Seasonal function succession and biogeographic zonation of assimilatory and dissimilatory nitrate-reducing bacterioplankton

Microbial interaction patterns and nitrogen cycling regularities in lake sediments under different trophic conditions

Exploring how nitrogen (N) cycling microbes interact in eutrophic lake sediments and how biogenic elements influence the nitrogen cycle is crucial for understanding biogeochemical cycles and nitrogen accumulation mechanisms. In this study, sediment samples were collected from various areas of Taihu Lake with different trophic conditions in all four seasons from 2015 to 2017. Using high-throughput sequencing and molecular ecological network analysis, we investigated the microbial interaction patterns and the role of nitrogen cycling in sediments from lakes with different trophic conditions. The results showed distinct structures of sediment microbial networks between lake areas with different trophic conditions. In the more eutrophic region, network indices indicate higher transfer efficiency of energy, material, and information, more significant competition, and weaker niche differentiation of the microbial community. The sedimentary environment in the moderately eutrophic area exhibited greater potential for denitrification, nitrification, and anammox compared to the mesotrophic area, but the inhibition between N functional microbes and limitations in N removal processes were also more likely to occur. The topological structure of the networks showed that the carbon (C), sulfur (S), and iron (Fe) cycles had a strong influence on the nitrogen cycle in both lake areas. In the moderately eutrophic lake area, C- and S-cycling functional bacteria facilitated a closed cycle of the coupled N fixation-nitrification-DNRA (dissimilatory nitrate reduction to ammonium) process and reduced N removal. In the mesotrophic lake area, C- and S-cycling functional bacteria promoted both N fixation and mineralization, and Fe-cycling functional bacteria coupled with denitrifiers enhanced the nitrogen removal process of products from nitrogen fixation and mineralization. This study improved the understanding of the nitrogen cycling mechanism in lake sediments under different trophic conditions.

Life strategies and metabolic interactions of core microbes during thiosulphate-based denitrification

Sulphur-driven denitrification is a low-cost process for the treatment of nitrate-contaminated water. However, a comprehensive understanding of core populations and microbial interactions of a sulphur-based denitrifying system is lacking. This study presents results from three replicated denitrifying systems amended with thiosulphate and operated under a low C/N ratio. Amplicon sequencing revealed gradual enrichments of a few abundant denitrifiers. Based on genome-centred metagenomics and metatranscriptomics, a core set of microbes was identified in the systems, with Pseudomonas 1 and Thauera 2 being the most abundant ones. Although the replicates showed different enrichments, generalized observations were summarized. Most core populations conserved energy from denitrification coupled with sulphur. Pseudomonas 1 and Thauera 2 were able to finish complete denitrification. Surprisingly, they were also able to synthesize almost all amino acids and vitamins. In contrast, less abundant members, including Pseudomonas 2, were relatively auxotrophic and required an exogenous supply of amino acids and vitamins. The high expression of enzymes involved in biosynthesis and transport systems indicated their syntrophic relationships. The genomic findings suggested life strategies and interactions of the core thiosulphate-based denitrifying microbiome, with implications for nitrate-polluted water remediation.

Effects of different soil water holding capacities on vegetable residue return and its microbiological mechanism

With the gradual expansion of the protected vegetable planting area, dense planting stubbles and increasing labor cost, the treatment of vegetable residues has become an urgent problem to be solved. Soil bacterial community structure plays an important role in vegetable residue return and is susceptible to environmental changes. Therefore, understanding the influences of different soil water holding capacities on plant residue decomposition and soil bacterial communities is important for biodegradation. During the whole incubation period, the weight loss ratio of plant residue with 100% water holding capacity was 69.60 to 75.27%, which was significantly higher than that with 60% water holding capacity in clay and sandy soil, indicating that high water holding capacity promoted the decomposition of plant residue. The degradation of lignin and cellulose was also promoted within 14 days. Furthermore, with the increase in soil water holding capacity, the contents of NH4+ increased to 5.36 and 4.54 times the initial value in the clay and sandy soil, respectively. The increase in napA and nrfA resulted in the conversion of NO3- into NH4+. The increase in water holding capacity made the bacterial network structure more compact and changed the keystone bacteria. The increase in water holding capacity also increased the relative abundance of Firmicutes at the phylum level and Symbiobacterium, Clostridium at the genus level, which are all involved in lignin and cellulose degradation and might promote their degradation. Overall, these findings provide new insight into the effects of different soil water holding capacities on the degradation of plant residues in situ and the corresponding bacterial mechanisms.

Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter

Suspended particulate matter (SPM) contributes to the loss of reactive nitrogen (Nr) in estuarine ecosystems. Although denitrification and anaerobic ammonium oxidation in SPM compensate for the current imbalance of global nitrogen (N) inputs and sinks, it is largely unclear whether other pathways for Nr transformation exist in SPM. Here, we combined stable isotope measurements with metagenomics and metatranscriptomics to verify the occurrence of dissimilatory nitrate reduction to ammonium (DNRA) in the SPM of the Pearl River Estuary (PRE). Surprisingly, the conventional functional genes of DNRA (nirBD) were abundant and highly expressed in SPM, which was inconsistent with a low potential rate. Through taxonomic and comparative genomic analyses, we demonstrated that nitrite reductase (NirBD) in conjunction with assimilatory nitrate reductase (NasA) performed assimilatory nitrate reduction (ANR) in SPM, and diverse alpha- and gamma-proteobacterial lineages were identified as key active heterotrophic ANR bacteria. Moreover, ANR was predicted to have a relative higher occurrence than denitrification and DNRA in a survey of Nr transformation pathways in SPM across the PRE spanning 65 km. Collectively, this study characterizes a previously overlooked pathway of Nr transformation mediated by heterotrophic ANR bacteria in SPM and has important implications for our understanding of N cycling in estuaries.

Using hierarchical stable isotope to reveal microbial food web structure and trophic transfer efficiency differences during lake melt season

The microbial food web (MFW) is a material and energy source in lake water ecosystems. Although it is crucial to determine its structure and function for water ecological health, MFW changes during lake melt period have not been well studied. In this study, the MFW was divided into three categories by analyzing its structure and trophic transfer efficiency using hierarchical C/N stable isotopes and eDNA sequencing techniques, including the detrital food web (DFC, 15 %), classical grazing food web (CFC, 60 %), and mixed trophic food web (MFC, 25 %). The trophic structure and type of MFW in ice-melting lakes are always in the process of succession and adaptation, which is in a relatively low trophic transfer efficiency stage under stable conditions (i.e. CFC), whereas the input of exogenous debris and organic pollutants may lead to an increase in MFW trophic transfer efficiency (i.e. MFC, DFC). The trophic transfer efficiency from the previous trophic level to protozoa and micrometazoa was 16.32 % and 20.77 % in DFC and 10.20 % and 29.43 % in MFC, respectively. Both are obviously higher than those of the CFC (11.69 % and 9.45 %, respectively). In terms of trophic structure, the community interaction and trophic cascade effect of DFC and MFC were enhanced but easily changed with environmental factors. In contrast, the core species and cascading effects of the CFC were clearer, and the MFW structure was relatively stable. Overall, this study reveals that the explosive increase in MFW trophic transfer efficiency induced by exogenous input during the lake melt period may subsequently lead to the destabilization of the microbial community structure and cause potential ecological risks. These are manifested in the absence of ecological trophic processes, the decrease in trophic structure complexity and stability, and the weakening of microecology self-adaptive regulation ability.

Metagenomic insights into comparative study of nitrogen metabolic potential and microbial community between primitive and urban river sediments

As a result of anthropogenic pollution, the nitrogen nutrients load in urban rivers has increased, potentially raising the risk of river eutrophication. Here, we studied how anthropogenic impacts alter nitrogen metabolism in river sediments by comparing the metagenomic function of microbial communities between relatively primitive and human-disturbed sediments. The contents of organic matter (OM), total nitrogen (TN), NO₃^--N and NO₂^--N were higher in primitive site than in polluted sites, which might be due to vegetation density, sediment type, hydrology, etc. Whereas, NH₄⁺-N content was higher in midstream and downstream, indicating that nitrogen loading increased in the anthropogenic regions and subsequently leading higher NH₄⁺-N. Hierarchical cluster analyses revealed significant changes in the community structure and functional potential between the primitive and human-affected sites. Metagenomic analysis demonstrated that Demequina, Streptomyces, Rubrobacter and Dechloromonas were the predominant denitrifiers. Ardenticatena and Dechloromonas species were the most important contributors to dissimilatory nitrate reduction. Furthermore, anthropogenic pollution significantly increased their abundance, and resulting in a decrease in NO₃^-, NO₂^--N and an increase in NH₄⁺-N contents. Additionally, the SOX metabolism of Dechloromonas and Sulfuritalea may involve in the sulfur-dependent autotrophic denitrification process by coupling the conversion of thiosulfate to sulfate with the reduction of NO₃^--N to N₂. From pristine to anthropogenic pollution sediments, the major nitrifying bacteria harboring Hao transitioned from Nitrospira to Nitrosomonas. This study sheds light on the consequences of anthropogenic activities on nitrogen metabolism in river sediments, allowing for better management of nitrogen pollution and eutrophication in river.

