Soil Organic Carbon Enrichment Triggers In Situ Nitrogen Interception by Phototrophic Biofilms at the Soil-Water Interface: From Regional Scale to Microscale.

Phototrophic biofilms are easy to grow at sediment/soil-water interfaces (SWIs) in shallow aquatic ecosystems and greatly impact nutrient biogeochemical cycles. However, the pathways by which they contribute to nitrogen interception and interact with sediment/soil remains largely unknown. Here, we conducted a field investigation in paddy fields in various regions of China and found that nitrogen immobilized in biofilm biomass significantly positively correlated with soil organic carbon (SOC) content. A microcosm experiment showed that this was due to increased bacterial and algal diversity, biomass accumulation, and inorganic nitrogen assimilation at high SOC, especially high dissolved organic carbon (DOC) levels. The metatranscriptomics results further verified that many KO groups of PSII, PSI, AP, and PC in antenna proteins and glutamate synthesis were distinctly expressed at elevated SOC and DOC levels. Our results elucidated the effects and possible pathways of how SOC enrichment triggers photosynthesis and nitrogen immobilization by phototrophic biofilms. The results will provide meaningful information for in situ nitrogen interception by using phototrophic biofilms at the SWI in human-made wetlands to change internal nitrogen cycling.

Occurrence and removal of micropollutants in full-scale aerobic, anaerobic and facultative wastewater treatment plants in Brazil.

This study aims to evaluate micropollutant occurrence and removal in a low-middle income country (LMIC) by investigating the occurrence of 28 chemicals from different classes (triclosan, 15 polycyclic aromatic hydrocarbons (PAHs), 4 estrogens and 8 polybrominated diphenyl ether (PBDE) congeners) in three technologically diverse full-scale Brazilian wastewater treatment plants (WWTPs). These chemicals were detected at concentrations similar to those reported in other low-middle income countries (LMICs) and high-income countries (HICs) (0.1-49 µg/L) indicating their widespread use globally and the need for more studies in LMICs that are typically characterized by relatively inadequate wastewater treatment barriers. Among the three different WWTPs investigated for removal of these chemicals, the least energy intensive system, waste stabilization ponds (WSPs), was the most effective (95-99%) compared to the activated sludge (79-94%), and Up-flow sludge blanket reactor (UASB) with trickling filters system (89-95%). These results highlight the potential of WSPs for micropollutant removal-especially in warm climates. However, the effluent from all three WWTP could pose a risk to aquatic organisms when discharged into the receiving waters as the effluent concentrations of triclosan, some estrogens, PAHs and BDE 209 were above European environmental quality standards (EQS) or predicted no effect concentration (PNEC values), indicating that receiving water bodies could benefit from further treatment. In combination, these results help to further understand prevailing concentrations of micropollutants globally and fate in current wastewater treatment systems.

Temperature and immigration effects on quorum sensing in the biofilms of anaerobic membrane bioreactors.

Quorum sensing (QS), a microbial communication mechanism modulated by acyl homoserine lactone (AHL) molecules impacts biofilm formation in bioreactors. This study investigated the effects of temperature and immigration on AHL levels and biofouling in anaerobic membrane bioreactors. The hypothesis was that the immigrant microbial community would increase the AHL-mediated QS, thus stimulating biofouling and that low temperatures would exacerbate this. We observed that presence of immigrants, especially when exposed to low temperatures indeed increased AHL concentrations and fouling in the biofilms on the membranes. At low temperature, the concentrations of the main AHLs observed, N-dodecanoyl-L-homoserine lactone and N-decanoyl-L-homoserine lactone, were significantly higher in the biofilms than in the sludge and correlated significantly with the abundance of immigrant bacteria. Apparently low temperature, immigration and denser community structure in the biofilm stressed the communities, triggering AHL production and excretion. These insights into the social behaviour of reactor communities responding to low temperature and influx of immigrants have implications for biofouling control in bioreactors.

