPs) and decreases in the formation of emerging high molecular weight DBPs. C17HnOmCl1-2 and C22HnNmOzCl were the highest relative abundances of emerging DBPs. The emerging DBPs were primarily generated through chlorine substitution reactions, with their precursors exhibiting higher H/Cwa (1.47) and O/Cwa (0.41) ratios under straw return. The molecular transformation ability and inactive molecules of soil DOM under long-term straw return were reduced after chlorination, resulting in increased DOM instability. Chlorination led to a shift in the thermodynamic processes of soil DOM molecules from thermodynamically limited to thermodynamically favorable processes, and lignin-like compounds displayed higher potentials for transformation into protein/amino sugar-like compounds. C19H26O6 was identified as a sensitive formula for tracing chlorine reactivity under straw return, and a network illustrating the generation of DBPs from C19H26O6 was established. Overall, these results highlighted the strong chlorine reactivity of soil DOM under long-term straw return.

Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient

Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.

Community successional patterns and inter-kingdom interactions during granular biofilm development

Aerobic granular sludge is a compact and efficient biofilm process used for wastewater treatment which has received much attention and is currently being implemented worldwide. The microbial associations and their ecological implications occurring during granule development, especially those involving inter-kingdom interactions, are poorly understood. In this work, we monitored the prokaryote and eukaryote community composition and structure during the granulation of activated sludge for 343 days in a sequencing batch reactor (SBR) and investigated the influence of abiotic and biotic factors on the granule development. Sludge granulation was accomplished with low-wash-out dynamics at long settling times, allowing for the microbial communities to adapt to the SBR environmental conditions. The sludge granulation and associated changes in microbial community structure could be divided into three stages: floccular, intermediate, and granular. The eukaryotic and prokaryotic communities showed parallel successional dynamics, with three main sub-communities identified for each kingdom, dominating in each stage of sludge granulation. Although inter-kingdom interactions were shown to affect community succession during the whole experiment, during granule development random factors like the availability of settlement sites or drift acquired increasing importance. The prokaryotic community was more affected by deterministic factors, including reactor conditions, while the eukaryotic community was to a larger extent shaped by biotic interactions (including inter-kingdom interactions) and stochasticity.

Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation

BACKGROUND

Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

RESULTS

During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.

CONCLUSIONS

All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.

Complexation with Metal Ions Affects Chlorination Reactivity of Dissolved Organic Matter: Structural Reactomics of Emerging Disinfection Byproducts

Metal ions are liable to form metal-dissolved organic matter [dissolved organic matter (DOM)] complexes, changing the chemistry and chlorine reactivity of DOM. Herein, the impacts of iron and zinc ions (Fe3+ and Zn2+) on the formation of unknown chlorinated disinfection byproducts (Cl-DBPs) were investigated in a chlorination system. Fe3+ preferentially complexed with hydroxyl and carboxyl functional groups, while Zn2+ favored the amine functional groups in DOM. As a consequence, electron-rich reaction centers were created by the C-O-metal bonding bridge, which facilitated the electrophilic attack of α-C in metal-DOM complexes. Size-reactivity continuum networks were constructed in the chlorination system, revealing that highly aromatic small molecules were generated during the oxidation and decarbonization of metal-DOM complexes. Molecular transformation related to C-R (R represents complex sites) loss was promoted via metal complexation, including decarboxylation and deamination. Consequently, complexation with Fe3+ and Zn2+ promoted hydroxylation by the C-O-metal bonding bridge, thereby increasing the abundances of unknown polychlorinated Cl-DBPs by 9.6 and 14.2%, respectively. The study provides new insights into the regulation of DOM chemistry and chlorine reactivity by metal ions in chlorination systems, emphasizing that metals increase the potential health risks of drinking water and more scientific control standards for metals are needed.

Disentangling drivers of mudflat intertidal DOM chemodiversity using ecological models

Microorganisms consume and transform dissolved organic matter (DOM) into various forms. However, it remains unclear whether the ecological patterns and drivers of DOM chemodiversity are analogous to those of microbial communities. Here, a large-scale investigation is conducted along the Chinese coasts to resolve the intrinsic linkages among the complex intertidal DOM pools, microbial communities and environmental heterogeneity. The abundance of DOM molecular formulae best fits log-normal distribution and follows Taylor's Law. Distance-decay relationships are observed for labile molecular formulae, while latitudinal diversity gradients are noted for recalcitrant molecular formulae. Latitudinal patterns are also observed for DOM molecular features. Negative cohesion, bacterial diversity, and molecular traits are the main drivers of DOM chemodiversity. Stochasticity analyses demonstrate that determinism dominantly shapes the DOM compositional variations. This study unveils the intrinsic mechanisms underlying the intertidal DOM chemodiversity and microbial communities from ecological perspectives, deepening our understanding of microbially driven chemical ecology.