Spatiotemporal correlations between water quality and microbial community of typical inflow river into Taihu Lake, China

Changxing River, which is a typical inflow river into Taihu Lake and occurs severe algae invasion, is selected to study the effect of different pollution sources on the water quality and ecological system. Four types of pollution sources, including the estuary of Taihu Lake, discharge outlets of urban wastewater treatment plants, stormwater outlets, and nonpoint source agricultural drainage areas, were chosen, and next-generation sequencing and multivariate statistical analyses were used to characterize the microbial communities and reveal their relationship with water physicochemical properties. The results showed that ammonia nitrogen (NH₄⁺-N), total nitrogen (TN), and total phosphorus (TP) were the main pollutants in Changxing River, especially at stormwater outlets. At the same time, the diversity of microbial communities was the highest in the summer, and dominant microbes included Proteobacteria (40.9%), Bacteroidetes (21.0%), and Euryarchaeota (6.1%). The results of BIOENV analysis showed that the major seasonal differences in the diversity of microbial community of Changxing river were explained by the combination of water temperature (T), air pressure (P), TP, and COD_Mn. From the perspective of different pollution types, relative abundances of Microcystis and Nostocaceae at the estuary of Taihu Lake were correlated positively with dissolved oxygen (DO) and pH, and relative abundances of Pseudomonas and Arcobacter were correlated positively with concentrations of TN and nitrate nitrogen (NO₃^--N) at stormwater outlets. This study provided a reference for the impact of pollution types on river microbial ecosystem under complex hydrological conditions and guidance for the selection of restoration techniques for polluted rivers entering the important lake.

Effect of sulfur sources on the competition between denitrification and DNRA

The fate of nitrogen is controlled by the competition between nitrate reduction pathways. Denitrification removes nitrogen in the system to the atmosphere, whereas dissimilatory nitrate reduction to ammonia (DNRA) retains nitrate in the form of ammonia. Different microbes specialize in the oxidation of different electron donors, thus electron donors might influence the outcomes of the competition. Here, we investigated the fate of nitrate with five forms of sulfur as electron donors. Chemoautotrophic nitrate reduction did not continue after the passages of the enrichments with sulfide, sulfite and pyrite. Nitrate reduction rate was the highest in the enrichment with thiosulfate. Denitrification was stimulated and no DNRA was observed with thiosulfate, while both denitrification and DNRA were stimulated with elemental sulfur. Metagenomes of the enrichments were assembled and binned into ten genomes. The enriched populations with thiosulfate included Thiobacillus, Lentimicrobium, Sulfurovum and Hydrogenophaga, all of which contained genes involved in sulfur oxidation. Elemental sulfur-based DNRA was performed by Thiobacillus (with NrfA and NirB) and Nocardioides (with only NirB). Our study established a link between sulfur sources, nitrate reduction pathways and microbial populations.

Denitrification and dissimilatory nitrate reduction to ammonia in long-term lake sediment microcosms with iron(II)

Nitrate is an abundant pollutant in aquatic environments. Competition between the nitrate reduction processes, denitrification, which converts nitrate into nitrogen gas, and dissimilatory nitrate reduction to ammonia (DNRA), which converts nitrate into ammonia, decides whether an ecosystem removes or retains nitrogen. The presence of iron was previously reported to stimulate DNRA while sometimes inhibiting denitrification in in-situ studies, but long-term effect of iron(II) inputs on the competition is unknown. Here we inoculated long-term microcosms with sediments from two freshwater lakes. During 540 days of incubations, the microcosms with nitrate and Fe(II) additions of both lakes were able to sustain high nitrate reduction rates. Lepidocrocite was produced as a product of iron oxidation. We found both denitrification and DNRA were stimulated by nitrate and iron in the absence of external organic carbon addition. Phylogenetic analysis of denitrification genes, nirK and nirS, and DNRA genes, nirB and nrfA, was performed with metagenomic sequencing results. Enrichment was shown for reported Fe(II)-dependent nitrate reducers associated with nirS and nirB. Most of these bacteria are affiliated with Betaproteobacteria. From 16S rRNA gene analysis, Betaproteobacteria was enriched as well. In parallel, heterotrophic denitrifiers and methanotrophic DNRA archaea increased in abundance. Our results suggested heterotrophic and Fe(II)-dependent nitrate reducers both contributed to denitrification and DNRA in long-term microcosm incubations provided with iron.

