Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system

Interactions between riverine sediment organic matter molecular structure and microbial community as regulated by heavy metals

Heavy metals (HMs) exert a profound influence on soil carbon storage potential. The microbially-mediated association between HM content and carbon structure in riverine sediments remains unclear in lotic ecosystems. We investigated the spatiotemporal variations of HMs content, carbon content and microbial communities in riverine surface sediments, and further explored the chemical structure of sediment organic carbon (OCsed), the molecular composition of dissolved organic matter (DOM), and their interactions with microorganisms. The spatial-temporal variations in the chemical structure of OCsed, excluding O-alkyl C, were minimal, whereas the molecular composition of DOM underwent substantial fluctuations with seasons and sites. Significantly positive correlations were observed between Cu, Zn, Pb, and OCsed content. However, within a certain content range, HMs can promote the mineralization risk of OCsed, as reflected in their ability to increase the proportion of unstable O-alkyl C and decrease the proportion of stable carbon fractions (aromatic C, alkyl C, and phenolic C). Additionally, appropriate contents of HMs also improved the abundance and diversity of bacteria and fungi. Bacteria consumed more stable OC under HMs enrichment, whereas fungi increased the consumption of DOM fractions (condensed aromatic hydrocarbons and amino sugars). Our findings contribute to the understanding of the molecular mechanisms of carbon storage in HM-rich riverine sediments.

Effects of DOM Chemodiversity on Microbial Diversity in Forest Soils on a Continental Scale

Soil dissolved organic matter (DOM) is a critical reservoir of carbon and nutrients in forest ecosystems, playing a central role in carbon cycling and microbial community dynamics. However, the influence of DOM molecular-level diversity (chemodiversity) on microbial community diversity and spatial distribution remains poorly understood. In this study, we used Fourier transform ion cyclotron resonance mass spectrometry and high-throughput sequencing to analyze soil DOM and microbial diversity along a ~4,000 km forest transect in China. We found that soil DOM chemodiversity varies significantly across sites, initially increasing and then decreasing with latitude. Additionally, we observed that the biogeographic distribution of DOM components has differential effects on bacterial and fungal diversity: lipid-like compounds are strongly associated with bacterial diversity, while aromatic-, carbohydrate-, and lipid-like compounds primarily influence fungal diversity. Linear models and structural equation modeling both reveal that DOM acts as a key intermediary, mediating the effects of temperature and soil properties on microbial spatial distribution. Our findings emphasize the importance of DOM molecular characteristics in shaping microbial community structure and functioning, providing new insights into how environmental factors influence microbial ecosystems and soil carbon cycles in forest ecosystems.

Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential

The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.

Disruptive effects of sewage intrusion into drinking water: Microbial succession and organic transformation at molecular level

Drinking water distribution systems are increasingly vulnerable to sewage intrusion due to aging water infrastructure and intensifying water stress. While the health risks associated with sewage intrusion have been extensively studied, little is known about the impacts of intruded bacteria and dissolved organic matter (DOM) on microbiology in drinking water. In this dynamic study, we demonstrate that the intrusion of 1 % sewage into tap water resulted in immediate contamination, including an 8-fold increase in biomass (TCC), a 48.9 % increase in bacterial species (ASVs), a 12.5 % increase in organic carbon content (DOC), and a 13.5 % increase in unique DOM molecular formulae. Over time, sewage intrusion altered tap water microbiology by accelerating bacterial growth rates (5-fold faster), selectively promoting ASVs in community succession, and producing 998 more unique DOM formulae. More significantly, statistical analysis revealed that the intrusion of 1 % sewage shifted the driving force of bacterial and DOM composition covariance from a DOM-dependent process in tap water to a bacterial-governed process post-intrusion. Our results clearly demonstrate the disruptive effects of sewage intrusion into tap water, emphasizing the urgent need to consider the long-lasting impacts of sewage intrusion in drinking water distribution systems, in addition to its immediate health risks.

Organic matter composition fluctuations disrupt free-living bacterial communities more than particle-associated bacterial communities in coastal waters

Marine organic matter fuels the growth of microbial communities, shaping the composition of bacteria that specialize in its breakdown. However, responses of free-living (FL) and particle-associated (PA) bacterial communities to the changing pools of dissolved organic matter (DOM) and particulate organic matter (POM) remained unclear. This study investigates the composition of size-fractionated bacterial communities, DOM and POM in coastal waters over a 22-day period that includes a diatom bloom. Co-occurrence analysis showed that the FL bacterial communities were significantly less stable than PA communities. During the diatom bloom, we observed a significant increase in DOM molecules, particularly those derived from amino acids and peptides. In contrast, the relative intensities of major POM molecule classes remained stable despite the algal bloom's influence. Our study revealed a strong negative correlation between bacterial alpha-diversity and the amount of molecules in the organic matter pool. Similarly, bacterial community beta-diversity was found to be related to the composition of organic matter pool. However, the composition of organic matter was more strongly related to the composition of FL bacterial communities compared to PA communities. This suggests that FL bacteria exhibit greater variations in temporal dynamics and higher sensitivity to the specific structure of organic matter molecules.

Long-Term Photochemical and Microbial Alterations Lead to the Compositional Convergence of Algal and Terrestrial Dissolved Organic Matter

Lakes are expected to become more active in processing dissolved organic matter (DOM), but the fate of DOM with different origins remains poorly constrained. We conducted long-term incubation experiments (∼1 year) with sole light, sole microbial, and combined light and microbial treatments using DOM from algal and terrestrial sources (DOMa and DOMt, respectively). Fourier transform ion cyclotron resonance mass spectrometry and 16s rRNA were used to analyze the DOM molecular composition and bacterial community, respectively. We observed that DOMa and DOMt converged toward a similar composition under the combined light and microbial treatment, driven by the removal of source-specific compositions along with the production of refractory, carboxylic-rich alicyclic molecules (CRAM). For CRAM enrichment, microbial processes played a greater role for DOMa, while phototransformation was more important for DOMt. The co-occurrence patterns between DOM molecules and bacteria showed that DOM molecular composition influenced the bacterial community. More complex DOM-bacteria interactions were observed for DOMt compared to DOMa, suggesting that greater bacterial cooperation was necessary for transforming DOMt. Collectively, these findings offer new insights into the mechanisms underlying the uniformity of DOM from various sources through prolonged environmental transformations in lakes.

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.

The Hunt for Chemical Dark Matter across a River-to-Ocean Continuum

Thousands of mass peaks emerge during molecular characterization of natural dissolved organic matter (DOM) using ultrahigh-resolution mass spectrometry. While mass peaks assigned to certain molecular formulas have been extensively studied, the uncharacterized mass peaks that represent a significant fraction of organic matter and convey biogenic elements and energy have been previously ignored. In this study, we introduce the term dark DOM (DDOM) for unassigned mass peaks and have explored its characteristics and environmental behaviors using a data set of 38 DOM extracts covering the Yangtze River-to-ocean continuum. We identified a total of 9141 DDOM molecules, which exhibited higher molecular weight and greater diversity than the DOM subset with assigned DOM formulas. Although DDOM contributed a smaller fraction of relative abundance, it significantly impacted the molecular weight and molecular composition of bulk DOM. A portion of DDOM with higher molecular weight was found to increase molecular abundance across the river-to-ocean continuum. These compounds could contain halogenated organic molecules and might have a high potential to contribute to the refractory organic carbon pool. With this study, we underline the contribution of dark matter to the total DOM pool and emphasize that more DDOM research is needed to understand its contribution to global biogeochemical cycles and carbon sequestration.