Low-Temperature Pretreatment of Organic Feedstocks with Selected Mineral Wastes Sustains Anaerobic Digestion Stability through Trace Metal Release.

A low-cost approach for enhancing mesophilic (37 °C) anaerobic digestion (AD) of organic waste using a low-temperature (37 °C) pretreatment with different mineral wastes (MW) was investigated. A higher and stable methane production rate, in comparison to MW-free controls, was achieved for 80 days at organic loading rates of 1-2 g VS/L·d, using a feed substrate pretreated with incinerator bottom ash (IBA). The boiler ash and cement-based waste pretreatments also produced high methane production rates but with some process instability. In contrast, an incinerator fly ash pretreatment showed a progressive decrease in methane production rates and poor process stability, leading to reactor failure after 40 days. To avoid process instability and/or reactor failure, two metrics had to be met: (a) a methanogenesis to fermentation ratio higher than 0.6 and (b) a cell-specific methanogenic activity to cell-specific fermentation activity ratio of >1000. The prevalence of Methanofastidiosum together with a mixed community of acetoclastic (Methanosaeta) and hydrogenotrophic (Methanobacterium) methanogens in the stable IBA treatment indicated the importance of Methanofastidiosum as a potential indicator of a healthy and stable reactor.

Dam Construction as an Important Anthropogenic Activity Disturbing Soil Organic Carbon in Affected Watersheds.

To explore whether and how anthropogenic activities related to surface water regulation (i.e., dam construction) disturb soil ecosystems in the surrounding uplands, a long-term monitoring program was conducted from 1998 to 2017 in the Three Gorges Reservoir Region, China. The Three Gorges Dam (TGD) is the largest hydraulic engineering project in the world. We present a direct, ecosystem-scale demonstration of changes in the soil organic carbon (SOC) content in the TGD watershed before and after the surface water was reshaped. The average SOC content decreased from 12.9 to 9.5 g/kg between 2004 and 2012 and then recovered to 13.8 g/kg in 2017. Dynamics of SOC were partly attributed to shifts in the composition of soil microbial communities responsible for carbon biogeochemistry. The shifts in microbial taxa were associated with the changed microclimate affected by the TGD as well as global and regional climate variability. The microclimate, soil microorganisms, and plant organic carbon input explained 40.2% of the variation in the SOC content. This study revealed that dam construction was an important and indirect driver for the SOC turnover, and the subsequent effects on the upland soil ecosystem must be considered when large-scale disturbance activities (such as dam construction) are conducted in the future.

The effect of anode potential on current production from complex substrates in bioelectrochemical systems: a case study with glucose.

Anode potential can affect the degradation pathway of complex substrates in bioelectrochemical systems (BESs), thereby influencing current production and coulombic efficiency. However, the intricacies behind this interplay are poorly understood. This study used glucose as a model substrate to comprehensively investigate the effect of different anode potentials (- 150 mV, 0 mV and + 200 mV) on the relationship between current production, the electrogenic pathway and the abundance of the electrogenic microorganisms involved in batch mode fed BESs. Current production in glucose-acclimatized reactors was a function of the abundance of Geobacteraceae and of the availability of acetate and formate produced by glucose degradation. Current production was increased by high anode potentials during acclimation (0 mV and + 200 mV), likely due to more Geobacteraceae developing. However, this effect was much weaker than a stimulus from an artificial high acetate supply: acetate was the rate-limiting intermediate in these systems. The supply of acetate could not be influenced by anode potential; altering the flow regime, batch time and management of the upstream fermentation processes may be a greater engineering tool in BES. However, these findings suggest that if high current production is the focus, it will be extremely difficult to achieve success with complex waste streams such as domestic wastewater.

Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers.

