Uncoupling of bacterial and terrigenous dissolved organic matter dynamics in decomposition experiments

Seasonal changes of dissolved organic matter chemistry and its linkage with greenhouse gas emissions in saltmarsh surface water and porewater interactions

Dissolved organic matter (DOM) is one of the largest reactive reservoirs of carbon on earth. Saltmarshes play an essential role in shaping the fate of DOM and greenhouse gas (GHG) production in surface water and groundwater interactions in coastal areas. However, the coupling mechanism between DOM and GHG production is poorly understood. In this study, DOM in both surface water and porewater were analyzed by 3D excitation-emission-matrix spectroscopy under different seasonal and tidal conditions in a saltmarsh. Protein-like DOM was likely to produce CH4, while humic-like DOM tended to produce CO2. CH4 concentration was highly enriched in porewater because increasing fresh groundwater flow introduced small-sized protein-like DOM. Based on the mass balance model, >98.5% of CH4 was oxidated to CO2 in sediment-water interface. The degradation of sediment-derived DOC (especially humic-like DOM) contributes ∼80% of the total amount of CO2 in surface water. Both hydrodynamics and chemical reactions are suggested to influence greenhouse gas (GHG) emissions. Hydrodynamics (e.g., tidal pumping) are controlling factors in short timescales (hourly/weekly) while chemical reactions become crucial in influencing DOM chemistry and related degradation rate on seasonal scales. These findings emphasize the importance of the coupling mechanism at different time scales between DOM characteristics and GHG emissions in saltmarshes.

Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates

Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.

Data evaluation strategy for identification of key molecular formulas in dissolved organic matter as proxies for biogeochemical reactivity based on abundance differences from ultrahigh resolution mass spectrometry

The molecular composition of dissolved organic matter (DOM) is of relevance for global carbon cycling and important for drinking water processing also. The detection of variation of DOM composition as function of time and space from a methodological viewpoint is essential to observe DOM processing and was addressed so far. High resolution concerning DOM quality was achieved with Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS). However almost none of the existing FTICR-MS data sets were evaluated addressing the fate of single mass features / molecular formulas (MFs) abundance during experiments. In contrast to former studies we analyze the function of MF abundance of time and space for such MFs which are present in all samples and which were formerly claimed as recalcitrant in not all but a great number of studies. For the first time the reactivity of MFs was directly compared by their abundance differences using a simple equation, the relative intensity difference (δRI). Search strategies to find out the maximum δRI values are introduced. The corresponding MFs will be regarded as key MFs (KEY-MFs). In order to test this new approach data from a recent photo degradation experiment were combined with monitoring surveys conducted in two drinking water reservoirs. The δRI values varied over one order of magnitude (more than five-fold). MFs like C₉H₁₂O₆ and C₁₀H₁₄O₆ revealed high biogeochemical reactivity as photo products. Some of the KEY-MFs were identical with MFs identified as disinfection byproducts precursors in recent studies. Other KEY-MFs were oxygen-rich and relatively unsaturated (poly-phenol-like) and hence relevant to flocculation procedures.

Distinct stages of the intestinal bacterial community of Ampullaceana balthica after salinization

Environmental disturbances influence bacterial community structure and functioning. To investigate the effect of environmental disturbance caused by changes in salinity on host-protected bacterial communities, we analyzed the microbiome within the gastrointestinal tract of Ampullaceana balthica in different salinities. A. balthica is a benthic gastropod found in fresh- and mesohaline waters. Whereas the total energy reserves of A. balthica were unaffected by an increase of salinity to 3, a high mortality rate was detected after a shift from freshwater to salinity 6 suggesting a major disruption of energy homeostasis. The shift to salinity 6 also caused a change in the gastrointestinal bacterial community composition. At salinity 3, the bacterial community composition of different host individuals was related either to the freshwater or salinity 6 gastrointestinal bacterial community, indicating an ambivalent nature of salinity 3. Since salinity 3 represents the range where aquatic gastropods are able to regulate their osmolarity, this may be an important tipping point during salinization. The change in the intestinal microbiome was uncoupled from the change in the water bacterial community and unrelated to the food source microbiome. Our study shows that environmental disturbance caused by salinity acts also on the host-protected microbiome. In light of the sea-level rise, our findings indicate that salinization of the near-shore freshwater bodies will cause changes in organisms' intestinal microbiomes if a critical salinity threshold (presumably ∼3) is exceeded.