The microbial carbon pump and climate change

The ocean has been a regulator of climate change throughout the history of Earth. One key mechanism is the mediation of the carbon reservoir by refractory dissolved organic carbon (RDOC), which can either be stored in the water column for centuries or released back into the atmosphere as CO2 depending on the conditions. The RDOC is produced through a myriad of microbial metabolic and ecological processes known as the microbial carbon pump (MCP). Here, we review recent research advances in processes related to the MCP, including the distribution patterns and molecular composition of RDOC, links between the complexity of RDOC compounds and microbial diversity, MCP-driven carbon cycles across time and space, and responses of the MCP to a changing climate. We identify knowledge gaps and future research directions in the role of the MCP, particularly as a key component in integrated approaches combining the mechanisms of the biological and abiotic carbon pumps for ocean negative carbon emissions.

Spatial distribution characteristics and interaction effects of DOM and microbial communities in kelp cultivation areas

The influence of macroalgae cultivation on aquaculture carbon sinks is significant, with microbial carbon (C) pumps contributing to a stable inert dissolved carbon pool in this context. Concurrently, dissolved organic matter (DOM) exchange at the marine sediment-water interface profoundly affects global ecosystem element cycling. However, the interactions between DOM and bacterial communities at the sediment-water interface in kelp cultivation areas, especially regarding microbial function prediction, have not been fully explored. This study analyzed the DOM characteristics, environmental factors, and bacterial community structure in the Tahewan kelp--Saccharina japonica cultivated area and compared them with those in non-cultivated areas. The results indicated significantly higher dissolved organic carbon (DOC) concentrations in the kelp culture area, particularly in surface seawater and overlying water. The dominant bacterial phyla in both regions included Pseudomonadota, Actinomycetota, and Bacteroidota in both regions, while Desulfobacterota was more prevalent in the sediment environment of the cultivated region. Parallel factor analysis (EEM-PARAFAC) was used to identify DOM components, among which component C2 (a microbial humic-like substance DOM) was highly resistant to microbial degradation. We infer that C2 has similar properties to recalcitrant dissolved organic matter (RDOM). Analysis of the predicted functional genes based on 16S rRNA gene data showed that methanol oxidation, methylotrophy, and methanotrophy were significant in the bottom seawater of the cultivation area. The carbon (C), nitrogen (N), and sulfur (S) cycle functional genes in the sediment environment of the kelp cultivation area were more active than those in other areas, especially in which sulfate reduction and denitrification were the two main processes. Furthermore, a DOM priming effect was identified in the cultivated sediment environment, where kelp-released labile dissolved organic matter (LDOM) stimulates rapid degradation of the original RDOM, potentially enhancing C sequestration.

Excessive Ozonation Stress Triggers Severe Membrane Biofilm Accumulation and Fouling

The established benefits of ozone on microbial pathogen inactivation, natural organic matter degradation, and inorganic/organic contaminant oxidation have favored its application in drinking water treatment. However, viable bacteria are still present after the ozonation of raw water, bringing a potential risk to membrane filtration systems in terms of biofilm accumulation and fouling. In this study, we shed light on the role of the specific ozone dose (0.5 mg-O3/mg-C) in biofilm accumulation during long-term membrane ultrafiltration. Results demonstrated that ozonation transformed the molecular structure of influent dissolved organic matter (DOM), producing fractions that were highly bioavailable at a specific ozone dose of 0.5, which was inferred to be a turning point. With the increase of the specific ozone dose, the biofilm microbial consortium was substantially shifted, demonstrating a decrease in richness and diversity. Unexpectedly, the opportunistic pathogen Legionella was stimulated and occurred in approximately 40% relative abundance at the higher specific ozone dose of 1. Accordingly, the membrane filtration system with a specific ozone dose of 0.5 presented a lower biofilm thickness, a weaker fluorescence intensity, smaller concentrations of polysaccharides and proteins, and a lower Raman activity, leading to a lower hydraulic resistance, compared to that with a specific ozone dose of 1. Our findings highlight the interaction mechanism between molecular-level DOM composition, biofilm microbial consortium, and membrane filtration performance, which provides an in-depth understanding of the impact of ozonation on biofilm accumulation.

Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis

Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1-C4) in the river, which were predominantly protein- (C1) and humic-like (C2-C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.

Terrestrial dissolved organic matter inputs drive the temporal dynamics of riverine bacterial ecological networks and assembly processes

Rivers receive, transport, and are reactors of terrestrial dissolved organic matter (DOM) and are highly influenced by changes in hydrological conditions and anthropogenic disturbances, but the effect of DOM composition on the dynamics of the bacterial community in rivers is poorly understood. We conducted a seasonal field sampling campaign at two eutrophic river mouth sites to examine how DOM composition influences the temporal dynamics of bacterial community networks, assembly processes, and DOM-bacteria associations. DOM composition and seasonal factors explained 34.7% of the variation in bacterial community composition, and 14.4% was explained purely by DOM composition where specific UV absorbance (SUVA254) as an indicator of aromaticity was the most important predictor. Significant correlations were observed between SUVA254 and the topological features of subnetworks of interspecies and DOM-bacteria associations, indicating that high DOM aromaticity results in more complex and connected networks of bacteria. The bipartite networks between bacterial taxa and DOM molecular formulae (identified by ultrahigh-resolution mass spectrometry) further revealed less specialized bacterial processing of DOM molecular formulae under the conditions of high water level and DOM aromaticity in summer than in winter. A shift in community assembly processes from stronger homogeneous selection in summer to higher stochasticity in winter correlated with changes in DOM composition, and more aromatic DOM was associated with greater similarity in bacterial community composition. Our results highlight the importance of DOM aromaticity as a predictor of the temporal dynamics of riverine bacterial community networks and assembly.

Disentangling Biological Transformations and Photodegradation Processes from Marine Dissolved Organic Matter Composition in the Global Ocean

Dissolved organic matter (DOM) holds the largest amount of organic carbon in the ocean, with most of it residing in the deep for millennia. Specific mechanisms and environmental conditions responsible for its longevity are still unknown. Microbial transformations and photochemical degradation of DOM in the surface layers are two processes that shape its molecular composition. We used molecular data (via Fourier transform ion cyclotron resonance mass spectrometry) from two laboratory experiments that focused on (1) microbial processing of fresh DOM and (2) photodegradation of deep-sea DOM to derive independent process-related molecular indices for biological formation and transformation (Ibio) and photodegradation (Iphoto). Both indices were applied to a global ocean data set of DOM composition. The distributions of Iphoto and Ibio were consistent with increased photodegradation and biological reworking of DOM in sunlit surface waters, and traces of these surface processes were evident at depth. Increased Ibio values in the deep Southern Ocean and South Atlantic implied export of microbially reworked DOM. Photodegraded DOM (increased Iphoto) in the deep subtropical gyres of Atlantic and Pacific oceans suggested advective transport in warm-core eddies. The simultaneous application of Iphoto and Ibio disentangled and assessed two processes that left unique molecular signatures in the global ocean.