Syntrophic acetate oxidation (SAO) plays a pivotal role in biogas production processes when aceticlastic methanogens are inhibited. Despite the importance of SAO, the metabolic interactions and syntrophic growth of the organisms involved are still poorly understood. Therefore, we studied growth parameters and interactions within constructed defined cocultures comprising the methanogen Methanoculleus bourgensis and one, or several, of the syntrophic acetate oxidizers Syntrophaceticus schinkii, [ Clostridium] ultunense, and Tepidanaerobacter acetatoxydans and a novel, uncharacterized bacterium. Cultivation experiments in a design-of-experiment approach revealed positive effects on methane production rate of increased ammonium levels (up to 0.2 M), temperature (up to 45 °C), and acetate concentrations (0.15-0.30 M). Molecular analyses and thermodynamic calculations demonstrated close interlinkages between the microorganisms, with available energies of -10 kJ/mol for acetate oxidation and -20 kJ/mol for hydrogenotrophic methanogenesis. The estimated generation time varied between 3 and 20 days for all syntrophic microorganisms involved, and the acetate minimum threshold level was 0.40-0.45 mM. The rate of methanogenesis depended on the SAO bacteria present in the culture. These data are beneficial for interpretation of SAO prevalence and competiveness against aceticlastic methanogens in anaerobic environments.

Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim.

Domestic wastes, ranging from sewage and sludge to municipal solid waste, are usually treated in bioprocessing systems. These systems are regarded as main conduits for the elevated levels of antibiotic resistance genes (ARGs) observed in the environment. This paper mainly reviews recent studies on the occurrence and dynamics of ARGs in wastewater bio-treatment systems and discusses the ins and outs of ARG dissemination from the perspective of the microbial community. Our analysis shows that concentration of antibiotics through adsorption to microbial aggregates triggers the bacteria to acquire ARGs, which can be facilitated by the presence of mobile genetic elements. Notably, the acquisition and flow of ARGs during the rapid dissemination process is directed towards and for the best interests of the microbial community as a whole, and is influenced by surrounding nutrient levels, toxicant types, and sensitivities of the species in the prevailing antibiotic-stressed conditions. Furthermore, our review argues that predation of ARG-carrying bacteria by bacteriophages does periodically enhance the accessibility of ARGs to bacteria, which indirectly facilitates the recruitment of ARGs into environmental microbial communities.

Perspective of harnessing energy from landfill leachate via microbial fuel cells: novel biofuels and electrogenic physiologies.

Organic carbon, nitrogen, and sulfur are highly concentrated in municipal solid waste (MSW) landfill leachate, which usually frustrates conventional leachate treatment technologies from the perspective of energy costs. Therefore, the possibility of converting leachate to a new energy source via microbial fuel cell (MFC) technology has been examined recently. This paper summarizes the power output and energy recovery efficiency of the leachate-fed MFCs according to different feeding patterns, cell structures, and loading rates. Also, we assess potential energy-generating chemicals in leachate like nitrogen and sulfur compounds and propose alternative pathways, which may lift strict ratios between organic carbon and nitrogen content in conventional denitrification of leachate and are expected to achieve a higher voltage than traditional organic-oxygen based cells. Although currently power output of leachate-fed MFCs is limited, it seems well possible that dynamic characteristics of MSW leachates and microbial physiologies underlying some bio-electrochemically efficient activities (e.g., direct interspecies electron transfer) could be stimulated in MFC systems to improve the present status.

The Gibbs free energy of formation of halogenated benzenes, benzoates and phenols and their potential role as electron acceptors in anaerobic environments.

The sequence of redox reactions in the natural environment generally follows the electron affinity of the electron acceptors present and can be rationalized by the redox potentials of the appropriate half-reactions. Answering the question how halogenated aromatics fit into this sequence requires information on their Gibbs free energy of formation values. In 1992 Gibbs free energy data for various classes of halogenated aromatic compounds were systematically explored for the first time based on Benson's group contribution method. Since then more accurate quantum chemical calculation methods have become available. Here we use these methods to estimate enthalpy and Gibbs free energy of formation values of all chlorinated and brominated phenols. These data and similar state-of-the-art datasets for halogenated benzenes and benzoates were then used to calculate two-electron redox potentials of halogenated aromatics for standard conditions and for pH 7. The results underline the need to take speciation into consideration when evaluating redox potentials at pH 7 and highlight the fact that halogenated aromatics are excellent electron acceptors in aqueous environments.