Response of Coastal Shewanella and Duganella Bacteria to Planktonic and Terrestrial Food Substrates

Global warming scenarios indicate that in subarctic regions, the precipitation will increase in the future. Coastal bacteria will thus receive increasing organic carbon sources from land runoff. How such changes will affect the function and taxonomic composition of coastal bacteria is poorly known. We performed a 10-day experiment with two isolated bacteria: Shewanella baltica from a seaside location and Duganella sp. from a river mouth, and provided them with a plankton and a river extract as food substrate. The bacterial growth and carbon consumption were monitored over the experimental period. Shewanella and Duganella consumed 40% and 30% of the plankton extract, respectively, while the consumption of the river extract was low for both bacteria, ∼1%. Shewanella showed the highest bacterial growth efficiency (BGE) (12%) when grown on plankton extract, while when grown on river extract, the BGE was only 1%. Duganella showed low BGE when grown on plankton extract (< 1%) and slightly higher BGE when grown on river extract (2%). The cell growth yield of Duganella was higher than that of Shewanella when grown on river extract. These results indicate that Duganella is more adapted to terrestrial organic substrates with low nutritional availability, while Shewanella is adapted to eutrophied conditions. The different growth performance of the bacteria could be traced to genomic variations. A closely related genome of Shewanella was shown to harbor genes for the sequestration of autochthonously produced carbon substrates, while Duganella contained genes for the degradation of relatively refractive terrestrial organic matter. The results may reflect the influence of environmental drivers on bacterial community composition in natural aquatic environments. Elevated inflows of terrestrial organic matter to coastal areas in subarctic regions would lead to increased occurrence of bacteria adapted to the degradation of complex terrestrial compounds with a low bioavailability.

Declining fungal diversity in Arctic freshwaters along a permafrost thaw gradient

Climate change-driven permafrost thaw has a strong influence on pan-Arctic regions, via, for example, the formation of thermokarst ponds. These ponds are hotspots of microbial carbon cycling and greenhouse gas production, and efforts have been put on disentangling the role of bacteria and archaea in recycling the increasing amounts of carbon arriving to the ponds from degrading watersheds. However, despite the well-established role of fungi in carbon cycling in the terrestrial environments, the interactions between permafrost thaw and fungal communities in Arctic freshwaters have remained unknown. We integrated data from 60 ponds in Arctic hydro-ecosystems, representing a gradient of permafrost integrity and spanning over five regions, namely Alaska, Greenland, Canada, Sweden, and Western Siberia. The results revealed that differences in pH and organic matter quality and availability were linked to distinct fungal community compositions and that a large fraction of the community represented unknown fungal phyla. Results display a 16%-19% decrease in fungal diversity, assessed by beta diversity, across ponds in landscapes with more degraded permafrost. At the same time, sites with similar carbon quality shared more species, aligning a shift in species composition with the quality and availability of terrestrial dissolved organic matter. We demonstrate that the degradation of permafrost has a strong negative impact on aquatic fungal diversity, likely via interactions with the carbon pool released from ancient deposits. This is expected to have implications for carbon cycling and climate feedback loops in the rapidly warming Arctic.

Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea)

Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may thus be affected. We studied the responses of bacterial community to inflow of terrestrial dissolved organic matter in a subarctic estuary in the northern Baltic Sea, using a 16S rRNA gene metabarcoding approach. Betaproteobacteria dominated during the spring river flush, constituting ~ 60% of the bacterial community. Bacterial diversity increased as the runoff decreased during summer, when Verrucomicrobia, Betaproteobacteria, Bacteroidetes, Gammaproteobacteria and Planctomycetes dominated the community. Network analysis revealed that a larger number of associations between bacterial populations occurred during the summer than in spring. Betaproteobacteria and Bacteroidetes populations appeared to display similar correlations to environmental factors. In spring, freshly discharged organic matter favoured specialists, while in summer a mix of autochthonous and terrestrial organic matter promoted the development of generalists. Our study indicates that increased inflows of terrestrial organic matter-loaded freshwater to coastal areas would promote specialist bacteria, which in turn might enhance the transformation of terrestrial organic matter in estuarine environments.

