Impacts of labile organic carbon concentration on organic and inorganic nitrogen utilization by a stream biofilm bacterial community

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

Although river ecosystems comprise less than 1% of Earth's total non-glaciated area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. As a result, the relevance of microbiome interactions and the impacts they have over time on biogeochemical cycles are poorly understood. To assess how viral and microbial communities change over time, we sampled surface water and pore water compartments of the wastewater-impacted River Erpe in Germany every 3 hours over a 48-hour period resulting in 32 metagenomes paired to geochemical and metabolite measurements. We reconstructed 6,500 viral and 1,033 microbial genomes and found distinct communities associated with each river compartment. We show that 17% of our vMAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to carbon and nitrogen cycling. Together, these findings demonstrate that microbial and viral communities in surface waters of this urban river can exist as stable communities along a flowing river; and raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment

Work on marine biofilms has primarily focused on host-associated habitats for their roles in larval recruitment and disease dynamics; little is known about the factors regulating the composition of reef environmental biofilms. To contrast the roles of succession, benthic communities and nutrients in structuring marine biofilms, we surveyed bacteria communities in biofilms through a six-week succession in aquaria containing macroalgae, coral, or reef sand factorially crossed with three levels of continuous nutrient enrichment. Our findings demonstrate how biofilm successional trajectories diverge from temporal dynamics of the bacterioplankton and how biofilms are structured by the surrounding benthic organisms and nutrient enrichment. We identify a suite of biofilm-associated bacteria linked with the orthogonal influences of corals, algae and nutrients and distinct from the overlying water. Our results provide a comprehensive characterization of marine biofilm successional dynamics and contextualize the impact of widespread changes in reef community composition and nutrient pollution on biofilm community structure.

Application of Machine Learning for eutrophication analysis and algal bloom prediction in an urban river: A 10-year study of the Han River, South Korea

The increasing release of nutrients to aquatic environments has led to great concern regarding eutrophication and the risk of unwanted algal blooms. Based on observational data of 20 water quality parameters measured on a monthly basis at 40 stations from 2011 to 2020, this study applied different Machine Learning (ML) algorithms to suggest the best option for algal bloom prediction in the Han River, a large river in South Korea. Eight different ML algorithms were categorized into several groups of statistical learning, regression family, and deep learning, and were then compared for their suitability to predict the chlorophyll-derived trophic index (TSI-Chla). ML algorithms helped identify the most important water quality parameters contributing to algal bloom prediction. The ML results confirmed that eutrophication and algal proliferation were governed by the complex interplay between nutrients (nitrogen and phosphorus), organic contaminants, and environmental factors. Of the models tested, the adaptive neuro-fuzzy inference system (ANFIS) exhibited the best performance owing to its consistent and outperforming prediction both quantitatively (i.e., via regression) and qualitatively (i.e., via classification), which was evidenced by the lowest value of mean absolute error (MAE) of 0.09, and the highest F1-score, Recall and Precision of 0.97, 0.98 and 0.96, respectively. In a further step, a representative web application was constructed to assist common users to predict the trophic status of the Han River. This study demonstrated that ML techniques are not only promising for highly accurate water quality modeling of urban rivers, but also reduce time and labor intensity for experiments, which decreases the number of monitored water quality parameters, providing further insights into the driving factors of water quality deterioration. They ultimately help devise proactive strategies for sustainable water management.

Interactions between Humic Substances and Microorganisms and Their Implications for Nature-like Bioremediation Technologies

The state of the art of the reported data on interactions between microorganisms and HSs is presented herein. The properties of HSs are discussed in terms of microbial utilization, degradation, and transformation. The data on biologically active individual compounds found in HSs are summarized. Bacteria of the phylum Proteobacteria and fungi of the phyla Basidiomycota and Ascomycota were found to be the main HS degraders, while Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were found to be the predominant phyla in humic-reducing microorganisms (HRMs). Some promising aspects of interactions between microorganisms and HSs are discussed as a feasible basis for nature-like biotechnologies, including the production of enzymes capable of catalyzing the oxidative binding of organic pollutants to HSs, while electron shuttling through the utilization of HSs by HRMs as electron shuttles may be used for the enhancement of organic pollutant biodegradation or lowering bioavailability of some metals. Utilization of HSs by HRMs as terminal electron acceptors may suppress electron transfer to CO2, reducing the formation of CH4 in temporarily anoxic systems. The data reported so far are mostly related to the use of HSs as redox compounds. HSs are capable of altering the composition of the microbial community, and there are environmental conditions that determine the efficiency of HSs. To facilitate the development of HS-based technologies, complex studies addressing these factors are in demand.