Low-temperature limitation of bioreactor sludge in anaerobic treatment of domestic wastewater.

Two strategies exist for seeding low-temperature anaerobic reactors: the use of specialist psychrophilic biomass or mesophilic bioreactor sludge acclimated to low temperature. We sought to determine the low-temperature limitation of anaerobic sludge from a bioreactor acclimated to UK temperatures (<15 °C). Anaerobic incubation tests using low-strength real domestic wastewater (DWW) and various alternative soluble COD sources were conducted at 4, 8 and 15 °C; methanogenesis and acidogenesis were monitored separately. Production of methane and acetate was observed; decreasing temperature resulted in decreased yields and increased 'start-up' times. At 4 °C methanogenesis not hydrolysis/acidogenesis was rate-limiting. The final methane yields at 4 °C were less than 35% of the theoretical potential whilst at 8 and 15 °C more than 75 and 100% of the theoretical yield was achieved respectively. We propose that the lower temperature limit for DWW treatment with anaerobic bioreactor sludge lies between 8 and 4 °C and that 8 °C is the threshold for reliable operation.

Dynamics and functions of biomarker taxa determine substrate-specific organic waste composting.

Bacteria are an influential component of diverse composting microbiomes, but their structure and underlying dynamics are poorly understood. This study analyzed the bacterial communities of 577 compost datasets globally and constructed a substrate-dependent catalog with more than 15 million non-redundant 16S rRNA gene sequences. Using a random-forest machine-learning model, 30 biomarker taxa were identified that accurately distinguish between the food, sludge and manure waste composting microbiomes (accuracy >98 %). These biomarker taxa were closely associated with carbon and nitrogen metabolic processes, during which they contributed to the predominant stochastic process and are influenced by different factors in the substrate-specific composts. This is corroborated by the community topological characteristics, which feature the biomarkers as keystone taxa maintaining the bacterial network stability. These findings provide a theoretical basis to identify and enhance the biomarker-functional bacteria for optimizing the composting performance of different organic wastes.

Catabolism and interactions of syntrophic propionate- and acetate oxidizing microorganisms under mesophilic, high-ammonia conditions.

Microbial inhibition by high ammonia concentrations is a recurring problem that significantly restricts methane formation from intermediate acids, i.e., propionate and acetate, during anaerobic digestion of protein-rich waste material. Studying the syntrophic communities that perform acid conversion is challenging, due to their relatively low abundance within the microbial communities typically found in biogas processes and disruption of their cooperative behavior in pure cultures. To overcome these limitations, this study examined growth parameters and microbial community dynamics of highly enriched mesophilic and ammonia-tolerant syntrophic propionate and acetate-oxidizing communities and analyzed their metabolic activity and cooperative behavior using metagenomic and metatranscriptomic approaches. Cultivation in batch set-up demonstrated biphasic utilization of propionate, wherein acetate accumulated and underwent oxidation before complete degradation of propionate. Three key species for syntrophic acid degradation were inferred from genomic sequence information and gene expression: a syntrophic propionate-oxidizing bacterium (SPOB) "Candidatus Syntrophopropionicum ammoniitolerans", a syntrophic acetate-oxidizing bacterium (SAOB) Syntrophaceticus schinkii and a novel hydrogenotrophic methanogen, for which we propose the provisional name "Candidatus Methanoculleus ammoniitolerans". The results revealed consistent transcriptional profiles of the SAOB and the methanogen both during propionate and acetate oxidation, regardless of the presence of an active propionate oxidizer. Gene expression indicated versatile capabilities of the two syntrophic bacteria, utilizing both molecular hydrogen and formate as an outlet for reducing equivalents formed during acid oxidation, while conserving energy through build-up of sodium/proton motive force. The methanogen used hydrogen and formate as electron sources. Furthermore, results of the present study provided a framework for future research into ammonia tolerance, mobility, aggregate formation and interspecies cooperation.