Wildfire Impacts on Molecular Changes of Dissolved Organic Matter during Its Passage through Soil

The frequency and intensity of global wildfires are escalating, leading to an increase in derived pyrogenic dissolved organic matter (pyDOM), which potentially influences the riverine carbon reservoir and poses risks to drinking water safety. However, changes in pyDOM properties as it traverses through soil to water bodies are highly understudied due to the challenges of simulating such processes under laboratory conditions. In this study, we extracted soil DOM along hillslope gradients and soil depths in both burned and unburned catchments post wildfire. Using high-resolution mass spectrometry and a substrate-explicit model, we observed significant increases in the relative abundance of condensed aromatics (ConAC) and tannins in wildfire-affected soil DOM. Wildfire-affected soil DOM also displayed a broader spectrum of molecular and thermodynamic properties, indicative of its diverse composition and reactivity. Furthermore, as the fire-induced weakening of topsoil microbial reprocessing abilities hindered the transformation of plant-derived DOM, the relative abundance of lignin-like compounds increased with soil depth in the fire regions. Meanwhile, the distribution of shared molecular formulas along the hillslope gradient (from shoulder to toeslope) exhibited analogous patterns in both burned and unburned catchments. Although there was an increased prevalence of ConAC and tannin in the burned catchments, the relative abundance of these fractions diminished along the hillslope in all three catchments. Based on the substrate-explicit model, the biodegradability exhibited by wildfire-affected DOM fractions offers the possibility of its conversion along hillslopes. Our findings reveal the spatial distribution of DOM properties after a wildfire, facilitating accurate evaluation of dissolved organic carbon composition involved in the watershed-scale carbon cycle.

Treeline displacement may affect lake dissolved organic matter processing at high latitudes and altitudes

Climate change induced shifts in treeline position, both towards higher altitudes and latitudes induce changes in soil organic matter. Eventually, soil organic matter is transported to alpine and subarctic lakes with yet unknown consequences for dissolved organic matter (DOM) diversity and processing. Here, we experimentally investigate the consequences of treeline shifts by amending subarctic and temperate alpine lake water with soil-derived DOM from above and below the treeline. We use ultra-high resolution mass spectrometry (FT-ICR MS) to track molecular DOM diversity (i.e., chemodiversity), estimate DOM decay and measure bacterial growth efficiency. In both lakes, soil-derived DOM from below the treeline increases lake DOM chemodiversity mainly through the enrichment with polyphenolic and highly unsaturated compounds. These compositional changes are associated with reductions in bulk and compound-level DOM reactivity and reduced bacterial growth efficiency. Our results suggest that treeline advancement has the potential to enrich a large number of lake ecosystems with less biodegradable DOM, affecting bacterial community function and potentially altering the biogeochemical cycling of carbon in lakes at high latitudes and altitudes.

Deciphering Microbe-Mediated Dissolved Organic Matter Reactome in Wastewater Treatment Plants Using Directed Paired Mass Distance

Understanding the reaction mechanism of dissolved organic matter (DOM) during wastewater biotreatment is crucial for optimal DOM control. Here, we develop a directed paired mass distance (dPMD) method that constructs a molecular network displaying the reaction pathways of DOM. It couples direction inference and PMD analysis to extract the substrate-product relationships and delta masses of potentially paired reactants directly from sequential mass spectrometry data without formula assignment. Using this method, we analyze the influent and effluent samples from the bioprocesses of 12 wastewater treatment plants (WWTPs) and build a dPMD network to characterize the core reactome of DOM. The network shows that the first step of the transformation triggers reaction cascades that diversify the DOM, but the highly overlapped subsequent reaction pathways result in similar effluent DOM compositions across WWTPs despite varied influents. Mass changes exhibit consistent gain/loss preferences (e.g., +3.995 and -16.031) but different occurrences across WWTPs. Combined with genome-centric metatranscriptomics, we reveal the associations among dPMDs, enzymes, and microbes. Most enzymes are involved in oxygenation, (de)hydrogenation, demethylation, and hydration-related reactions but with different target substrates and expressed by various taxa, as exemplified by Proteobacteria, Actinobacteria, and Nitrospirae. Therefore, a functionally diverse community is pivotal for advanced DOM degradation.

Environment-specific virocell metabolic reprogramming

Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.

Fertilization Weakens the Ecological Succession of Dissolved Organic Matter in Paddy Rice Rhizosphere Soil at the Molecular Level

Dissolved organic matter (DOM) is involved in numerous biogeochemical processes, and understanding the ecological succession of DOM is crucial for predicting its response to farming (e.g., fertilization) practices. Although plentiful studies have examined how fertilization practice affects the content of soil DOM, it remains unknown how long-term fertilization drives the succession of soil DOM over temporal scales. Here, we investigated the succession of DOM in paddy rice rhizosphere soils subjected to different long-term fertilization treatments (CK: no fertilization; NPK: inorganic fertilization; OM: organic fertilization) along with plant growth. Our results demonstrated that long-term fertilization significantly promoted the molecular chemodiversity of DOM, but it weakened the correlation between DOM composition and plant development. Time-decay analysis indicated that the DOM composition had a shorter halving time under CK treatment (94.7 days), compared to NPK (337.4 days) and OM (223.8 days) treatments, reflecting a lower molecular turnover rate of DOM under fertilization. Moreover, plant development significantly affected the assembly process of DOM only under CK, not under NPK and OM treatments. Taken together, our results demonstrated that long-term fertilization, especially inorganic fertilization, greatly weakens the ecological succession of DOM in the plant rhizosphere, which has a profound implication for understanding the complex plant-DOM interactions.