Influence of the flooded time on the performance of a tidal flow constructed wetland treating urban stream water

A vertical subsuperficial tidal flow constructed wetland (TFCW) operated under flooded time (FT) variation, was evaluated in the removal of carbonaceous, nitrogenous, and phosphorous matter from urban stream water. The TFCW downflow (117 L) was filled with bricks (44% porosity) and vegetated with Althernanthera philoxeroides (32 plants m^-2). The TFCW was operated under different flooded times - Stage A (48 h), B (36 h), C (24 h), and D (12 h), organic loading rates of 19.58-43.83 gCOD m^-2 d^-1, 3.68-6.94 gTN m^-2 d^-1 and 0.93-2.00 gTP m^-2 d^-1 and volumetric load rates of 46.8, 58.5, 78.0 and 11.7 L d^-1. No significant differences were observed in the removal efficiencies to Chemical Oxygen Demand (COD 66 to 94%), Total Ammonia Nitrogen (TAN 58 to 87%), and Total Nitrogen (TN 53 to 78%) among the stages, and nitrate concentrations lower than 6 mg L^-1 in the effluent. High Total Phosphorus removal was obtained in FT of 48 h (TP 79%). Total phosphorus loading rate was a limiting factor in TP removal, which reduced along with the reduction of FT. The nitrifying community was present over time since ammonia-oxidizing bacteria (Nitrosospira) and nitrite-oxidizing bacteria (Nitrobacter and Nitrospira) were identified in operational stages with variation in relative abundance, but TAN removal efficiency did not show significant differences. There was no change in the denitrifying community structure, indicating that FT did not influence the TN removal. A. philoxeroides was responsible for phytoextraction of 2.1% of TN and 2.7% of TP from the total removed by TFCW. TN removal (65%) was attributed to adsorption in the filtering material and microbial metabolism during the rest time. The findings of this study suggest FT of 12 h to remove COD and TN, and equal to or higher than 48 h to remove TP.

Two Food Waste By-Products Selectively Stimulate Beneficial Resident Citrus Host-Associated Microbes in a Zero-Runoff Indoor Plant Production System

The global production of food waste is a far-reaching problem with sizable financial, ethical, social, and environmental costs. Over 66 million tons of food waste is produced annually in the United States alone. This waste can be converted into valuable digestate by-products that promote a circular economy within agri-food systems. The present work investigated the use of two liquid digestates of microaerobic fermentation from mixed food waste and beer mash, respectively, as biostimulants for non-bearing citrus plants (nursery stock) grown in a zero-runoff greenhouse system with recirculating irrigation. The digestates' impact on the structure and diversity of the microbiota was determined on the irrigation water, soil, leaves, roots, and rhizosphere of citrus plants. A combination of culture-dependent (selective media) and culture-independent approaches (Next-Generation Sequencing) was used to assess the composition of the microbial communities and to single out the presence of foodborne pathogens. Our results suggest that the use of digestates is safe (i.e., no human or plant pathogens were present in the digestates or enriched in the plant production system following amendments). Digestates application to the irrigation water reduced the bacterial diversity within 24–48 h and selectively and significantly stimulated beneficial resident host-associated microorganisms (Pseudomonas putida) by two to three orders of magnitude. Carbon dynamics were analyzed in the nutrient solutions by measuring dissolved organic carbon and characterizing carbon species through gas chromatography-electron ionization-mass spectrometry. Our results indicate that dissolved organic carbon in the recirculating irrigation water spikes after each digestate amendment and it is quickly metabolized by bacteria, plateauing 24 h after application. Soil carbon, nitrogen, and nutrient dynamics were also analyzed, and results suggest that digestates increased the concentration of some plant nutrients in soils without causing a surge of potentially toxic elements. This study represents a proof-of-concept for the safe re-use of organic wastes, from farming and consumers, in agriculture. Implementing this type of integrated plant production system could reduce the environmental impact of food waste and benefit the public by improving soil health, reducing agricultural footprint, and increasing crop fitness by deploying a method based on a circular economy and sustainable food production approaches.