Applying fluorescence spectroscopy and DNA pyrosequencing with 2D-COS and co-occurrence network to deconstruct dynamical DOM degradation of air-land-water sources in an urban river

In an urban river, comprehending the interplay between dissolved organic matter (DOM) and atmospheric, terrestrial, and aquatic sources is crucial. This encompassed investigating temporal variations in DOM and its association with the bacterioplankton community to gain profound insights into the biogeochemical dynamics and biodegradability of DOM. DOM was extracted from PM2.5, soil, sediment, bait, and terrestrial/aquatic plant residuals collected along the Wenyuhe River in Beijing, China - a region predominantly supplied with reclaimed water. Subsequently, mixed microbial communities from the river were introduced into DOM samples originating from each source and incubated for 10 days. Principal component analysis (PCA) applied to reassembled excitation-emission matrix (EEM) data revealed two distinct clusters: cluster 1 comprising soil, sediment, and PM2.5 samples; and cluster 2 consisting of bait as well as terrestrial/aquatic plant residuals. According to parallel factor analysis, C1 (microbial humic-like) and C2-C3 (fulvic-like) dominated the DOM from soil, sediment, and PM2.5. These components were continuously degraded during incubation, except for PM2.5. DOM from bait and terrestrial/aquatic plants contained representative components of C6 (phenolic-like) and C7 (tryptophan-like), which underwent extensive decomposition. Interestingly, DOM in PM2.5 contained aliphatic compounds and polycyclic aromatic hydrocarbons (PAHs) but exhibited weak degradation with the complete disappearance of C6 and C7. Rhodococcus was a unique species capable of degrading PAHs, which might be particularly important considering the specificity of PM2.5 pollution. Based on two-dimensional correlation spectroscopy (2D-COS), variations in DOM components such as C6, and C7 were significantly larger compared to those of C1, C2, C3, and C5 (terrestrial humic-like) from bait samples, sediments, and residual terrestrial plants. MW-2D-COS analysis revealed that DOM from bait samples and terrestrial/aquatic plants experienced substantial degradation by the second day while DOM from soil or sediment decomposed mainly on the fourth day. Notably, the decomposition of DOM fractions in PM2.5 occurred throughout the entire four-day period. Co-occurrence network analysis classified sources of DOM into two clusters similar to PCA results: cluster 1 showed significant microbial degradation of fulvic-like compounds while cluster 2 demonstrated deep microbial decomposition of tyrosine-like and phenolic compounds. Therefore, the artificial loading of DOM into rivers not only expands the chemical diversity within DOM but also perturbs bacterioplankton diversities.

Soil microbial community, dissolved organic matter and nutrient cycling interactions change along an elevation gradient in subtropical China

To identify possible dominating processes involved in soil microbial community assembly, dissolved organic matter (DOM) and multi-nutrient cycling (MNC) interactions and contribute to understanding of climate change effects on these important cycles, we investigated the interaction of soil chemistry, DOM components and microbial communities in five vegetation zones - ranging from evergreen broad-leaved forest to alpine meadow - along an elevation gradient of 290-1960 m in the Wuyi Mountains, Fujian Province, China. Soil DOM composition and microbial community assembly were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and Illumina MiSeq high-throughput sequencing, respectively. Sloan's neutral model and the modified stochasticity ratio were used to infer community assembly processes. Key microbial drivers of the soil MNC index were identified from partial least squares path models. Our results showed that soil DOM composition is closely related to the vegetation types along an elevation gradient, the structure and composition of the microbial community, and soil nutrient status. Overall, values of the double bond equivalent (DBE), modified aromaticity index (AImod) increased, and H/C ratio and molecular lability boundary (MLBL) percentage decreased with elevation. Lignins/CRAM-like structures compounds dominated soil DOM in each vegetation type and its relative abundance decreased with elevation. Aliphatic/protein and lipids components also decreased, but the relative abundance of aromatic structures and tannin increased with elevation. The alpha diversity index of soil bacteria gradually decreased with elevation, with deterministic processes dominating the microbial community assembly in the highest elevation zone. Bacterial communities were conducive to the decomposition of labile degradable DOM compounds (H/C ≥ 1.5) at low elevation. In the cooler and wetter conditions at higher-elevation sites the relative abundance of potentially resistant soil DOM components (H/C < 1.5) gradually increased. Microbial community diversity and composition were important predictors of potential soil nutrient cycling. Although higher elevation sites have higher nutrient cycling potential, soil DOM was assessed to be a more stable carbon store, with apparent lower lability and bioavailability than at lower elevation sites. Overall, this study increases understanding of the potential linkage between soil microbial community, multiple nutrient cycling and DOM fate in subtropical mountain ecosystems that can help predict the effect of climate change on soil carbon sequestration and thus inform ecosystem management.

Coupling effect of DOM and microbe on arsenic speciation and bioavailability in tailings soil after the addition of different biologically stabilized sludges

Dissolved organic matter (DOM) and microbes co-mediate the transformation of heavy metals in soil. However, few previous studies have investigated the effects of interaction between DOM and microbes on the transformation and bioavailability of heavy metals in tailings soil at the molecular level after the addition of organic wastes. This study used co-occurrence network analysis based on Fourier-transform ion cyclone resonance mass spectrometry and high-throughput sequencing to investigate the molecular mechanisms of different bio-stabilized sludge addition on arsenic fraction transformation and bioavailability in tailings soil. It was found that sludge amendments decreased the arsenic bioavailable fraction from 3.62% to 1.74% and 1.68% and promoted humification of DOM in soil. The extra inorganic salt ions introduced with sludge desorb the adsorbed As(V) into soil solution. Specifically, bio-stabilized sludge increased the contents of labile compounds that provided nutrients for microbial metabolism and shaped the microbial community composition into a more copiotrophic state, which increased the abundance of As(V)-reducing bacteria and then converted the As(V) into As(III) and precipitated as As₂S₃. This work innovatively explores the transformation mechanisms of As fractions through the perspectives of microbial community and DOM molecular characterization, providing an important basis for the remediation of As-contaminated soil using biosolids.

Dissolved organic matter defines microbial communities during initial soil formation after deglaciation

Ecosystem succession and pedogenesis reshuffle the composition and turnover of dissolved organic matter (DOM) and its interactions with soil microbiome. The changes of these connections are especially intensive during initial pedogenesis, e.g. in young post-glacial areas. The temporal succession and vertical development of DOM effects on microbial community structure remains elusive. Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS), high-throughput sequencing, and molecular ecological networks, we characterized the molecular diversity of water-extractable DOM and identified its links to microbial communities in soil profiles along deglaciation chronosequence (12, 30, 40, 52, 80, and 120 years) in the southeastern Tibetan Plateau. Low-molecular-weight compound content decreased, whereas the mid- and high-molecular-weight compounds increased with succession age and soil depth. This was confirmed by the increase in double bond equivalents and averaged oxygen-to‑carbon ratios (O/C), and decrease in hydrogen-to‑carbon ratios (H/C), which reflect DOM accumulation and stabilization. Microbial community succession shifted towards the dominance of oligotrophic Acidobacteria and saprophytic Mortierellomycota, reflecting the increase of stable DOM components (H/C < 1.5 and wider O/C). Less DOM-bacterial positive networks during the succession reduced specialization of labile DOM production (such as lipid- and protein-like compounds), whereas more DOM-fungal negative networks increased specialization of stable DOM decomposition (such as tannin- and condensed aromatic-like compounds). Consequently, DOM stability is not intrinsic during initial pedogenesis: stable DOM compounds remain after fast bacterial utilization of labile DOM compounds, whereas fungi decompose slowly the remaining DOM pools.

Determinants of Microbial-Derived Dissolved Organic Matter Diversity in Antarctic Lakes

Identifying drivers of the molecular composition of dissolved organic matter (DOM) is essential to understand the global carbon cycle, but an unambiguous interpretation of observed patterns is challenging due to the presence of confounding factors that affect the DOM composition. Here, we show, by combining ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, that the DOM molecular composition varies considerably among 43 lakes in East Antarctica that are isolated from terrestrial inputs and human influence. The DOM composition in these lakes is primarily driven by differences in the degree of photodegradation, sulfurization, and pH. Remarkable molecular beta-diversity of DOM was found that rivals the dissimilarity between DOM of rivers and the deep ocean, which was driven by environmental dissimilarity rather than the spatial distance. Our results emphasize that the extensive molecular diversity of DOM can arise even in one of the most pristine and organic matter source-limited environments on Earth, but at the same time the DOM composition is predictable by environmental variables and the lakes' ecological history.