Quantifying Stochastic Processes in Shaping Dissolved Organic Matter Pool with High-Resolution Mass Spectrometry

Natural dissolved organic matter (DOM) represents a ubiquitous molecular mixture, progressively characterized by spatiotemporal resolution. However, an inadequate comprehension of DOM molecular dynamics, especially the stochastic processes involved, hinders carbon cycling predictions. This study employs ecological principles to introduce a neutral theory to elucidate the fundamental processes involving molecular generation, degradation, and migration. A neutral model is thus formulated to assess the probability distribution of DOM molecules, whose frequencies and abundances follow a β-distribution relationship. The neutral model is subsequently validated with high-resolution mass spectrometry (HRMS) data from various waterbodies, including lakes, rivers, and seas. The model fitting highlights the prevalence of molecular neutral distribution and quantifies the stochasticity within DOM molecular dynamics. Furthermore, the model identifies deviations of HRMS observations from neutral expectations in photochemical and microbial experiments, revealing nonrandom molecular transformations. The ecological null model further validates the neutral modeling results, demonstrating that photodegradation reduces molecular stochastic dynamics at the surface of an acidic pit lake, while random distribution intensifies at the river surface compared with the porewater. Taken together, the DOM molecular neutral model emphasizes the significance of stochastic processes in shaping a natural DOM pool, offering a potential theoretical framework for DOM molecular dynamics in aquatic and other ecosystems.

Mechanisms shaping dissolved organic matter and microbial community in lake ecosystems

Lakes are active components of the global carbon cycle and host a range of processes that degrade and modify dissolved organic matter (DOM). Through the degradation of DOM molecules and the synthesis of new compounds, microbes in aquatic environments strongly and continuously influence chemodiversity, which can feedback to influence microbial diversity. Developing a better understanding of the biodiversity patterns that emerge along spatial and environmental gradients is one of the key objectives of community ecology. A changing climate may affect ecological feedback, including those that affect microbial communities. To maintain the function of a lake ecosystem and predict carbon cycling in the environment, it is increasingly important to understand the coupling between microbial and DOM diversity. To unravel the biotic and abiotic mechanisms that control the structure and patterns of DOM and microbial communities in lakes, we combined high-throughput sequencing and ultra-high resolution mass spectrometry together with a null modeling approach. The advantage of null models is their ability to evaluate the relative influences of stochastic and deterministic assembly processes in both DOM and microbial community assemblages. The present study includes spatiotemporal signatures of DOM and the microbial community in six temperate lakes contrasting continental and Mediterranean climates during the productive season. Different environmental conditions and nutrient sources characterized the studied lakes. Our results have shown high covariance between molecular-level DOM diversity and the diversity of individual microbial communities especially with diversity of microeukaryotes and free-living bacteria indicating their dynamic feedback. We found that the differences between lakes and climatic regions were mainly reflected in the diversity of DOM at the molecular formula-level and the microeukaryota community. Furthermore, using null models the DOM assembly was governed by deterministic variable selection operating consistently and strongly within and among lakes. In contrast, microbial community assembly processes were highly variable across lakes with different trophic status and climatic regions. Difference in the processes governing DOM and microbial composition does not indicate weak coupling between these components, rather it suggests that distinct factors may be influencing microbial communities and DOM assemblages separately. Further understanding of the DOM-microbe coupling (or lack thereof) is key to formulating predictive models of future lake ecology and function.

Chemodiversity of Dissolved Organic Matter Is Governed by Microbial Biogeography in Inland Waters

Dissolved organic matter (DOM) is crucial for the carbon biogeochemical cycle and has a close link with microbiome in aquatic ecosystems; however, the causal relationship between DOM and microbial diversity in inland waters is not very clear so far. Therefore, a national survey of China's inland waters was conducted, and the DOM chemical composition and microbial community composition were determined by Fourier transform ion cyclotron resonance mass spectrometry and high-throughput sequencing to clarify the abovementioned question. Here, we found that DOM chemodiversity was governed by microbial community assembly in inland waters, not vice versa. Under the control of microbial biogeography, DOM chemodiversity showed a clear geographical distribution difference. Water DOM chemodiversity was mainly constrained by bacterial and archaeal community composition, whereas sediment DOM chemodiversity was mainly controlled by eukaryotic and fungal community composition. In addition, the sediment DOM chemical composition was also affected by the interaction of different microbial groups between waters and sediments. The study is the first to clarify the causal relationship and proposes a microbial regulatory mechanism on the geographical distribution pattern of DOM chemodiversity, thus further deepening the understanding of the DOM biogeochemical cycle.