Available Dissolved Organic Carbon Alters Uptake and Recycling of Phosphorus and Nitrogen from River Sediments

Concurrent with nutrient pollution, agriculture has significantly impacted the quantity, composition, and bioavailability of catchment-derived dissolved organic carbon (DOC) in stream ecosystems. Based on the stoichiometric theory, we tested the hypothesis that bioavailable DOC will stimulate the heterotrophic uptake of soluble reactive P (SRP) and inorganic nitrogen in stream sediments. In a simplified laboratory column flow-through study, we exposed stream sediments to additions of glucose, nitrate, and phosphate alone and in combination (+C, +NP, +CNP), and calculated gross and net changes in DOC and nutrients via a mass balance approach. Our results show that glucose-C increased nutrient uptake, but also that NP additions resulted in the enhanced consumption of both native and added organic C. The effects of C addition were stronger on N than P uptake, presumably because labile C stimulated both assimilation and denitrification, while part of the P uptake was due to adsorption. Internal cycling affected net nutrient uptake due to losses of dissolved organically-complexed P and N (DOP and DON). Overall, our study shows that increases in the stoichiometric availability of organic carbon can stimulate N and P sequestration in nutrient-polluted stream sediments. Future studies are required to assess the effects of complex organic carbon sources on nutrient uptake in stream sediments under different environmental conditions, and whether these stoichiometric relations are relevant for ecosystem management.

Effects of terrigenous organic substrates and additional phosphorus on bacterioplankton metabolism and exoenzyme stoichiometry

Bamboo, as a pioneer vegetation, often forms forests on bare lands after catastrophic landslides. Compared to evergreen forest soil, bamboo forest soil is much more labile, with a higher percentage of microbially derived organic carbon (OC), lower molecular weight, and lower humic acid content. We hypothesised that different terrigenous organic matter (tOM) sources with varying lability and phosphorus (P) availability select for bacterioplankton with distinct metabolic pathways.We incubated natural bacterioplankton assemblages with tOM leached from bamboo forest soil (BOM) and evergreen forest soil (EOM) and compared these to a lake water control. To test if microbial metabolism would be limited by OC or P availability of each tOM treatment, we used acetate as an extra labile OC source and phosphate as an inorganic P source. Bacterial metabolism was measured by analysing respiration via O2 consumption and production via tritiated thymidine (TdR) assimilation.Bacterioplankton metabolism is limited by the availability of P in BOM substrates. When using BOM, bacteria had higher enzymatic activities for phosphatase. The nutrients required for bacterial biomass seemed to be derived from organic matter. Under BOM treatment, bacterial production (BP) (0.92 ± 0.13 μg C L-1 hr-1) and cell specific TdR assimilation rates (0.015 ± 0.002 10-18 M TdR cell-1 hr-1) were low. Adding P enhanced BP (BOM+P 1.52 ± 0.31 and BOM+C+P 2.25 ± 0.37 μg C L-1 hr-1) while acetate addition had no significant effect on BOM treatment.This indicated that the bacteria switched to using added inorganic P to respire a P-limited BOM substrate, which increased total BP and abundance, resulting in even more active respiration and lower growth efficiency. We also found higher activities for chitin-degrading enzyme β-N-acetylglucosaminidase, which is associated with N mining from aminosaccharides.Microbes using EOM, however, did not change metabolic strategies with additional acetate or/and inorganic P. This is due to higher concentrations of organic P in EOM substrates and the presence of inorganic N in the EOM leachates an alternative nutrient source. Bacteria produced β-glucosidase and leucyl-aminopeptidase in order to utilise the humic substances, which sustained greater bacterial abundance, higher BP (2.64 ± 0.39 μg C L-1 hr-1), and lower cell-specific respiration. This yielded a much higher bacterial growth efficiency (15 ± 9.2%) than the lake water control.Our study demonstrated the aquatic metabolic discrepancy between tOM of different forest types. Bacterioplankton in BOM and EOM exhibit distinct metabolic responses. Bacterial metabolic strategy when using BOM implied that the supposedly stabilised biomass OM might be efficiently used by aquatic bacterioplankton. As the labile and nutrient-deficient BOM is more susceptible to the influence of additional nutrients, fertiliser residues in bamboo forest catchments might have a stronger effect on aquatic bacterial metabolic pathways. Thus, it is important to take tOM differences into consideration when building models to estimate soil carbon turnover rates along a terrestrial-aquatic continuum.