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.

Terrestrial dissolved organic matter inputs accompanied by dissolved oxygen depletion and declining pH exacerbate CO2 emissions from a major Chinese reservoir.

Terrestrial inputs and subsequent degradation of dissolved organic matter (DOM) in lake ecosystems can result in rapid depletion of dissolved oxygen (DO). Inputs of terrestrial DOM including organic acids can also lead to decreases in pH. However, to date, few studies have investigated the linkages between terrestrial DOM inputs, DO and pH levels in the water column, and carbon dioxide (CO2) emissions from lake ecosystems. Based on monthly field sampling campaigns across 100 sites in Lake Qiandao, a major man-made drinking water reservoir in China, from May 2020 to April 2021, we estimated an annual CO2 efflux (FCO2) of 37.2 ± 29.0 gC m-2 yr-1, corresponding to 0.02 ± 0.02 TgC yr-1 from this lake. FCO2 increased significantly with decreasing DO, chlorophyll-a (Chl-a) and δ2H-H2O, while FCO2 increased with increasing specific UV absorbance (SUVA254) and a terrestrial humic-like component (C2). We found that DO concentration and pH declined with increasing terrestrial DOM inputs, i.e. increased SUVA254 and terrestrial humic-like C2 levels. Vertical profile sampling revealed that the partial pressure of CO2 (pCO2) increased with increasing terrestrial DOM fluorescence (FDOM), while DO, pH, and δ13C-CO2 declined with increasing terrestrial FDOM. These results highlight the importance of terrestrial DOM inputs in altering physico-chemical environments and fueling CO2 emissions from this lake and potentially other aquatic ecosystems.

Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions.

Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.

Distribution of methanogenic and methanotrophic consortia at soil-water interfaces in rice paddies across climate zones.

Periphytic biofilms (PB) at the soil-water interface contributes 7-38% of the methane emission from rice paddies, yet the biogeographical mechanism underlying and affecting the process remain elusive. In this study, rice fields along an edapho-vclimatic gradient were sampled, and the environmental drivers affecting distribution of methanogenic and methanotrophic communities were evaluated. The methanogenic and methanotrophic communities at soil-water interface showed less complex inter/intra-generic interactions than those in soil, and their relative abundances were weakly driven by spatial distance, soil organic carbon, soil total nitrogen and pH. The nutrient supply and buffering capacity of extracellular polymeric substance released by PB reduced their interaction and enhanced the resilience on edaphic environment changes. Climate affected soil metal content, extracellular polymeric substance content, and thus the methane-related communities, and caused geographical variation in the impacts of PB on methane emissions from rice paddies. This study facilitates our understanding of geographical differences in the contribution of PB to methane emission.

Thermodynamic restrictions determine ammonia tolerance of methanogenic pathways in Methanosarcina barkeri.

Ammonia is a ubiquitous potential inhibitor of anaerobic digestion processes, mainly exhibiting inhibition towards methanogenic activity. However, knowledge as to how ammonia affects the methanogens is still limited. In this study, we cultured a multitrophic methanogen, Methanosarcina barkeri DSM 800, with acetate, H2/CO2, and methanol to evaluate the influence of ammonia on different methanogenic pathways. Aceticlastic methanogenesis was more sensitive to increased ammonia concentrations than hydrogenotrophic and methylotrophic methanogenesis. Theoretical maximum NH3 tolerances of M. barkeri fed with acetate, H2/CO2, and methanol were calculated to be 39.1 ± 9.0, 104.3 ± 7.4, and 85.7 ± 1.0 mg/L, respectively. The order of the ΔG range of M. barkeri under three methanogenic pathways reflected the order of ammonia tolerance of M. barkeri. Our results provide insights into the role of the thermodynamic potential of methanogenesis on the tolerance of ammonia stress; and shed light on the mechanism of ammonia inhibition on anaerobic digestion.

Explaining the resistomes in a megacity's water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria.

Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|ßNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 106 cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff ß = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.