Comparison of Myriophyllum Spicatum and artificial plants on nutrients removal and microbial community in constructed wetlands receiving WWTPs effluents

The impacts of WWTPs effluents on nutrients removal and epiphytic microbial community in constructed wetlands dominated by submersed macrophytes remain to be fully illustrated. In this study, compared to M. Spicatum, artificial submersed macrophytes (control) generally had higher NH₄⁺-N (78.35% vs 80.52%) and TN (73.35% vs 90.25%) removal rates and similar COD (70.64% vs 70.80%) and TP (59.86% vs 60.82%) removal rates in wetlands receiving simulated effluents of WWTPs (GB18918-2002). Microbial population richness was higher in epiphytic biofilms on M. Spicatum than artificial ones, and substrates played the most decisive role in determining the microbial diversities. Network analysis revealed that there were more complex interactions among environmental parameters, bacteria and eukaryotes in M. Spicatum systems than in artificial ones. Nutrients in effluents could cause damage to M. Spicatum. The results highlight that artificial plants have better performance on effluents deep treatments than submerged plants.

Processing of dissolved organic matter from surface waters to sediment pore waters in a temperate coastal wetland

Coastal wetlands are active transitional ecotones between land and ocean, and are considered as hot spots of organic matter processing within the global carbon cycle, which dissolved organic matter (DOM) plays a critical role. In this study, combined use of ultrahigh-resolution mass spectrometry (FT-ICR MS) and complementary optical techniques was conducted to assess the detailed molecular composition of DOM in the temperate Liaohe coastal wetland (LCW), NE China in respect to the differences in DOM composition from surface water to sediment pore water. Significant positive correlations between salinity and dissolved organic carbon (DOC) concentrations were observed in both surface waters and pore waters. Pore water DOM is generally characterized by lower protein-like fluorescence and biological index, but higher humification and humic-like fluorescent components than those in surface water DOM. Corresponding to the optical properties, FT-ICR MS measurements show that pore water DOM has higher proportions of heteroatoms, aromaticity index, O/C ratios, unsaturated aliphatics, and peptides, but lower average H/C ratios compared to surface water DOM across locations with different marsh plant species (rice (Oryza sativa), reed (Phragmites australis), Seablite (Suaeda Salsa)) and salinity (0.5 to 51.5 psu). The results suggest that selective preservation for polyphenols, lignin degradation intermediates (highly unsaturated compounds), and microbial resynthesis of heteroatomic compounds are involved in the processing of DOM from surface water to pore water, leading to the formation of higher molecular weight and sulfur-containing molecules. The abundant CHOS compounds could be related to the early diagenetic sulfurization of DOM in sediments. Our unique data set should provide new clues for a comprehensive understanding of the molecular dynamics of DOM in coastal wetlands.

Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter

BACKGROUND

The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river.

RESULTS

We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.

CONCLUSIONS

Our work contributes to expand significantly our comprehension of the world's largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers. Video abstract.

Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes

Lakes receive large amounts of terrestrially derived dissolved organic matter (tDOM). However, little is known about how aquatic microbial communities interact with tDOM in lakes. Here, by performing microcosm experiments we investigated how microbial community responded to tDOM influx in six Tibetan lakes of different salinities (ranging from 1 to 358 g/l). In response to tDOM addition, microbial biomass increased while dissolved organic carbon (DOC) decreased. The amount of DOC decrease did not show any significant correlation with salinity. However, salinity influenced tDOM transformation, i.e., microbial communities from higher salinity lakes exhibited a stronger ability to utilize tDOM of high carbon numbers than those from lower salinity. Abundant taxa and copiotrophs were actively involved in tDOM transformation, suggesting their vital roles in lacustrine carbon cycle. Network analysis indicated that 66 operational taxonomic units (OTUs, affiliated with Alphaproteobacteria, Actinobacteria, Bacteroidia, Bacilli,  Gammaproteobacteria, Halobacteria, Planctomycetacia, Rhodothermia, and Verrucomicrobiae) were associated with degradation of CHO compounds, while four bacterial OTUs (affiliated with Actinobacteria, Alphaproteobacteria, Bacteroidia and Gammaproteobacteria) were highly associated with the degradation of CHOS compounds. Network analysis further revealed that tDOM transformation may be a synergestic process, involving cooperation among multiple species. In summary, our study provides new insights into a microbial role in transforming tDOM in saline lakes and has important implications for understanding the carbon cycle in aquatic environments.