Molecular Diversity and Biochemical Content in Two Invasive Alien Species: Looking for Chemical Similarities and Bioactivities

The biochemical composition, molecular diversity, and two different bioactivities of Asparagopsis armata and Rugulopteryx okamurae (two alien species with different invasive patterns in the southern Iberian Peninsula) were analyzed through spectrophotometric methods and Fourier transform ion cyclotron mass spectroscopy (FT-ICR-MS). A total of 3042 molecular formulas were identified from the different extracts. The dH2O extracts were the most molecularly different. A. armata presented the highest content of nitrogenous compounds (proteins, CHON) and sulphur content, whereas R. okamurae was rich in carbonated compounds (total carbon, lipids, CHO, and CHOP). Antioxidant capacity and phenolic content were higher in R. okamurae than in A. armata. Antimicrobial activity was detected from both species. A. armata showed capacity to inhibit human and fish pathogens (e.g., Staphylococcus aureus or Vibrio anguillarum), whereas R. okamurae only showed inhibition against human bacteria (Staphylococcus aureus and Cutibacterium acnes). In R. okamurae, molecules with a great number of pharmaceutical activities (e.g., anti-inflammatory or antitumoral), antibacterial, biomaterial, and other utilities were found. The main molecules of A. armata had also pharmaceutical applications (e.g., antimalarian, antithrombotic, anti-inflammatory, or antiarthritis). The valorization of these species can help to counteract the environmental effects of the bioinvasions.

ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction

Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for entire subnetworks. By limiting annotation propagation to only structural classes which are identical for the majority of ion features within a subnetwork, ConCISE maintains a true positive rate greater than 95% across all levels of the ChemOnt hierarchical ontology used by the ClassyFire annotation software (superclass, class, subclass). The ConCISE framework expanded the proportion of reliable and consistent ion feature annotation up to 76%, allowing for improved assessment of the chemo-diversity of dissolved organic matter pools from three complex marine metabolomics datasets comprising dominant reef primary producers, five species of the diatom genus Pseudo-nitzchia, and stromatolite sediment samples.

Experimental Insight into the Enigmatic Persistence of Marine Refractory Dissolved Organic Matter

More than 90% of marine dissolved organic matter (DOM) is biologically recalcitrant. This recalcitrance has been attributed to intrinsically refractory molecules or to low concentrations of molecules, but their relative contributions are a long-standing debate. Characterizing the molecular composition of marine DOM and its bioavailability is critical for understanding this uncertainty. Here, using different sorbents, DOM was solid-phase extracted from coastal, epipelagic, and deep-sea water samples for molecular characterization and was subjected to a 180-day incubation. ¹H nuclear magnetic resonance spectroscopy and ultra-high-resolution mass spectrometry (UHRMS) analyses revealed that all of the DOM extracts contained refractory carboxyl-rich alicyclic molecules, accompanied with minor bio-labile components, for example, carbohydrates. Furthermore, dissolved organic carbon concentration analysis showed that a considerable fraction of the extracted DOM (86-95%) amended in the three seawater samples resisted microbial decomposition throughout the 180-day heterotrophic incubation, even when concentrated threefold. UHRMS analysis revealed that DOM composition remained mostly invariant in the 180-day deep-sea incubations. These results underlined that the dilution and intrinsic recalcitrance hypotheses are not mutually exclusive in explaining the recalcitrance of oceanic DOM, and that the intrinsically refractory DOM likely has a relatively high contribution to the solid-phase extractable DOM in the ocean.

Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea)

Because of their recognized global importance, there is now the urgent need to map diversity and distribution patterns of marine microbial communities. Even if available studies provided some advances in the understanding the biogeographical patterns of marine microbiomes at the global scale, their degree of plasticity at the local scale it is still underexplored, and functional implications still need to be dissected. In this scenario here we provide a synoptical study on the microbiomes of the water column and surface sediments from 19 sites in a 130 km2 area located 13.5 km afar from the coast in the North-Western Adriatic Sea (Italy), providing the finest-scale mapping of marine microbiomes in the Mediterranean Sea. Pelagic and benthic microbiomes in the study area showed sector specific-patterns and distinct assemblage structures, corresponding to specific variations in the microbiome network structure. While maintaining a balanced structure in terms of potential ecosystem services (e.g., hydrocarbon degradation and nutrient cycling), sector-specific patterns of over-abundant modules—and taxa—were defined, with the South sector (the closest to the coast) characterized by microbial groups of terrestrial origins, both in the pelagic and the benthic realms. By the granular assessment of the marine microbiome changes at the local scale, we have been able to describe, to our knowledge at the first time, the integration of terrestrial microorganisms in the marine microbiome networks, as a possible natural process characterizing eutrophic coastal area. This raises the question about the biological threshold for terrestrial microorganisms to be admitted in the marine microbiome networks, without altering the ecological balance.

Molecular and spectroscopic changes of peat-derived organic matter following photo-exposure: Effects on heteroatom composition of DOM

The temporal evolution of molecular compositions and changes in structural features of Hillsboro Canal (Florida, USA) dissolved organic matter (DOM) was studied with an emphasis on nitrogen and sulfur containing molecules, after a 13 day time-series exposure to simulated sunlight. The Hillsboro Canal drains from the ridge and slough wetland environment underlain by peat soils from the northern extent of the Greater Everglades Ecosystem. The Hillsboro Canal-DOM was characterized by combining ultrahigh-resolution mass spectrometry (FT-ICR-MS), high-field nuclear magnetic resonance spectroscopy (¹H NMR), size exclusion chromatography (SEC) with UV detection, and ultraviolet/visible (UV/vis) absorbance and excitation emission matrix (EEM) fluorescence spectroscopy. Size exclusion chromatography (SEC) demonstrated progressive depletion of higher mass molecules and a concomitant decrease of absorbance during photo-irradiation. NMR and FT-ICR-MS revealed nonlinear temporal evolution of DOM. In fact, FT-ICR-MS showed an initial depletion of supposedly chromophoric molecules often carrying major unsaturation accompanied by an uneven evolution of numbers of CHO, CHOS and CHNO compounds. While CHNO compounds continually increased throughout the entire photo-exposure time, CHO and CHOS compounds temporarily increased but declined after further light exposure. Progressive loss of highly unsaturated compounds was accompanied by production of low mass CHO and CHNO compounds with high O/C ratios. Area-normalized ¹H NMR spectra of DOM in water and of the water insoluble fraction (~5%) in methanol revealed clear distinctions between irradiated and non-irradiated samples and congruent evolution of DOM structural features during irradiation, with more uniform trends in methanolic-DOM. Photoirradiation caused initial photoproduction of oxygenated aliphatic compounds, continued depletion of phenols and oxygenated aromatics, substantial change from initial natural product derived olefins to photoproduced olefins, and uneven evolution of carboxylated and alkylated benzene derivatives. This study demonstrates longer-term heteroatom-dependent photochemistry of DOM, which will affect the speciation of N and S heteroatoms, their connections to inorganic nutrients, and potentially their bioavailability.

Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies

Microbial communities, through their metabolism, drive carbon cycling in marine environments. These complex communities are composed of many different microorganisms including heterotrophic bacteria, each with its own nutritional needs and metabolic capabilities. Yet, models of ecosystem processes typically treat heterotrophic bacteria as a “black box,” which does not resolve metabolic heterogeneity nor address ecologically important processes such as the successive modification of different types of organic matter. Here we directly address the heterogeneity of metabolism by characterizing the carbon source utilization preferences of 63 heterotrophic bacteria representative of several major marine clades. By systematically growing these bacteria on 10 media containing specific subsets of carbon sources found in marine biomass, we obtained a phenotypic fingerprint that we used to explore the relationship between metabolic preferences and phylogenetic or genomic features. At the class level, these bacteria display broadly conserved patterns of preference for different carbon sources. Despite these broad taxonomic trends, growth profiles correlate poorly with phylogenetic distance or genome-wide gene content. However, metabolic preferences are strongly predicted by a handful of key enzymes that preferentially belong to a few enriched metabolic pathways, such as those involved in glyoxylate metabolism and biofilm formation. We find that enriched pathways point to enzymes directly involved in the metabolism of the corresponding carbon source and suggest potential associations between metabolic preferences and other ecologically relevant traits. The availability of systematic phenotypes across multiple synthetic media constitutes a valuable resource for future quantitative modeling efforts and systematic studies of interspecies interactions.

IMPORTANCE Half of the Earth’s annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. Here, we characterize the diversity of metabolic preferences across many representative heterotrophs by systematically growing them on different fractions of dissolved organic carbon. Our analysis suggests that different clades of bacteria have substantially distinct preferences for specific carbon sources, in a way that cannot be simply mapped onto phylogeny. These preferences are associated with the presence of specific genes and pathways, reflecting an association between metabolic capabilities and ecological lifestyles. In addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprint we obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans.

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.

Impact of Quorum Sensing and Tropodithietic Acid Production on the Exometabolome of Phaeobacter inhibens

Microbial interactions shape ecosystem diversity and chemistry through production and exchange of organic compounds, but the impact of regulatory mechanisms on production and release of these exometabolites is largely unknown. We studied the extent and nature of impact of two signaling molecules, tropodithietic acid (TDA) and the quorum sensing molecule acyl homoserine lactone (AHL) on the exometabolome of the model bacterium Phaeobacter inhibens DSM 17395, a member of the ubiquitous marine Roseobacter group. Exometabolomes of the wild type, a TDA and a QS (AHL-regulator) negative mutant were analyzed via Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Based on a total of 996 reproducibly detected molecular masses, exometabolomes of the TDA and QS negative mutant were ∼70% dissimilar to each other, and ∼90 and ∼60% dissimilar, respectively, to that of the wild type. Moreover, at any sampled growth phase, 40–60% of masses detected in any individual exometabolome were unique to that strain, while only 10–12% constituted a shared “core exometabolome.” Putative annotation revealed exometabolites of ecological relevance such as vitamins, amino acids, auxins, siderophore components and signaling compounds with different occurrence patterns in the exometabolomes of the three strains. Thus, this study demonstrates that signaling molecules, such as AHL and TDA, extensively impact the composition of bacterial exometabolomes with potential consequences for species interactions in microbial communities.

Insight into the effect of wastewater-derived dissolved organic matter composition on norgestrel degradation in activated sludge: Coupled bacterial community and molecular characteristics

Dissolved organic matter (DOM) mediates the microbial transformation of micropollutants, including norgestrel (NGT) in natural waters. However, little is known of the effect of complex and variable wastewater-derived DOM composition on NGT degradation during wastewater treatment. In this study, the relationship between the compositions of initial DOM and NGT removal efficiencies of 17 wastewater treatment plants (WWTPs) in spring and summer were analyzed. The different molecular composition of DOM was selected in the lab to further explore its effect on NGT degradation by activated sludge. Results indicated that the DOM composition was a substantial driver of NGT removal in WWTPs. The discrepancies in the initial DOM composition contributed to the differences in the kinetics of NGT degradation by activated sludge. The larger rapid decay phase rates of NGT are usually accompanied by a large proportion of labile substances in DOM. High-throughput sequencing and ultrahigh-resolution mass spectrometry were used to further analyze the evolution of bacterial communities and DOM molecular composition were combined with network analysis to reveal the intrinsic relationship that how DOM composition affected NGT degradation by regulating core microbes. Eighty-nine core OTUs were significantly associated with NGT degradation, and 73 occurred in the rapid decay phase, implying that NGT degradation was mainly regulated by the initial composition of DOM. Nine major transformation products were identified in different groups with widely varying concentrations or relative abundances of these transformation products. This work provides valuable insights into the effects of wastewater-derived DOM composition on NGT degradation by activated sludge and innovatively explores the influence mechanisms from the bacterial community and molecular characterization perspectives.

Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment

Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source. The DOM composition, community structure, and metabolic pathways were characterised using multi-omics approaches. The addition of diatom lysate introduced a mass of labile DOM into the incubation seawater, which led to a low degradation index (I_DEG) and refractory molecular lability boundary (RMLB) on days 1 and 18. The molecular compositions of the DOM molecules in the later incubation period (from day 120 to day 220) were more similar in composition to those on day 0, suggesting a rapid turnover of phytoplankton debris by microbial communities. Taxonomically, while Alpha proteobacteria dominated during the entire incubation period, Gamma proteobacteria became more sensitive and abundant than the other bacterial groups on days 1 and 18. Recalcitrant measurements such as I_DEG and RMLB were closely related to the DOM molecules, bacterial community, and Kyoto encyclopaedia of Genes and Genomes (KEGG) modules, suggesting close associations between RDOM accumulation and microbial metabolism. KEGG modules that showed strong positive correlation with CRAMs were identified using a microbial ecological network approach. The identified KEGG modules produced the substrates, such as the acetyl-CoA or 3‑hydroxy-3-methylglutaryl-CoA, which could participate in the mevalonate pathway to generate the precursor of CRAM analogues, isopentenyl-PP, suggesting a potential generation pathway of CRAM analogues in bacteria and archaea. This study revealed the potential genetic and molecular processes involved in the microbial origin of CRAM analogues, and thus indicated a vital ecological role of bacteria and archaea in RDOM production. This study also offered new perspectives on the carbon sequestration in the ocean.

Linking Microbial Population Succession and DOM Molecular Changes in Synechococcus-Derived Organic Matter Addition Incubation

The molecular-level interactions between phytoplankton-derived dissolved organic matter (DOM) and heterotrophic prokaryotes represent a fundamental and yet poorly understood component of the marine elemental cycle. Here, we investigated the degradation of Synechococcus-derived organic matter (SynOM) by coastal microorganisms using spectroscopic and ultrahigh-resolution mass spectrometry analyses coupled with high-throughput sequencing. The added SynOM showed a spectrum of reactivity during a 180-day dark incubation experiment. Along with the decrease in DOM bioavailability, the chemical properties of DOM molecules overall showed increases in oxidation state and aromaticity. Both the microbial community and DOM molecular compositions became more homogeneous toward the end of the incubation. The experiment was partitioned into three phases (I, II, and III) based on the total organic carbon consumption rates from 7.0 ± 1.0 to 1.0 ± 0.1 and to 0.1 ± 0.0 μmol C L-1 day-1, respectively. Diverse generalists with low abundance were present in all three phases of the experiment, while a few abundant specialists dominated specific phases, suggesting their diverse roles in the transformation of DOM molecules from labile and semilabile to recalcitrant. The changes of organic molecules belonging to CHO, CHNO, and CHOS containing formulas were closely associated with specific microbial populations, suggesting close interactions between the different bacterial metabolic potential for substrates and DOM molecular compositional characteristics. This study sheds light on the interactions between microbial population succession and DOM molecular changes processes and collectively advances our understanding of microbial processing of the marine elemental cycle. IMPORTANCE Phytoplankton are a major contributor of labile dissolved organic matter (DOM) in the upper ocean, fueling tremendous marine prokaryotic activity. Interactions between microorganisms and algae-derived DOM regulate biogeochemical cycles in the ocean, but key aspects of their interactions remain poorly understood. Under global warming and eutrophication scenarios, Synechococcus blooms are commonly observed in coastal seawaters, and they significantly influence the elemental biogeochemistry cycling in eutrophic ecosystems. To understand the interactions between Synechococcus-derived DOM and heterotrophic prokaryotes as well as their influence on the coastal environment, we investigated the degradation of DOM by coastal microbes during a 180-day dark incubation. We showed substantial DOM compositional changes that were closely linked to the developments of microbial specialists and generalists. Our study provides information on the interactions between microbial population succession and DOM molecular changes, thereby advancing our understanding of microbial processing of the marine DOM pool under the influence of climate change.