Priming effect of autochthonous organic matter on enhanced degradation of 17α-ethynylestradiol in water-sediment system of one eutrophic lake

Climate change and increasing eutrophication are expected to increase the release of autochthonous organic matter (OM) to sediments, where most contaminants are transformed or mineralized in freshwater lakes. This study sought to evaluate how cyanobacteria- and macrophyte-derived OM (COM and MOM) affected the microbial attenuation of 17α-ethinylestradiol (EE2) in the sediment from eutrophic Lake Taihu in China. In two months of water-sediment microcosm experiments, the input of COM and MOM both promoted EE2 degradation more strongly than humic acids, and the degradation efficiency was significantly and positively correlated with the cometabolism of increasing organic carbon in sediments (P < 0.001). The enhanced degradation was explained by responses of indigenous bacterial community to OM amendment as a priming effect. The immediate breakdown of biodegradable components such as proteinaceous substances in COM and MOM remarkably augmented the metabolic activity of bacteria in terms of the stimulated activity of extracellular enzymes including fluorescein diacetate and dehydrogenase, as well as the elevated production of proteins and polysaccharides in extracellular polymeric substances. In the meantime, the bacterial community composition was reshaped toward a more eutrophic state, leading to the clear upregulation of metabolic function genes of organic carbon and xenobiotics. Correlation-based network analysis further determined the strong facilitative coordination between the community members and the compositional variability of OM in the cometabolism. These results suggest that cyanobacterial blooms-dominated zones are potential hotspot areas for steroid estrogen attenuation, a finding of significance for the control and management of complex pollution in freshwater lakes.

Differences in bioavailability of canonical and non-canonical D-amino acids for marine microbes

Dissolved organic matter (DOM) accounts for >95% of total marine organic matter, and >95% of marine DOM is refractory to biodegradation. The recalcitrancy of DOM determines its residence time and thus is of great concern regarding to carbon sequestration in the ocean. However, the recalcitrancy of DOM not only varies among different compounds but also within different conformations of a same molecule such as L-amino acids (L-AAs) and D-amino acids (D-AAs). While the former is labile, the latter is refractory and used as a proxy for estimation of bacterial refractory DOM in the ocean. However, some D-AAs are also reported to be bioavailable. To clarify the controversy, we examined the bioavailability of two types of D-AAs: canonical D-AAs, which mainly present as bacterial cell wall components, and non-canonical D-AAs (NCDAAs), which are secreted by various bacteria as signaling molecules in bacterial physiology. Bioassay experiments were conducted with nine marine bacterial strains and a natural microbial community. D-AAs were poorly utilized by the strains as sole carbon or nitrogen sources compared with L-AAs, in addition, NCDAAs were barely used compared with canonical D-AAs. In comparison, the microbial community consumed all three canonical D-AAs (D-alanine, D-aspartic acid and D-glutamic acid) as efficiently as their corresponding L-AAs when supplied separately; however, L-AAs were preferentially used over D-AAs when both forms were provided simultaneously. Remarkably, two NCDAAs, D-methionine and D-leucine, were poorly utilized regardless of the presence of the L-enantiomers. It was found for the first time that NCDAAs are relatively more refractory than canonical D-AAs to microbial utilization. This novel recognition of difference in recalcitrancy between NCDAAs and canonical D-AAs lays the foundation for a better understanding of carbon cycling and more accurate estimation of carbon storage in the ocean.

Inhibitory effect of phenol on wastewater ammonification

This study aimed to elucidate inhibitory effect of phenol on ammonification of dissolved organic nitrogen (DON) in wastewater. Laboratory incubation experiments were conducted using primary and secondary effluent samples spiked with phenol (100-1000 mg/L) and inoculated with mixed cultures, pure strains of phenol-degrading bacteria (Acinetobacter sp. and Pseudomonas putida F1), and/or an ammonia oxidizing bacterium (Nitrosomonas europaea). DON concentration was monitored with incubation time. Phenol suppressed the ammonification rate of DON up to 62.9%. No or minimal ammonification inhibition was observed at 100 mg/L of phenol while the inhibition increased with increasing phenol concentration from 250 to 1000 mg/L. The inhibition was curtailed by the presence of the phenol-degrading bacteria. DON was ammonified in the samples inoculated with only N. europaea and the ammonification was also inhibited by phenol. The findings suggest that high phenol in wastewater could result in low ammonification and high DON in the effluent.