Epiphytic bacterial community shift drives the nutrient cycle during Potamogeton malaianus decomposition

Epiphytic bacteria on submerged macrophytes play important roles in the nutrient cycle in freshwater ecosystems. However, little is known about the composition and role of epiphytic bacteria during the decomposition of submerged macrophytes. In this study, the alterations in epiphytic bacterial composition, abundances of nitrogen cycle-related genes and nutrient release were investigated in a 56-day decomposition process of Potamogeton malaianus. The total reduced biomass was positively related to the contents of carbon, nitrogen and phosphorus released from plant residues. Nutrient released from plant litter showed a positively effect on the concentrations of carbon, nitrogen and phosphorus in the overlying water (p < 0.01). The carbon, phosphorus and nitrogen decreased with decomposition process in both plant debris and overlying water. Humic acid-like substances were the main component of dissolved organic matter in the conditioning stage, whereas fulvic acid-like substances dominated in the fragmentation stage. Results from network analysis and canonical correspondence analysis showed dominant bacterial clades changed with decomposition process. Bacteroidetes was the most abundant phylum in the leaching stage and Spirochaetes, Chlorobi, and Bacteroidetes dominated in the conditioning stage, while Chlorobi dominated in the fragmentation stage. The highest abundance of cnorB and nosZ were detected in the leaching and fragmentation stage, respectively. Bacterial denitrification contributed to nitrogen removal and might be promoted by high ORP and DOC concentration. Our results indicate that epiphytic bacterial community shift drived the metabolism of nutrients C, N, and S during the decomposition of P. malaianus.

Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations

Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures.IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects ("bottle effect") may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called "bottle effect," which is well known to occur during enclosure experiments.

Compositional changes of dissolved organic carbon during its dynamic desorption from hyporheic zone sediments

Dissolved organic matter (DOM) is an important driver for biogeochemical reactions that affect microbial community function, and regulate changes in porewater chemical composition and redox properties in the environment. This study investigated the variation in DOM molecular composition during the detachment of organic matter (OM) from hyporheic zone (HZ) sediments using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS). Diffusive mass transfer and microbial degradation were the two primary processes controlling the rate of OM release and molecular composition changes during the detachment from sediments. The diffusive mass transfer process limited the rate of OM release from the sediments, but had negligible effect on the molecular signature of the released OM. Microbial degradation on the other hand preferentially consumed the protein- and lipid-like fractions of the DOM, characterized by lower nominal oxidation states of carbon (NOSC), lower molecular weight, and a higher saturation of chemical bonds. The results have strong implication to the organic carbon dynamics and related microbial activities and contaminant transformation in hyporheic zones, an important critical area in river systems.

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change

Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environmental change is not well known. Metagenomes allow examination of genetic responses of the entire microbial community to environmental change. However, it is challenging to link metagenomes directly to biogeochemical process rates. Here, we investigate metagenomic responses in natural bacterioplankton communities to simulated environmental stressors in the Baltic Sea, including increased river water input, increased nutrient concentration, and reduced oxygen level. This allowed us to identify informative prokaryotic gene markers, responding to environmental perturbation. Our results demonstrate that metagenomic and metabolic changes in bacterial communities in response to environmental stressors are influenced both by the initial community composition and by the biogeochemical factors shaping the functional response. Furthermore, the different sources of dissolved organic matter (DOM) had the largest impact on metagenomic blueprint. Most prominently, changes in DOM loads influenced specific transporter types reflecting the substrate availability and DOC assimilation and consumption pathways. The results provide new knowledge for developing models of ecosystem structure and biogeochemical cycling in future climate change scenarios and advance our exploration of the potential use of marine microorganisms as markers for environmental conditions.

A new approach for evaluating transformations of dissolved organic matter (DOM) via high-resolution mass spectrometry and relating it to bacterial activity

Streams are important sites of transformation of dissolved organic matter (DOM). The molecular characterization of DOM-quality changes requires sophisticated analytical evaluation techniques. The goal of our study was to link molecular DOM transformation with bacterial activity. We measured the degradation of leaf leachate over a gradient of bacterial production obtained by different rates of percolation of sediments in seven experimental flumes on five sampling dates. We developed a new strategy for evaluating molecular formula data sets obtained by ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS), in which the time-dependent change of component abundance was fitted by a linear regression model after normalization of mass peak intensities. All components were categorized by calculating the slope (change of percent intensity per day) in each of the seven flumes. These slopes were then related to cumulative bacterial production. The concentration of DOM decreased quickly in all flumes. Bacterial activity was higher in flumes with percolated sediment than in those without percolation, whereas plankton bacterial activity was higher in flumes without percolation or without sediment. There were no differences in molecular-DOM characteristics between flumes, but there were distinct changes over time. Positive slopes, i.e. increasing intensities over time, were found for small molecules (MW < 450 Da) and high O/C ratios, whereas decreasing intensities were observed less often and only for large molecules and low O/C ratios. The positive slopes of produced components showed a positive relationship to bacterial production for small and for oxygen-rich components. The negative slopes of degraded components were negatively related to bacterial production for large and for oxygen-deficient molecules. Overall, the approach provided new insights into the transformation of specific molecular DOM components.