Changes of Soil Dissolved Organic Matter and Its Relationship with Microbial Community along the Hailuogou Glacier Forefield Chronosequence

Glacier-retreated areas are ideal areas to study soil biogeochemical processes during vegetation succession, because of the limited effect of other environmental and climatic factors. In this study, the changes of soil dissolved organic matter (DOM) and its relationship with microbial communities along the Hailuogou Glacier forefield chronosequence were investigated. Both microbial diversity and DOM molecular chemodiversity recovered rapidly at the initial stage, indicating the pioneering role of microorganisms in soil formation and development. The chemical stability of soil organic matter enhanced with vegetation succession due to the retaining of compounds with high oxidation state and aromaticity. The molecular composition of DOM affected microbial communities, while microorganisms tended to utilize labile components to form refractory components. This complex relationship network between microorganisms and DOM components played an important role in the development of soil organic matter as well as the formation of stable soil carbon pool in glacier-retreated areas.

Dark Matter Enhances Interactions within Both Microbes and Dissolved Organic Matter under Global Change

There are vast but uncharacterized microbial taxa and chemical metabolites (that is, dark matter) across the Earth's ecosystems. A lack of knowledge about dark matter hinders a complete understanding of microbial ecology and biogeochemical cycles. Here, we examine sediment bacteria and dissolved organic matter (DOM) in 300 microcosms along experimental global change gradients in subtropical and subarctic climate zones of China and Norway, respectively. We develop an indicator to quantify the importance of dark matter by comparing co-occurrence network patterns with and without dark matter in bacterial or DOM assemblages. In both climate zones, dark matter constitutes approximately 30-56% of bacterial taxa and DOM metabolites and changes connectivity within bacterial and DOM assemblages by between -15.5 and +61.8%. Dark matter is generally more important for changing network connectivity within DOM assemblages than those of microbes, especially in the subtropical zone. However, the importance of dark matter along global change gradients is strongly correlated between bacteria and DOM and consistently increased toward higher primary productivity because of increasing temperatures and nutrient enrichment. Our findings highlight the importance of microbial and chemical dark matter for changing biogeochemical interactions under global change.

Deciphering the Fingerprint of Dissolved Organic Matter in the Soil Amended with Biodegradable and Conventional Microplastics Based on Optical and Molecular Signatures

Biodegradable polymers are promoted as promising alternatives for conventional non-degradable plastics, but they may also negatively impact soil ecosystems. Here, we estimated the effects of biodegradable (polylactide (PLA) and polybutylene succinate (PBS)) and non-biodegradable (polyethylene (PE) and polystyrene (PS)) microplastics at a concentration of 1% (w/w) on dissolved organic matter (DOM) in two soil types, a black soil (BS) and a yellow soil (YS), by using fluorescence excitation-emission matrix spectroscopy and ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). PBS significantly increased the contents of soil dissolved organic carbon (DOC) and the relative intensities of protein-like components. The turnover rates of soil DOM were statistically higher in PBS treatments (0.106 and 0.196, p < 0.001) than those in other microplastic groups. The FT-ICR-MS results indicated that more labile-active DOM molecules were preferentially obtained in biodegradable microplastic treatments, which may be attributed to the polymer degradation. The conventional microplastics showed no significant effects on the optical characteristics but changed the molecular compositions of the soil DOM. More labile DOM molecules were observed in BS samples treated with PE compared to the control, while the conventional microplastics decreased the DOM lability in YS soil. The distinct priming effects of plastic-leached DOM may trigger the DOM changes in different soils. This study provided important information for further understanding the impact of microplastics on soil carbon processes.

Groundwater metabolome responds to recharge in fractured sedimentary strata

Understanding the sources, structure and fate of dissolved organic matter (DOM) in groundwater is paramount for the protection and sustainable use of this vital resource. On its passage through the Critical Zone, DOM is subject to biogeochemical conversions. Therefore, it carries valuable cross-habitat information for monitoring and predicting the stability of groundwater ecosystem services and assessing these ecosystems' response to fluctuations caused by external impacts such as climatic extremes. Challenges arise from insufficient knowledge on groundwater metabolite composition and dynamics due to a lack of consistent analytical approaches for long-term monitoring. Our study establishes groundwater metabolomics to decipher the complex biogeochemical transport and conversion of DOM. We explore fractured sedimentary bedrock along a hillslope recharge area by a 5-year untargeted metabolomics monitoring of oxic perched and anoxic phreatic groundwater. A summer with extremely high temperatures and low precipitation was included in the monitoring. Water was accessed by a monitoring well-transect and regularly collected for liquid chromatography-mass spectrometry (LC-MS) investigation. Dimension reduction of the resulting complex data set by principal component analysis revealed that metabolome dissimilarities between distant wells coincide with transient cross-stratal flow indicated by groundwater levels. Time series of the groundwater metabolome data provides detailed insights into subsurface responses to recharge dynamics. We demonstrate that dissimilarity variability between groundwater bodies with contrasting aquifer properties coincides with recharge dynamics. This includes groundwater high- and lowstands as well as recharge and recession phases. Our monitoring approach allows to survey groundwater ecosystems even under extreme conditions. Notably, the metabolome was highly variable lacking seasonal patterns and did not segregate by geographical location of sampling wells, thus ruling out vegetation or (agricultural) land use as a primary driving factor. Patterns that emerge from metabolomics monitoring give insight into subsurface ecosystem functioning and water quality evolution, essential for sustainable groundwater use and climate change-adapted management.