Microbial explanation to performance stratification along up-flow solid-phase denitrification column packed with polycaprolactone

In this study, the fluctuating profiles of physicochemical and microbial characterizations along different filling heights of continuously up-flow solid-phase denitrification (SPD) columns packed with polycaprolactone (PCL) were investigated. It was found both the PCL filling area and non-filling area made significant contributions to treatment performance and denitrification mainly occurred near the bottom of the filling column. Nitrate displayed a high proportional removal (≥98.7%) among all the cases except the one with the lowest filling ratio (FR30) and highest NLR (3.99 ± 0.12 gN/(L·d)), while nitrite and ammonium displayed a weak accumulation in final effluents (nitrite ≤ 0.40 mg/L; ammonium ≤ 0.98 mg/L). The intensity of PCL hydrolysis in the top substrate was stronger than those in the middle or bottom. Both dissimilatory nitrate reduction to ammonium (DNRA) and microbial lysis contributed to ammonium accumulation, and nitrate was mainly removed via traditional denitrification and DNRA. JGI_0000069-P22_unclassified and Gracilibacteria_unclassified might contribute to denitrification.

Improving the outcomes from electroactive constructed wetlands by mixing wastewaters from different beverage-processing industries

Denitrification in electroactive constructed wetland (EW) systems is constrained by the carbon source and the carbon/nitrogen (C/N) ratio (the COD/TN ratio). In this study, wastewater with a high C/N from a brewery was added to wastewater with a low C/N (dairy wastewater) in an EW system, and the pollutant removal, bioelectricity generation, transformations of dissolved organic matter, and microbial community structures were evaluated. The results showed that the average removal rates of ammonium nitrogen, total nitrogen, and chemical oxygen demand from the wastewater mixture were 6.40%, 46.44%, and 23.85% higher than those from the wastewater with a low C/N, respectively. Dissimilatory nitrate reduction to ammonium was effectively inhibited, and the NH₄⁺-N removal was 25.52% higher, when the wastewater mixture was used instead of the high C/N wastewater. Similarly, the output voltage was significantly increased, and the internal resistance of the device was reduced, for the wastewater mixture. The structure of the microbial community improved, the relative abundance of electrochemically active bacteria was higher, and the protein-like and humic-like components were lower, in the mixture treatment than in the individual treatment. The results show that the nitrogen removal and biopower generation improved in an EW system when high C/N wastewater was used as the carbon source.

Comparative analysis of bacterioplankton assemblages from two subtropical karst reservoirs of southwestern China with contrasting trophic status

Although bacterioplankton play an important role in aquatic ecosystems, less is known about bacterioplankton assemblages from subtropical karst reservoirs of southwestern China with contrasting trophic status. Here, 16S rRNA gene next-generation sequencing coupled with water chemistry analysis was applied to compare the bacterioplankton communities from a light eutrophic reservoir, DL Reservoir, and a mesotrophic reservoir, WL Reservoir, in subtropical karst area of southwestern China. Our findings indicated that Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia dominated bacterioplankton community with contrasting relative frequency in the two subtropical karst reservoirs. Proteobacteria and Bacteroidetes were the core communities, which played important roles in karst biogeochemical cycles. Though WT, TN and DOC play the decisive role in assembling karst aquatic bacterioplankton, trophic status exerted significantly negative direct effects on bacterioplankton community composition and alpha diversity. Due to contrasting trophic status in the two reservoirs, the dominant taxa such as Enterobacter, Clostridium sensu stricto, Candidatus Methylacidiphilum and Flavobacteriia, that harbor potential functions as valuable and natural indicators of karst water health status, differed in DL Reservoir and WL Reservoir.

Dredging mitigates cyanobacterial bloom in eutrophic Lake Nanhu: Shifts in associations between the bacterioplankton community and sediment biogeochemistry