Differential responses of marine, mesohaline and oligohaline bacterial communities to the addition of terrigenous carbon

In response to global warming, increasing quantities of tDOM are transported through estuaries from land to the sea. In this study, we investigated microbial responses to increased tDOM concentrations in three salinity regimes (salinity: 32, 7 and 3) characteristic of the Baltic Sea. Mesocosm experiments performed in May and November revealed low (0-6%) dissolved organic carbon (DOC) utilisation. Molecular DOM analyses using ultrahigh-resolution mass spectrometry identified the terrigenous signal in the tDOM manipulation, but the molecular changes in DOM levels over the course of the experiment were subtle. However, tDOM had significant stimulatory effects on bacterial production in the oligohaline mesocosms. The shift in the bacterial community composition was especially prominent in the tDOM-amended marine and mesohaline mesocosms, but not in the oligohaline mesocosms after 7 and 11 days of incubation. These results suggested the inherent ability of oligohaline bacterial communities to adapt to high tDOM concentrations and therefore to use tDOM. The higher rates of bacterial activity and DOC removal in mesocosms containing UV-pretreated tDOM supported the increased bioavailability of photoinduced, modified tDOM. The overall low rates of microbial tDOM utilisation highlights the importance of abiotic factors in determining the distribution and dynamics of tDOM in estuaries.

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

Dissolved organic matter (DOM) is the main substrate and energy source for heterotrophic bacterioplankton. To understand the interactions between DOM and the bacterial community (BC), it is important to identify the key factors on both sides in detail, chemically distinct moieties in DOM and the various bacterial taxa. Next-generation sequencing facilitates the classification of millions of reads of environmental DNA and RNA amplicons and ultrahigh-resolution mass spectrometry yields up to 10 000 DOM molecular formulae in a marine water sample. Linking this detailed biological and chemical information is a crucial first step toward a mechanistic understanding of the role of microorganisms in the marine carbon cycle. In this study, we interpreted the complex microbiological and molecular information via a novel combination of multivariate statistics. We were able to reveal distinct relationships between the key factors of organic matter cycling along a latitudinal transect across the North Sea. Total BC and DOM composition were mainly driven by mixing of distinct water masses and presumably retain their respective terrigenous imprint on similar timescales on their way through the North Sea. The active microbial community, however, was rather influenced by local events and correlated with specific DOM molecular formulae indicative of compounds that are easily degradable. These trends were most pronounced on the highest resolved level, that is, operationally defined 'species', reflecting the functional diversity of microorganisms at high taxonomic resolution.

Use of ESI-FTICR-MS to Characterize Dissolved Organic Matter in Headwater Streams Draining Forest-Dominated and Pasture-Dominated Watersheds