Using Potential Molecular Transformation To Understand the Molecular Trade-Offs in Soil Dissolved Organic Matter

Understanding the chemical composition and molecular transformation in soil dissolved organic matter (DOM) is important to the global carbon cycle. To address this issue, ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) was applied to investigate DOM molecules in 36 paddy soils collected from subtropical China. All the detected 7576 unique molecules were divided into seven compound groups, and nine trade-off relationships between different compound groups were revealed based on principal component analysis and Pearson's correlation. An optimized method was developed to evaluate all potential molecular transformations in DOM samples. The concept of thermodynamics was introduced to evaluate the identified molecular transformations and classify them as thermodynamically favorable (TFP) and thermodynamically limited (TLP) processes. Here, we first tried to understand the molecular trade-offs by using the potential molecular transformations. All the nine trade-offs could be explained by molecular transformations. Six trade-offs had bases of biochemical reactions, and the trade-off-related direct transformations could explain the content variations of carbohydrate-like, condensed aromatic-like, tannin-like, and lignin-like compounds in TLP. More reasonable explanations existed in the TLP rather than TFP, which demonstrated the critical role of external energy in the molecular transformation of soil DOM.

Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data

Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical barriers to the wider adoption of this technology. To help the user community overcome these barriers, we have made major updates to the well-established MetaboAnalyst platform ( www.metaboanalyst.ca ). This protocol extends the previous 2011 Nature Protocol by providing stepwise instructions on how to use MetaboAnalyst 5.0 to: optimize parameters for LC-HRMS spectra processing; obtain functional insights from peak list data; integrate metabolomics data with transcriptomics data or combine multiple metabolomics datasets; conduct exploratory statistical analysis with complex metadata. Parameter optimization may take ~2 h to complete depending on the server load, and the remaining three stages may be executed in ~60 min.

Microbial and Environmental Processes Shape the Link between Organic Matter Functional Traits and Composition

Dissolved organic matter (DOM) is a large and complex mixture of molecules that fuels microbial metabolism and regulates biogeochemical cycles. Individual DOM molecules have unique functional traits, but how their assemblages vary deterministically under global change remains poorly understood. Here, we examine DOM and associated bacteria in 300 aquatic microcosms deployed on mountainsides that span contrasting temperatures and nutrient gradients. Based on molecular trait dimensions of reactivity and activity, we partition the DOM composition into labile-active, recalcitrant-active, recalcitrant-inactive, and labile-inactive fractions and quantify the relative influences of deterministic and stochastic processes governing the assembly of each. At both subtropical and subarctic study sites, the assembly of labile or recalcitrant molecules in active fractions is primarily governed by deterministic processes, while stochastic processes are more important for the assembly of molecules within inactive fractions. Surprisingly, the importance of deterministic selection increases with global change gradients for recalcitrant molecules in both active and inactive fractions, and this trend is paralleled by changes in the deterministic assembly of microbial communities and environmental filtering, respectively. Together, our results highlight the shift in focus from potential reactivity to realized activity and indicate that active and inactive fractions of DOM assemblages are structured by contrasting processes, and their recalcitrant components are consistently sensitive to global change. Our study partitions the DOM molecular composition across functional traits and links DOM with microbes via a shared ecological framework of assembly processes. This integrated approach opens new avenues to understand the assembly and turnover of organic carbon in a changing world.

Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems

BACKGROUND

Rhizodeposits regulate rhizosphere interactions, processes, nutrient and energy flow, and plant-microbe communication and thus play a vital role in maintaining soil and plant health. However, it remains unclear whether and how alteration in belowground carbon allocation and chemodiversity of rhizodeposits influences microbiome functioning in the rhizosphere ecosystems. To address this research gap, we investigated the relationship of rhizosphere carbon allocation and chemodiversity with microbiome biodiversity and functioning during peanut (Arachis hypogaea) continuous mono-cropping. After continuously labeling plants with ¹³CO₂, we studied the chemodiversity and composition of rhizodeposits, along with the composition and diversity of active rhizosphere microbiome using metabolomic, amplicon, and shotgun metagenomic sequencing approaches based on DNA stable-isotope probing (DNA-SIP).

RESULTS

Our results indicated that enrichment and depletion of rhizodeposits and active microbial taxa varied across plant growth stages and cropping durations. Specifically, a gradual decrease in the rhizosphere carbon allocation, chemodiversity, biodiversity and abundance of plant-beneficial taxa (such as Gemmatimonas, Streptomyces, Ramlibacter, and Lysobacter), and functional gene pathways (such as quorum sensing and biosynthesis of antibiotics) was observed with years of mono-cropping. We detected significant and strong correlations between rhizodeposits and rhizosphere microbiome biodiversity and functioning, though these were regulated by different ecological processes. For instance, rhizodeposits and active bacterial communities were mainly governed by deterministic and stochastic processes, respectively. Overall, the reduction in carbon deposition and chemodiversity during peanut continuous mono-cropping tended to suppress microbial biodiversity and its functions in the rhizosphere ecosystem.