Seagrass litter decomposition: an additional nutrient source to shallow coastal waters

Seagrass ecosystems are vital for its regulatory services yet, highly threatened by degradation due to human pressures. Decomposition of two tropical seagrass species (Cymodocea serrulata and Cymodocea rotundata) was studied and compared, to understand their potential in generating additional nutrients to coastal waters. Release of carbon, nitrogen and phosphorus during the decomposition process of seagrass wracks was estimated in bacteria-active (non-poisoned) and bacteria-inhibited (poisoned) conditions from shore-washed fresh seagrass, sampled from Palk Bay, India. Incubation experiments for 25 days indicated a near three times higher concentration of dissolved organic carbon (DOC) in bacteria-inhibited flasks compared to bacteria-active conditions for both species. The maximum leaching rates of DOC, TDN and TDP were found to be 294, 65.1 and 11.2 μM/g dry wt/day, respectively. Further, higher release of dissolved inorganic nitrogen (DIN) (> 1.3 times) was documented from the bacteria-active flask, highlighting the significance of microbial process in generating bio-available nutrients from decaying seagrass. Faster decomposition (0.014 ± 0.004 day^-1) in the initial stages (up to 8 days) compared to the later stages (0.005 ± 0.001 day^-1) indicated a rapid loss of biomass carbon during the initial leaching process and its relative importance in the decomposition pathway. The decomposition rate is best described by a single-stage exponential decay model with a half-life of 41 days. It is estimated that the total seagrass litter available along the Palk Bay coast is about ~ 0.3 Gg with high potential of additional nitrogen (0.9 ± 0.5 Mg) and phosphorus (0.3 ± 0.1 Mg) supply to the adjacent coastal waters.

Trophic Strategies Influence Metal Bioaccumulation in Detritus-Based, Aquatic Food Webs

Metal accumulation in aquatic food webs is mediated by physiochemical parameters of the environment and organismal traits. Trophic strategies influence an organisms' exposure to metal pollution, but links between trophic ecology and exposure to divalent metals are relatively understudied. While organically bound metals are typically considered unavailable for uptake, organisms directly consuming dissolved organic carbon (DOC) and bacteria-via the microbial loop-must also be consuming organically bound metals. Hence, we predicted animals feeding within the microbial loop would accumulate metals through their diet. To test this prediction, we exploited dietary differences between two organisms, Simulium vittatum, a filter-feeding black fly and Hyalella azteca, a shredding detritivore. We exposed both species to three treatments of DOC (labile, recalcitrant, and no additional DOC) that were crossed with exposure to variable copper (Cu) concentrations (2-14 μg L^-1) in laboratory microcosms. As predicted, H. azteca experienced a buffering effect by DOC. However, this pattern was not apparent for S. vittatum. Our results highlight the importance of considering trophic strategies when examining the impacts of metal pollution on aquatic communities, and demonstrate the potential for the microbial loop to facilitate metal uptake in freshwater food webs.

Investigation of an early season river flood pulse: Carbon cycling in a subtropical estuary

The January 2016 Bonnet Carré Spillway (BCS) opening resulted in a large-scale Mississippi River (MR) flood discharge that qualitatively and quantitatively impacted the dissolved organic matter (DOM) cycling in the Lake Pontchartrain Estuary (LPE) located in Louisiana, USA. This early season flood event was a result of the delay of snow formation caused by warmer than normal watershed temperatures. During the diversion period and the subsequent weeks, the LPE water temperature remained lower than pre-flood water temperatures, suppressing carbon cycling. Following that period, the water temperature increased, leading to an increase in the rate of abiotic and biological carbon processing (i.e., mineralization, degradation, and consumption). There were multiple and abnormally high discharges into LPE from the northern tributaries, totaling 43% of the MR flood discharge. As a secondary DOM source, the northern tributaries discharge was qualitatively and quantitatively different from the discharge originating from the river or estuarine sources. The dominant DOM source was determined using satellite images in conjunction with UV-Vis, fluorescence EEMs, and PARAFAC indicators. Overall, the three sources (MR, northern tributaries, and LPE) characteristics were identified by UV-Vis, fluorescence EEMs, and PARAFAC parameters, namely: i) spectral slope (S₂₇₅), serving as an indicator of lignin-like compounds' molecular weights, with a trend of MR > northern tributaries > LPE; ii) biological index (BIX), indicating freshness of DOM, with a trend of LPE > MR > northern tributaries; and iii) Fluorophore T intensity, serving as an indicator of the amount of terrestrial-like sourced DOM, with a trend of northern tributaries > LPE > MR. It was possible to identify DOM sources and monitor DOM transformation in the water column, increasing our understanding of DOM, carbon, and nitrogen ecological processing.