A new conceptual framework for the transformation of groundwater dissolved organic matter

Groundwater comprises 95% of the liquid fresh water on Earth and contains a diverse mix of dissolved organic matter (DOM) molecules which play a significant role in the global carbon cycle. Currently, the storage times and degradation pathways of groundwater DOM are unclear, preventing an accurate estimate of groundwater carbon sources and sinks for global carbon budgets. Here we reveal the transformations of DOM in aging groundwater using ultra-high resolution mass spectrometry combined with radiocarbon dating. Long-term anoxia and a lack of photodegradation leads to the removal of oxidised DOM and a build-up of both reduced photodegradable formulae and aerobically biolabile formulae with a strong microbial signal. This contrasts with the degradation pathway of DOM in oxic marine, river, and lake systems. Our findings suggest that processes such as groundwater extraction and subterranean groundwater discharge to oceans could result in up to 13 Tg of highly photolabile and aerobically biolabile groundwater dissolved organic carbon released to surface environments per year, where it can be rapidly degraded. These findings highlight the importance of considering groundwater DOM in global carbon budgets.

Marine Dissolved Organic Matter Shares Thousands of Molecular Formulae Yet Differs Structurally across Major Water Masses

Most oceanic dissolved organic matter (DOM) is still not fully molecularly characterized. We combined high-field nuclear magnetic resonance (NMR) and ultrahigh-resolution mass spectrometry (Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) for the structural and molecular formula-level characterization of solid-phase extracted (SPE) DOM from surface, mesopelagic, and bathypelagic Atlantic and Pacific Ocean samples. Using a MicroCryoProbe, unprecedented low amounts of SPE-DOM (∼1 mg carbon) were sufficient for two-dimensional NMR analysis. Low proportions of olefinic and aromatic relative to aliphatic and carboxylated structures (NMR) at the sea surface were likely related to photochemical transformations. This was consistent with lower molecular masses and higher degrees of saturation and oxygenation (FT-ICR-MS) compared to those of the deep sea. Carbohydrate structures in the mesopelagic North Pacific Ocean suggest export and release from sinking particles. In our sample set, the universal molecular DOM composition, as captured by FT-ICR-MS, appears to be structurally more diverse when analyzed by NMR, suggesting DOM variability across oceanic provinces to be more pronounced than previously assumed. As a proof of concept, our study takes advantage of new complementary approaches resolving thousands of structural and molecular DOM features while applying reasonable instrument times, allowing for the analysis of large oceanic data sets to increase our understanding of marine DOM biogeochemistry.

Evidence of Covid-19 lockdown effects on riverine dissolved organic matter dynamics provides a proof-of-concept for needed regulations of anthropogenic emissions

The fast spread of SARS-CoV-2 virus in Italy resulted in a 3-months lockdown of the entire country. During this period, the effect of the relieved anthropogenic activities on the environment was plainly clear all over the country. Herein, we provide the first evidence of the lockdown effects on riverine dissolved organic matter (DOM) dynamics. The strong reduction in anthropogenic activities resulted in a marked decrease in dissolved organic carbon (DOC) concentration in the Arno River (-44%) and the coastal area affected by its input (-15%), compared to previous conditions. The DOM optical properties (absorption and fluorescence) showed a change in its quality, with a shift toward smaller and less aromatic molecules during the lockdown. The reduced human activity and the consequent change in DOM dynamics affected the abundance and annual dynamics of heterotrophic prokaryotes. The results of this study highlight the extent to which DOM dynamics in small rivers is affected by secondary and tertiary human activities as well as the quite short time scales to return to the impacted conditions. Our work also supports the importance of long-term research to disentangle the effects of casual events from the natural variability.

Linkages Among Dissolved Organic Matter Export, Dissolved Metabolites, and Associated Microbial Community Structure Response in the Northwestern Sargasso Sea on a Seasonal Scale

Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016-2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.

Adaptations of microbial communities and dissolved organics to seasonal pressures in a mesotrophic coastal Mediterranean lake

In lake ecosystems, changes in eukaryotic and prokaryotic microbes and the concentration and availability of dissolved organic matter (DOM) produced within or supplied to the system by allochthonous sources are components that characterize complex processes in the microbial loop. We address seasonal changes of microbial communities and DOM in the largest Croatian lake, Vrana. This shallow lake is connected to the Adriatic Sea and is impacted by agricultural activity. Microbial community and DOM structure were driven by several environmental stressors, including drought, seawater intrusion, and heavy precipitation events. Bacterial composition of different lifestyles (free-living and particle-associated) differed and only a part of the particle-associated bacteria correlated with microbial eukaryotes. Oscillations of cyanobacterial relative abundance along with chlorophyll a revealed a high primary production season characterized by increased levels of autochthonous DOM that promoted bacterial processes of organic matter degradation. From our results, we infer that in coastal freshwater lakes dependent on precipitation-evaporation balance, prolonged dry season coupled with heavy irrigation impact microbial communities at different trophic levels even if salinity increases only slightly and allochthonous DOM inputs decrease. These pressures, if applied more frequently or at higher concentrations, could have the potential to overturn the trophic state of the lake. This article is protected by copyright. All rights reserved.

Extensive primary production promoted the recovery of the Ediacaran Shuram excursion

Member IV of the Ediacaran Doushantuo Formation records the recovery from the most negative carbon isotope excursion in Earth history. However, the main biogeochemical controls that ultimately drove this recovery have yet to be elucidated. Here, we report new carbon and nitrogen isotope and concentration data from the Nanhua Basin (South China), where δ¹³C values of carbonates (δ¹³C_carb) rise from − 7‰ to −1‰ and δ¹⁵N values decrease from +5.4‰ to +2.3‰. These trends are proposed to arise from a new equilibrium in the C and N cycles where primary production overcomes secondary production as the main source of organic matter in sediments. The enhanced primary production is supported by the coexisting Raman spectral data, which reveal a systematic difference in kerogen structure between depositional environments. Our new observations point to the variable dominance of distinct microbial communities in the late Ediacaran ecosystems, and suggest that blooms of oxygenic phototrophs modulated the recovery from the most negative δ¹³C_carb excursion in Earth history.

Variable dominance of distinct microbial communities during the late Ediacaran, recorded in C and N cycles perturbations and in Raman structural heterogeneities of organic matter, modulated the recovery from the most negative δ¹³C_carb excursion in Earth’s history.

Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network

During transit from soils to the ocean, microbial communities are modified and re-assembled, generating complex patterns of ecological succession. The potential effect of upstream assembly on downstream microbial community composition is seldom considered within aquatic networks. Here, we reconstructed the microbial succession along a land-freshwater-estuary continuum within La Romaine river watershed in Northeastern Canada. We captured hydrological seasonality and differentiated the total and reactive community by sequencing both 16 S rRNA genes and transcripts. By examining how DNA- and RNA-based assemblages diverge and converge along the continuum, we inferred temporal shifts in the relative importance of assembly processes, with mass effects dominant in spring, and species selection becoming stronger in summer. The location of strongest selection within the network differed between seasons, suggesting that selection hotspots shift depending on hydrological conditions. The unreactive fraction (no/minor RNA contribution) was composed of taxa with diverse potential origins along the whole aquatic network, while the majority of the reactive pool (major RNA contribution) could be traced to soil/soilwater-derived taxa, which were distributed along the entire rank-abundance curve. Overall, our findings highlight the importance of considering upstream history, hydrological seasonality and the reactive microbial fraction to fully understand microbial community assembly on a network scale.