CONCLUSIONS

Our results, for the first time, provide the evidence underlying the mechanism of rhizosphere microbiome malfunctioning in mono-cropped systems. Our study opens new avenues to deeply disentangle the complex plant-microbe interactions from the perspective of rhizodeposits chemodiversity and composition and will serve to guide future microbiome research for improving the functioning and services of soil ecosystems. Video abstract.

Ecological networks of dissolved organic matter and microorganisms under global change

Microbes regulate the composition and turnover of organic matter. Here we developed a framework called Energy-Diversity-Trait integrative Analysis to quantify how dissolved organic matter and microbes interact along global change drivers of temperature and nutrient enrichment. Negative and positive interactions suggest decomposition and production processes of organic matter, respectively. We applied this framework to manipulative field experiments on mountainsides in subarctic and subtropical climates. In both climates, negative interactions of bipartite networks were more specialized than positive interactions, showing fewer interactions between chemical molecules and bacterial taxa. Nutrient enrichment promoted specialization of positive interactions, but decreased specialization of negative interactions, indicating that organic matter was more vulnerable to decomposition by a greater range of bacteria, particularly at warmer temperatures in the subtropical climate. These two global change drivers influenced specialization of negative interactions most strongly via molecular traits, while molecular traits and bacterial diversity similarly affected specialization of positive interactions.

Microbes are intimately linked with the fate of organic matter. Here the authors develop an ecological network framework and show how microbes and dissolved organic matter interact along global change drivers of temperature and nutrient enrichment via manipulative field experiments on mountains.

Bulk and Spatially Resolved Extracellular Metabolome of Free-Living Nitrogen Fixation

Soil nitrogen (N) transformations constrain terrestrial net primary productivity and are driven by the activity of soil microorganisms. Free-living N fixation (FLNF) is an important soil N transformation and key N input to terrestrial systems, but the forms of N contributed to soil by FLNF are poorly understood. To address this knowledge gap, a focus on microorganisms and microbial scale processes is needed that links N-fixing bacteria and their contributed N sources to FLNF process rates. However, studying the activity of soil microorganisms in situ poses inherent challenges, including differences in sampling scale between microorganism and process rates, which can be addressed with culture-based studies and an emphasis on microbial-scale measurements. Culture conditions can differ significantly from soil conditions, so it also important that such studies include multiple culture conditions like liquid and solid media as proxies for soil environments like soil pore water and soil aggregate surfaces. Here we characterized extracellular N-containing metabolites produced by two common, diazotrophic soil bacteria in liquid and solid media, with or without N, across two sampling scales (bulk via GC-MS and spatially resolved via MALDI mass spec imaging). We found extracellular production of inorganic and organic N during FLNF, indicating terrestrial N contributions from FLNF occur in multiple forms not only as ammonium as previously thought. Extracellular metabolite profiles differed between liquid and solid media supporting previous work indicating environmental structure influences microbial function. Metabolite profiles also differed between sampling scales underscoring the need to quantify microbial scale conditions to accurately interpret microbial function.

IMPORTANCE Free-living nitrogen-fixing bacteria contribute significantly to terrestrial nitrogen availability; however, the forms of nitrogen contributed by this process are poorly understood. This is in part because of inherent challenges to studying soil microorganisms in situ, such as vast differences in scale between microorganism and ecosystem and complexities of the soil system (e.g., opacity, chemical complexity). Thus, upscaling important ecosystem processes driven by soil microorganisms, like free-living nitrogen fixation, requires microbial-scale measurements in controlled systems. Our work generated bulk and spatially resolved measurements of nitrogen released during free-living nitrogen fixation under two contrasting growth conditions analogous to soil pores and aggregates. This work allowed us to determine that diverse forms of nitrogen are likely contributed to terrestrial systems by free-living nitrogen bacteria. We also demonstrated that microbial habitat (e.g., liquid versus solid media) alters microbial activity and that measurement of microbial activity is altered by sampling scale (e.g., bulk versus spatially resolved) highlighting the critical importance of quantifying microbial-scale processes to upscaling of ecosystem function.

Implications of sample treatment on characterization of riverine dissolved organic matter

High-resolution mass spectrometry techniques are widely used in the environmental sciences to characterize natural organic matter and, when utilizing these instruments, researchers must make multiple decisions regarding sample pre-treatment and the instrument ionization mode. To identify how these choices alter organic matter characterization and resulting conclusions, we analyzed a collection of 17 riverine samples from East River, CO (USA) under four PPL-based Solid Phase Extraction (SPE) treatment and electrospray ionization polarity (e.g., positive and negative) combinations: SPE (+), SPE (-), non-SPE (-), and non-SPE (+). The greatest number of formula assignments were achieved with SPE-treated samples due to the removal of compounds that could interfere with ionization. Furthermore, the SPE (-) treatment captured the most formulas across the widest chemical compound diversity. In addition to a reduced number of assigned formulas, the non-SPE datasets resulted in altered thermodynamic interpretations that could cascade into incomplete assumptions about the availability of organic matter pools for heterotrophic microbial respiration. Thus, we infer that the SPE (-) treatment is the best single method for characterizing environmental organic matter pools unless the focus is on lipid-like compounds, in which case we recommend a combination of SPE (-) and SPE (+) to adequately characterize these molecules.