Differences in N loading affect DOM dynamics during typhoon events in a forested mountainous catchment

The dissolved organic matter (DOM) and nutrient dynamics in small mountainous rivers (SMRs) strongly depend on hydrologic conditions, and especially on extreme events. Here, we investigated the quantity and quality of DOM and inorganic nutrients during base-flow and typhoon events, in a chronically N-saturated mainstream and low N-loaded tributaries of a forested small mountainous reservoir catchment in Taiwan. Our results suggest that divergent transport mechanisms were triggered in the mainstream vs. tributaries during typhoons. The mainstream DON increased from 3.4 to 34.7% of the TDN pool with a static DOC:NO₃-N ratio and enhanced DOM freshness, signalling a N-enriched DOM transport. Conversely, DON decreased from 46 to 6% of the TDN pool in the tributaries and was coupled with a rapid increase of the DOC:NO₃-N ratio and humified DOM signals, suggesting the DON and DOC were passively and simultaneously transported. This study confirmed hydrology and spatial dimensions being the main drivers shaping the composition and concentration of DOM and inorganic nutrients in small mountainous catchments subject to hydrologic extremes. We highlighted that the dominant flow paths largely controlled the N-saturation status and DOM composition within each sub-catchment, the effect of land-use could therefore be obscured. Furthermore, N-saturation status and DOM composition are not only a result of hydrologic dynamics, but potential agents modifying the transport mechanism of solutes export from fluvial systems. We emphasize the importance of viewing elemental dynamics from the perspective of a terrestrial-aquatic continuum; and of taking hydrologic phases and individual catchment characteristics into account in water quality management.

Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater.

Extractable pool of biochar controls on crop productivity rather than greenhouse gas emission from a rice paddy under rice-wheat rotation

The role of extractable pool of biochar in crop productivity and soil greenhouse gas (GHGs) emission is not yet clear. In this study, two biochars with and without extraction was added to a paddy before rice transplantation at 20 t·ha^-1. Crop yield, plant traits and greenhouse gas emission monitored throughout a rice-wheat rotation. Between the biochar treatments, changes in bulk density and microbial biomass carbon were insignificant. However, the increase in organic carbon was similar between maize and wheat biochars while higher under bulk wheat biochar than extracted one. The increase in available P and K was higher under wheat than maize biochar regardless of extraction. Moreover, the increase in plant traits and grain yield, in rice season only, was higher under bulk than extracted biochars. Yet, there was no difference in changes in GHGs emission between bulk and extracted biochars regardless of feedstock. Nevertheless, increased methane emission for rice season was lower under extracted biochars than bulk ones. Overall, crop productivity rather than GHGs emission was affected by treatment of extraction of biochars. Thus, use of unextracted biochar is recommended for improving soil crop productivity in the paddy soils.

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates

Background

The nitrogen (N) cycle consists of complex microbe-mediated transformations driven by a variety of factors, including diversity and concentrations of N compounds. In this study, we examined taxonomic diversity and N substrate utilization by heterotrophic bacteria isolated from streams under complex and simple N-enrichment conditions.

Results

Diversity estimates differed among isolates from the enrichments, but no significant composition were detected. Substrate utilization and substrate range of bacterial assemblages differed within and among enrichments types, and not simply between simple and complex N-enrichments.

Conclusions

N substrate use patterns differed between isolates from some complex and simple N-enrichments while others were unexpectedly similar. Taxonomic composition of isolates did not differ among enrichments and was unrelated to N use suggesting strong functional redundancy. Ultimately, our results imply that the available N pool influences physiology and selects for bacteria with various abilities that are unrelated to their taxonomic affiliation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0993-7) contains supplementary material, which is available to authorized users.