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) has proven to be a powerful technique revealing complexity and diversity of natural DOM molecules, but its application to DOM analysis in grazing-impacted agricultural systems remains scarce. In the present study, we presented a case study of using ESI-FTICR-MS in analyzing DOM from four headwater streams draining forest- or pasture-dominated watersheds in Virginia, USA. In all samples, most formulas were CHO compounds (71.8–87.9%), with other molecular series (CHOS, CHON, CHONS, and CHOP (N, S)) accounting for only minor fractions. All samples were dominated by molecules falling in the lignin-like region (H/C = 0.7–1.5, O/C = 0.1–0.67), suggesting the predominance of allochthonous, terrestrial plant-derived DOM. Relative to the two pasture streams, DOM formulas in the two forest streams were more similar, based on Jaccard similarity coefficients and nonmetric multidimensional scaling calculated from Bray-Curtis distance. Formulas from the pasture streams were characterized by lower proportions of aromatic formulas and lower unsaturation, suggesting that the allochthonous versus autochthonous contributions of organic matter to streams were modified by pasture land use. The number of condensed aromatic structures (CAS) was higher for the forest streams, which is possibly due to the controlled burning in the forest-dominated watersheds and suggests that black carbon was mobilized from soils to streams. During 15-day biodegradation experiments, DOM from the two pasture streams was altered to a greater extent than DOM from the forest streams, with formulas with H/C and O/C ranges similar to protein (H/C = 1.5–2.2, O/C = 0.3–0.67), lipid (H/C = 1.5–2.0, O/C = 0–0.3), and unsaturated hydrocarbon (H/C = 0.7–1.5, O/C = 0–0.1) being the most bioreactive groups. Aromatic compound formulas including CAS were preferentially removed during combined light+bacterial incubations, supporting the contention that black carbon is labile to light alterations. Collectively, our data demonstrate that headwater DOM composition contains integrative information on watershed sources and processes, and the application of ESI-FTICR-MS technique offers additional insights into compound composition and reactivity unrevealed by fluorescence and stable carbon isotopic measurements.

Pyrolysis-gas chromatography-mass spectrometry with electron-ionization or resonance-enhanced-multi-photon-ionization for characterization of polycyclic aromatic hydrocarbons in the Baltic Sea

Polycyclic aromatic hydrocarbons (PAH), as a part of dissolved organic matter (DOM), are environmental pollutants of the marine compartment. This study investigates the origin of PAH, which is supposed to derive mainly from anthropogenic activities, and their alteration along the salinity gradient of the Baltic Sea. Pyrolysis in combination with gas chromatography and two mass selective detectors in one measurement cycle are utilized as a tool for an efficient trace analysis of such complex samples, by which it is possible to detect degradation products of high molecular structures. Along the north-south transect of the Baltic Sea a slightly rising trend for PAH is visible. Their concentration profiles correspond to the ship traffic as a known anthropogenic source, underlined by the value of special isomer ratios such as phenanthrene and anthracene (0.31-0.45) or pyrene and fluoranthene (0.44-0.53). The detection of naphthalene and the distribution of its alkylated representatives support this statement.

Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance.

Pre-treatments, characteristics, and biogeochemical dynamics of dissolved organic matter in sediments: A review

Dissolved organic matter (DOM) in sediments, termed here sediment DOM, plays a variety of important roles in global biogeochemical cycling of carbon and nutrients as well as in the fate and transport of xenobiotics. Here we reviewed sediment DOM, including pore waters and water extractable organic matter from inland and coastal sediments, based on recent literature (from 1996 to 2014). Sampling, pre-treatment, and characterization methods for sediment DOM were summarized. The characteristics of sediment DOM have been compared along an inland to coastal ecosystems gradient and also with the overlying DOM in water column to distinguish the unique nature of it. Dissolved organic carbon (DOC) from inland sediment DOM was generally higher than coastal areas, while no notable differences were found for their aromaticity and apparent molecular weight. Fluorescence index (FI) revealed that mixed sources are dominant for inland sediment DOM, but marine end-member prevails for coastal sediment DOM. Many reports showed that sediments operate as a net source of DOC and chromophoric DOM (CDOM) to the water column. Sediment DOM has shown more enrichment of nitrogen- and sulfur-containing compounds in the elemental signature than the overlying DOM. Fluorescent fingerprint investigated by excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC) further demonstrated the characteristics of sediment DOM lacking in the photo-oxidized and the intermediate components, which are typically present in the overlying surface water. In addition, the biogeochemical changes in sediment DOM and the subsequent environmental implications were discussed with the focus on the binding and the complexation properties with pollutants.

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring

Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open oceans have been the primary focus of studies on aquatic microbes, coastal and brackish ecosystems are now being surveyed. Here, we review so far published studies on microbes in the Baltic Sea, one of the world's largest brackish water bodies, using high throughput sequencing of environmental DNA and RNA. Collectively the data illustrate that Baltic Sea microbes are unique and highly diverse, and well adapted to this brackish-water ecosystem, findings that represent a novel base-line knowledge necessary for monitoring purposes and a sustainable management. More specifically, the data relate to environmental drivers for microbial community composition and function, assessments of the microbial biodiversity, adaptations and role of microbes in the nitrogen cycle, and microbial genome assembly from metagenomic sequences. With these discoveries as background, prospects of using metagenomics for Baltic Sea environmental monitoring are discussed.