Stabilizing microbial communities by looped mass transfer

Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates μ′. Subsets of cells that did not show net growth μ′SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.

Niche differentiation drives microbial community assembly and succession in full-scale activated sludge bioreactors

Network models and community phylogenetic analyses are applied to assess the composition, structure, and ecological assembly mechanisms of microbial communities. Here we combine both approaches to investigate the temporal dynamics of network properties in individual samples of two activated sludge systems at different adaptation stages. At initial assembly stages, we observed microbial communities adapting to activated sludge, with an increase in network modularity and co-exclusion proportion, and a decrease in network clustering, here interpreted as a consequence of niche specialization. The selective pressure of deterministic factors at wastewater treatment plants produces this trend and maintains the structure of highly functional and specialized communities responding to seasonal environmental changes.

Metabolomics insight into the influence of environmental factors in responses of freshwater biofilms to the model herbicide diuron

Freshwater biofilms have been increasingly used during the last decade in ecotoxicology due to their ecological relevance to assess the effect(s) of environmental stress at the community level. Despite growing knowledge about the effect of various stressors on the structure and the function of these microbial communities, a strong research effort is still required to better understand their response to chemical stress and the influence of environmental stressors in this response. To tackle this challenge, untargeted metabolomics is an approach of choice because of its capacity to give an integrative picture of the exposure to multiple stress and associated effect as well as identifying the molecular pathways involved in these responses. In this context, the present study aimed to explore the use of an untargeted metabolomics approach to unravel at the molecular/biochemical level the response of the whole biofilm to chemical stress and the influence of various environmental factors in this response. To this end, archived high-resolution mass spectrometry data from previous experiments at our laboratory on the effect of the model photosynthesis inhibitor diuron on freshwater biofilm were investigated by using innovative solutions for OMICs data (e.g., DRomics) and more usual chemometric approaches (multivariate and univariate statistical analyses). The results showed a faster (1 min) and more sensitive response of the metabolome to diuron than usual functional descriptors, including photosynthesis. Also, the metabolomics response to diuron resulted from metabolites following various trends (increasing, decreasing, U/bell shape) along increasing concentration and time. This metabolomics response was influenced by the temperature, photoperiod, and flow. A focus on a plant-specific omega-3 (eicosapentaenoic acid) playing a key role in the trophic chain highlighted the potential relevance of metabolomics approach to establish the link between molecular alteration and ecosystem structure/functioning impairment but also how complex is the response and the influence of all the tested factors on this response at the metabolomics level. Altogether, our results underline that more fundamental researches are needed to decipher the metabolomics response of freshwater biofilm to chemical stress and its link with physiological, structural, and functional responses toward the unraveling of adverse outcome pathways (AOP) for key ecosystem functions (e.g., primary production).

Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly

Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTI_feat), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTI_feat, we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTI_feat can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTI_feat values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTI_feat offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.

Functional metabolome profiling may improve individual outcomes in colorectal cancer management implementing concepts of predictive, preventive, and personalized medical approach

Objectives

Colorectal cancer (CRC) is one of the most common solid tumors worldwide, but its diagnosis and treatment are limited. The objectives of our study were to compare the metabolic differences between CRC patients and healthy controls (HC), and to identify potential biomarkers in the serum that can be used for early diagnosis and as effective therapeutic targets. The aim was to provide a new direction for CRC predictive, preventive, and personalized medicine (PPPM).

Methods

In this study, CRC patients (n = 30) and HC (n = 30) were recruited. Serum metabolites were assayed using an ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) technology. Subsequently, CRC cell lines (HCT116 and HCT8) were treated with metabolites to verify their function. Key targets were identified by molecular docking, thermal shift assay, and protein overexpression/inhibition experiments. The inhibitory effect of celastrol on tumor growth was also assessed, which included IC50 analysis, nude mice xenografting, molecular docking, protein overexpression/inhibition experiments, and network pharmacology technology.

Results

In the CRC group, 15 serum metabolites were significantly different in comparison with the HC group. The level of glycodeoxycholic acid (GDCA) was positively correlated with CRC and showed high sensitivity and specificity for the clinical diagnostic reference (AUC = 0.825). In vitro findings showed that GDCA promoted the proliferation and migration of CRC cell lines (HCT116 and HCT8), and Poly(ADP-ribose) polymerase-1 (PARP-1) was identified as one of the key targets of GDCA. The IC50 of celastrol in HCT116 cells was 121.1 nM, and the anticancer effect of celastrol was supported by in vivo experiments. Based on the potential of GDCA in PPPM, PARP-1 was found to be significantly correlated with the anticancer functions of celastrol.