Chemodiversity of Dissolved Organic Matter and Its Molecular Changes Driven by Rhizosphere Activities in Fe Ore Tailings Undergoing Eco-Engineered Pedogenesis

Dissolved organic matter (DOM) plays an important role in soil structure and biogeochemical function development, which are fundamental for the eco-engineering of tailings-soil formation to underpin sustainable tailings rehabilitation. In the present study, we have characterized the DOM composition and its molecular changes in an alkaline Fe ore tailing primed with organic matter (OM) amendment and plant colonization. The results demonstrated that microbial OM decomposition dramatically increased DOM richness and average molecular weight, as well as its degree of unsaturation, aromaticity, and oxidation in the tailings. Plant colonization drove molecular shifts of DOM by depleting the unsaturated compounds with a high value of nominal oxidation state of carbon (NOSC), such as tannin-like and carboxyl-rich polycyclic-like compounds. This may be partially related to their sequestration by secondary Fe-Si minerals formed from rhizosphere-driven mineral weathering. Furthermore, the molecular shifts of DOM may have also resulted from plant-regulated microbial community changes, which further influenced DOM molecules through microbial-DOM interactions. These findings contribute to the understanding of DOM biogeochemistry and ecofunctionality in the tailings during early pedogenesis driven by OM input and pioneer plant/microbial colonization, providing an important basis for the development of strategies and technologies toward the eco-engineering of tailings-soil formation.

Correspondence between DOM molecules and microbial community in a subtropical coastal estuary on a spatiotemporal scale

Dissolved organic matter (DOM) changes in quantity and quality over time and space, especially in highly dynamic coastal estuaries. Bacterioplankton usually display seasonal and spatial variations in abundance and composition in the coastal regions, and influence the DOM pool via assimilation, transformation and release of organic molecules. The change in DOM can also affect the composition of bacterial community. However, little is known on the correspondence between DOM molecules and bacterial composition, particularly through a systematic field survey. In this study, the spatiotemporal signatures of microbial communities and DOM composition in the subtropical coastal estuary of Xiamen are investigated over one and half years. The co-occurrence analysis between bacteria and DOM suggested microorganisms likely transformed the DOM from a relatively high (>400 Da) to a low (<400 Da) molecular weight, corresponding to an apparent increase in overall aromaticity. This might be the reason why microbial transformation renders "dark" organic matter visible in mass spectrometry due to more efficient ionization of microbial metabolites, as well as photodegradation processes. K- and r-strategists exhibited different correlations with two-size categories of DOM molecules owing to their different lifestyles and responses to environmental nutrient conditions. A comparison of the environmental variables and DOM composition with the microbial communities showed that the environmental/DOM variations played a more important role in shaping the microbial communities than vice versa. This study sheds light on the interactions between microbial populations and DOM molecules at the spatiotemporal scale, improving our understanding of microbial roles in marine biogeochemical cycles.

Multiple thresholds and trajectories of microbial biodiversity predicted across browning gradients by neural networks and decision tree learning

Ecological association studies often assume monotonicity such as between biodiversity and environmental properties although there is growing evidence that nonmonotonic relations dominate in nature. Here, we apply machine-learning algorithms to reveal the nonmonotonic association between microbial diversity and an anthropogenic-induced large-scale change, the browning of freshwaters, along a longitudinal gradient covering 70 boreal lakes in Scandinavia. Measures of bacterial richness and evenness (alpha-diversity) showed nonmonotonic trends in relation to environmental gradients, peaking at intermediate levels of browning. Depending on the statistical methods, variables indicative for browning could explain 5% of the variance in bacterial community composition (beta-diversity) when applying standard methods assuming monotonic relations and up to 45% with machine-learning methods taking non-monotonicity into account. This non-monotonicity observed at the community level was explained by the complex interchangeable nature of individual taxa responses as shown by a high degree of nonmonotonic responses of individual bacterial sequence variants to browning. Furthermore, the nonmonotonic models provide the position of thresholds and predict alternative bacterial diversity trajectories in boreal freshwater as a result of ongoing climate and land-use changes, which in turn will affect entire ecosystem metabolism and likely greenhouse gas production.

Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach

Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM.

Vertical Stratification of Dissolved Organic Matter Linked to Distinct Microbial Communities in Subtropic Estuarine Sediments

Dissolved organic matter (DOM) provides carbon substrates and energy sources for sediment microbes driving benthic biogeochemical processes. The interactions between microbes and DOM are dynamic and complex and require the understanding based on fine-scale microbial community and physicochemical profiling. In this study, we characterized the porewater DOM composition in a 300-cm sediment core from the Pearl River estuary, China, and examined the interactions between DOM and archaeal and bacterial communities. DOM composition were highly stratified and associated with changing microbial communities. Compared to bacteria, the amplicon sequence variants of archaea showed significant Pearson correlations (r ≥ 0.65, P < 0.01) with DOM molecules of low H/C ratios, high C number and double bond equivalents, indicating that the distribution of archaea was closely correlated to recalcitrant DOM while bacteria were associated with relatively labile compounds. This was supported by the presence of auxiliary enzyme families essential for lignin degradation and bcrABCD, UbiX genes for anaerobic aromatic reduction in metagenome-assembled genomes of Bathyarchaeia. Our study demonstrates that niche differentiation between benthic bacteria and archaea may have important consequences in carbon metabolism, particularly for the transformation of recalcitrant organic carbon that may be predominant in aged marine sediments.

Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

Urbanization along coastlines alters marine ecosystems including contributing molecules of anthropogenic origin to the coastal dissolved organic matter (DOM) pool. A broad assessment of the nature and extent of anthropogenic impacts on coastal ecosystems is urgently needed to inform regulatory guidelines and ecosystem management. Recently, non-targeted tandem mass spectrometry approaches are gaining momentum for the analysis of global organic matter composition (chemotypes) including a wide array of natural and anthropogenic compounds. In line with these efforts, we developed a non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) workflow that utilizes advanced data analysis approaches such as feature-based molecular networking and repository-scale spectrum searches. This workflow allows the scalable comparison and mapping of seawater chemotypes from large-scale spatial surveys as well as molecular family level annotation of unknown compounds. As a case study, we visualized organic matter chemotype shifts in coastal environments in northern San Diego, USA, after notable rain fall in winter 2017/2018 and highlight potential anthropogenic impacts. The observed seawater chemotype, consisting of 4384 LC-MS/MS features, shifted significantly after a major rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, including pesticides (Imazapyr and Isoxaben), cleaning products (Benzyl-tetradecyl-dimethylammonium) and chemical additives (Hexa (methoxymethyl)melamine) and potential degradation products. By expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we further contextualized their possible origin and show their importance in other ecosystems. The mass spectrometry and data analysis pipelines applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which will contribute to a deliberate assessment of how chemical pollution impacts our oceans.

Microbial transformation of distinct exogenous substrates into analogous composition of recalcitrant dissolved organic matter

Oceanic dissolved organic matter (DOM) comprises a complex molecular mixture which is typically refractory and homogenous in the deep layers of the ocean. Though the refractory nature of deep-sea DOM is increasingly attributed to microbial metabolism, it remains unexplored whether ubiquitous microbial metabolism of distinct carbon substrates could lead to similar molecular composition of refractory DOM. Here, we conducted microbial incubation experiments using four typically bioavailable substrates (L-alanine, trehalose, sediment DOM extract, and diatom lysate) to investigate how exogenous substrates are transformed by a natural microbial assemblage. The results showed that although each-substrate-amendment induced different changes in the initial microbial assemblage and the amended substrates were almost depleted after 90 days of dark incubation, the bacterial community compositions became similar in all incubations on day 90. Correspondingly, revealed by ultra-high resolution mass spectrometry, molecular composition of DOM in all incubations became compositionally consistent with recalcitrant DOM and similar toward that of DOM from the deep-sea. These results indicate that while the composition of natural microbial communities can shift with substrate exposures, long-term microbial transformation of distinct substrates can ultimately lead to a similar refractory DOM composition. These findings provide an explanation for the homogeneous and refractory features of deep-sea DOM.