Conclusion

These findings suggest that GDCA is an abnormally produced metabolite of CRC, which may provide an innovative molecular biomarker for the predictive identification and targeted prevention of CRC. In addition, PARP-1 was found to be an important target of GDCA that promotes CRC; therefore, celastrol may be a potential targeted therapy for CRC via its effects on PARP-1. Taken together, the pathophysiology and progress of tumor molecules mediated by changes in metabolite content provide a new perspective for predictive, preventive, and personalized medical of clinical cancer patients based on the target of metabolites in vivo.Clinical trials registration number: ChiCTR2000039410.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-021-00269-8.

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing

BACKGROUND

Sequential membrane filtration as a pre-processing step for capturing sediment-associated microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques. However, the effects of sample pre-processing via filtration on DNA-based profiling of sediment-associated microbial community diversity and composition are poorly understood. Specifically, the influences of pre-processing on the quality and quantity of extracted DNA, high-throughput DNA sequencing reads, and detected microbial taxa need further evaluation.

RESULTS

We assessed the impact of pre-processing freshwater sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size) for 16S rRNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the qualities and quantities of extracted DNA and PCR amplicons, and the read abundance after bioinformatics processing (i.e., denoising and chimeric-read filtering steps) between the two methods. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods' absolute read abundance. More so, at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition.

CONCLUSIONS

Our observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.

Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties

Stream and river systems transport and process substantial amounts of dissolved organic matter (DOM) from terrestrial and aquatic sources to the ocean, with global biogeochemical implications. However, the underlying mechanisms affecting the spatiotemporal organization of DOM composition are under-investigated. To understand the principles governing DOM composition, we leverage the recently proposed synthesis of metacommunity ecology and metabolomics, termed 'meta-metabolome ecology.' Applying this novel approach to a freshwater ecosystem, we demonstrated that despite similar molecular properties across metabolomes, metabolite identity significantly diverged due to environmental filtering and variations in putative biochemical transformations. We refer to this phenomenon as 'thermodynamic redundancy,' which is analogous to the ecological concept of functional redundancy. We suggest that under thermodynamic redundancy, divergent metabolomes can support equivalent biogeochemical function just as divergent ecological communities can support equivalent ecosystem function. As these analyses are performed in additional ecosystems, potentially generalizable concepts, like thermodynamic redundancy, can be revealed and provide insight into DOM dynamics.

Analysis of Sour Porridge Microbiota and Improvement of Cooking Quality via Pure Culture Fermentation Using Lacticaseibacillus paracasei Strain SZ02

The microbial composition of sour porridge at different fermentation times was analyzed through high-throughput sequencing, and a pure culture fermentation process was established to optimize production process and improve the edible quality of the porridge. In natural fermentation, Firmicutes and Proteobacteria were abundant throughout the process. Specifically, Aeromonas, Acinetobacter, and Klebsiella were dominant on fermentation days 1–5 (groups NF-1, NF-3, and NF-5), while Lactobacillus and Acetobacter gradually became the dominant bacteria on fermentation day 7 (group NF-7). Further, we isolated one strain of acid-producing bacteria from sour porridge, identified as Lacticaseibacillus paracasei by 16SrRNA sequencing and annotated as strain SZ02. Pure culture fermentation using this strain significantly increased the relative starch and amylose contents of the porridge, while decreasing the lipid, protein, and ash contents (P < 0.05). These findings suggest that sour porridge produced using strain SZ02 has superior edible qualities and this strategy may be exploited for its industrial production.

Identification of novel 1,4-dioxane degraders and related genes from activated sludge by taxonomic and functional gene sequence analysis

This study used integrated omics technologies to investigate the potential novel pathways and enzymes for 1,4-dioxane degradation by a consortium enriched from activated sludge of a domestic wastewater treatment plant. An unclassified genus belonging to Xanthobacteraceae increased significantly after magnetic nanoparticle-mediated isolation for 1,4-dioxane degraders. Species with relatively higher abundance (> 0.3%) were identified to present high metabolic activities in the biodegradation process through shotgun sequencing. The functional gene investigations revealed that Xanthobacter sp. 91, Xanthobacter sp. 126, and a Rhizobiales strain carried novel 1,4-dioxane-hydroxylating monooxygenase genes. Xanthobacter sp. 126 contained the genes coding for glycolate oxidase, which was the main enzyme responsible for utilization of 1,4-dioxane intermediates through the TCA cycle, and further proven by the specific glycolate oxidase inhibitor, α-hydroxy-2-pyridinemethanesulfonic acid. An expanded and detailed degradation pathway of 1,4-dioxane was proposed on the basis of the three major intermediates (2-hydroxy-1,4-dioxane, ethylene glycol, and oxalic acid) confirmed by metabolomics. These findings of microbial community and function as well as the novel pathway will be valuable in predicting natural attenuation or reconstruction of a bacterial consortium for enhanced remediation of 1,4-dioxane-contaminated sites as well as wastewater treatment.

Seeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell

Synthetic metagenomics could potentially unravel the complexities of microbial ecosystems by revealing the simplicity of microbial communities captured in a single cell. Conceptionally, a yeast cell carrying a representative synthetic metagenome could uncover the complexity of multi-species interactions, illustrated here with wine ferments.