Resource aromaticity affects bacterial community successions in response to different sources of dissolved organic matter

Microbe-mediated transformation of dissolved organic matter (DOM) contributes substantially to the carbon dynamics and energy flow of aquatic ecosystems; yet, the temporal dynamics of bacterial communities in response to diverse DOM sources are scarcely known. Here, we supplied four distinct sources of DOM (algae-derived, macrophyte-derived, sewage-derived, and soil-derived) to the same bacterial community to track the effects of these DOM sources on the carbon processing and successional dynamics of bacterial communities. Although by the end of the incubation the proportion of bio-degraded DOM was significantly lower in the soil-derived DOM treatment than for the other sources, rapid initial metabolism of protein-like and aliphatic compounds and increasing aromaticity and humification degree of DOM during the incubation period were observed for all sources. The role of stochastic processes in governing the community assembly decreased substantially from 61.4% on the first day to 16.7% at the end of the incubation. Moreover, stronger deterministic selection and lower temporal turnover rate were observed for the soil-derived than the other DOM sources, indicating stronger environmental filtering by the more aromatic DOM. Significant correlations were also observed between the humification index (HIX) of DOM and bacterial community diversities, co-occurrence patterns, habitat niche breadths, and the contribution of deterministic ecological processes. In addition, we demonstrated that taxa with different abundance patterns all play crucial but different roles in the response to DOM variation. Our results indicate the importance of DOM aromaticity as a predictor of the outcome of different DOM sources on bacterial community dynamics.

Evaluation of the Production of Dissolved Organic Matter by Three Marine Bacterial Strains

A large part of marine dissolved organic matter (DOM) is considered to be recalcitrant DOM (RDOM) produced by marine bacteria. However, it is still unclear whether differences in bacterial species and/or physiology control the efficiency of RDOM production. Here, batch culture experiments with glucose as the sole carbon source were carried out using three model marine bacterial strains, namely, Alteromonas macleodii (Alt), Vibrio splendidus (Vib), and Phaeobacter gallaeciensis (Pha). Dissolved organic carbon (DOC) concentrations drastically decreased during the exponential growth phases of these bacteria due to the consumption of glucose. The efficiency of bacterial DOC production at the end of incubation was largely different among the strains and was higher for Vib (20%) than for the other two strains (Alt, 4%; Pha, 6%). All strains produced fluorescent DOM (FDOM), including humic-like FDOM which is considered as recalcitrant component in the ocean, even though the composition of bacterial FDOM was also different among the strains. The efficiency of humic-like FDOM production during the exponential growth phase was different among the bacterial strains; that is, Pha produced humic-like FDOM efficiently compared with the other two species. The efficiency of humic-like FDOM production with mineralization of organic matter was lower during the exponential growth phase than during the stationary phase of Alt and Pha. Four processes for the production of bacterially derived recalcitrant humic-like FDOM are suggested from this study: (1) production during active growing (in all strains), (2) production with the reutilization of bacterial DOM (Alt), (3) production with the consumption of cellular materials (Pha), and (4) release from lysis (Vib). Our results suggest that bacterial species and physiology can regulate RDOM production and accumulation in the ocean.

Genome-Wide Identification and Functional Characterization of β-Agarases in Vibrio astriarenae Strain HN897

The genus Vibrio is a genetically and metabolically versatile group of heterotrophic bacteria that are important contributors to carbon cycling within marine and estuarine ecosystems. HN897, a Vibrio strain isolated from the coastal seawater of South China, was shown to be agarolytic and capable of catabolizing D-galactose. Herein, we used Illumina and PacBio sequencing to assemble the whole genome sequence for the strain HN897, which was comprised of two circular chromosomes (Vas1 and Vas2). Genome-wide phylogenetic analysis with 140 other Vibrio sequences firmly placed the strain HN897 into the Marisflavi clade, with Vibrio astriarenae strain C7 being the closest relative. Of all types of carbohydrate-active enzyme classes, glycoside hydrolases (GH) were the most common in the HN897 genome. These included eight GHs identified as putative β-agarases belonging to GH16 and GH50 families in equal proportions. Synteny analysis showed that GH16 and GH50 genes were tandemly arrayed on two different chromosomes consistent with gene duplication. Gene knockout and complementation studies and phenotypic assays confirmed that Vas1_1339, a GH16_16 subfamily gene, exhibits an agarolytic phenotype of the strain. Collectively, these findings explained the agar-decomposing of strain HN897, but also provided valuable resources to gain more detailed insights into the evolution and physiological capability of the strain HN897, which was a presumptive member of the species V. astriarenae.

Molecular Characteristics of Dissolved Organic Nitrogen and Its Interaction with Microbial Communities in a Prechlorinated Raw Water Distribution System

Dissolved organic nitrogen (DON) represents a unique challenge in prechlorinated raw water distribution systems (PRWDSs) because of its contribution to the formation of harmful nitrogen-disinfection byproducts, influence upon biogeochemical processes, and unclear molecular characteristics. Here, Fourier transform ion cyclotron resonance mass spectrometry in combination with high-throughput sequencing was applied to elucidate the molecular changes of DON and biofilm microbial communities in a PRWDS in Yixing, China. Our study revealed that dynamic characteristics of DON are significantly correlated with the biofilm. The accumulation of refractory lignin-like compounds and C_nH_mO_pN₁ contributes to the higher recalcitrance molecular characteristics of DON in the effluent associated with Alphaproteobacteria, Planctomycetes, and Bacteroidetes. Additionally, with the help of prechlorination, the biofilm may change the DON characteristics and lead to higher oxygenation, higher m/z, and lower saturation during transportation. Despite the promotion of C_nH_mO_pN₁ and C_nH_mO_pN₃ at the early stage, we suggest that appropriate concentration of chlorine can add to the front end of raw water distribution pipes. Prechlorination may control the nitrification process and stabilize the rapid growth of diversity and concentration of low molecular weight DON, especially the refractory C_nH_mO_pN₁ in the effluent, which may help to improve treatment efficiency of drinking water treatment plants.

A Collection of 13 Archaeal and 46 Bacterial Genomes Reconstructed from Marine Metagenomes Derived from the North Sea

Marine bacteria are key drivers of ocean biogeochemistry. Despite the increasing number of studies, the complex interaction of marine bacterioplankton communities with their environment is still not fully understood. Additionally, our knowledge about prominent marine lineages is mostly based on genomic information retrieved from single isolates, which do not necessarily represent these groups. Consequently, deciphering the ecological contributions of single bacterioplankton community members is one major challenge in marine microbiology. In the present study, we reconstructed 13 archaeal and 46 bacterial metagenome-assembled genomes (MAGs) from four metagenomic data sets derived from the North Sea. Archaeal MAGs were affiliated to Marine Group II within the Euryarchaeota. Bacterial MAGs mainly belonged to marine groups within the Bacteroidetes as well as alpha- and gammaproteobacteria. In addition, two bacterial MAGs were classified as members of the Actinobacteria and Verrucomicrobiota, respectively. The reconstructed genomes contribute to our understanding of important marine lineages and may serve as a basis for further research on functional traits of these groups.