Cyanobacterial blooms are a worldwide environmental problem, which is partly attributed to their access to excessive nitrogen (N) and phosphorus (P). Preventing the blooms by reducing N and P from internal inputs is viewed as a challenge. To evaluate the effects of dredging on cyanobacterial abundances and bacterioplankton communities, water and sediment samples were collected from eutrophic Lake Nanhu (Wuhan, China) before dredging (2017) and after dredging (2018). After dredging, significant decreases were observed for sediment nutrients (e.g., C, N, and P sources); C-, N-, P-, and S-cycling-related enzyme activity; N- and P-cycling-related gene abundance; microbial abundance; and dramatic changes were observed in the composition of the sediment microbial community. The release rates of nutrient including nitrogen, phosphorus, and organic matter decreased after dredging, and sediment biogeochemistry was closely correlated to nutrient release rates. Additionally, our observations and analyses indicated that the abundance and diversity of the bacterioplankton community decreased significantly, the composition and interaction of the bacterioplankton community dramatically changed, and the bacterioplankton community function (e.g., N, P-cycling-related enzymes and proteins) down regulated after dredging. Water and sediment physicochemical factors explained 72.28% variation in bacterioplankton community composition, and these physicochemical factors were significantly correlated with diversity, composition, and function of bacterioplankton community. Our findings emphasized that cyanobacterial blooms in freshwater ecosystems were closely correlated with noncyanobacterial bacterioplankton that were largely conserved at the phylum level, with Proteobacteria, Actinobacteria, and Bacteroidetes as the main taxa. To our knowledge, this is the first report clarifying the mechanism of cyanobacterial blooms mitigation by dredging, via changing the association between the bacterioplankton community and sediment biogeochemistry. Our findings are of significance and indicate that dredging is effective for mitigating cyanobacterial blooms.

Wastewater treatment plant upgrade induces the receiving river retaining bioavailable nitrogen sources

Currently, wastewater treatment plant (WWTP) upgrades have been implemented in various countries to improve the water quality of the receiving ecosystems and protect aquatic species from potential deleterious effects. The impact of WWTP upgrades on biological communities and functions in receiving waters is a fundamental issue that remains largely unaddressed, especially for microbial communities. Here, we selected two wastewater-dominant rivers in Beijing (China) as study sites, i.e., one river receiving water from an upgraded WWTP to explore the impacts of upgrade on aquatic ecosystems and another river receiving water from a previously upgraded WWTP as a reference. After a five-year investigation, we found that WWTP upgrade significantly decreased total organic nitrogen (N) in the receiving river. As a biological response, N-metabolism-related bacterioplankton are accordingly altered in composition and tend to intensively interact according to the network analysis. Metagenomic analysis based on the N-cycling genes and metagenomic-assembled genomes revealed that WWTP upgrade decreased the abundance of nitrifying bacteria but increased that of denitrifying and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in the receiving river, according to their marker gene abundances. After calculation of the ratios between DNRA and denitrifying bacteria and quantification of genes/bacteria related to ammonium cycling, we deduced the changes in N-metabolism-related bacteria are likely an attempt to provide enough bioavailable N for plankton growth as conservation of ammonium was enhanced in receiving river after WWTP upgrade.

Survey of dissimilatory nitrate reduction to ammonium microbial community at national wetland of Shanghai, China

Dissimilatory nitrate reduction to ammonia (DNRA) process is an important nitrate reduction pathway in the environment. Numerous studies focused on the DNRA, especially in various natural habitats. However, little is known about the envrionmental parameters driving the DNRA process in anthropogenic ecosystem. Human activities put forward significant influence on nitrogen cycle and bacterial communities of sediment. This study aimed to assess the DNRA potential rates, nrfA gene abundance, DNRA bacterial community's diversity and influencing factors in a national wetland park near the Yangtze River estuary, Shanghai. The results of ¹⁵N isotope tracer experiments showed that DNRA potential rates from 0.13 to 0.44 μmol N/kg/h and contribution of nitrate reduction varied from 1.56% to 7.47%. The quantitative real-time PCR results showed that DNRA functional gene nrfA abundances ranged from 9.87E+10 to 1.98E+11 copies/g dry weight. The results of nrfA gene pyrosequencing analysis showed that Lacunisphaera (10.4-13.4%), Sorangium (7.1-10.7%), Aeromonas (4.2-6.8%), Corallococcus (1.8-6.9%), and Geobacter (3.3-6.6%) showed higher relative abundances in their genus levels. Combined with environmental parameters of sediments, redundancy analysis indicated that the nrfA functional gene was positively correlated with moisture content, the concentration of NO₂^--N and NO₃^-N; the DNRA rates was positively correlated with sediment organic carbon (SOC), C/NO₃^- ratio and salinity (ranked by explains %). This study is the first simultaneous determination of nitrate reduction pathways including denitrification, anammox and DNRA rates to assess the role of DNRA in a national wetland park and revealed the community abundance, diversity of DNRA bacteria and its relationship with environmental factors.

Seasonal operation of dual-mode biofilters: The influence of plant species on stormwater and greywater treatment

The use of stormwater biofilters (also known as bioretention systems and raingardens), in tropical and semi-arid areas is hindered by seasonal rainfall patterns which cause extended dry periods. These periods can result in plant die-off, long-term damage to system health and leaching of pollutants when stormwater inflows resume. Using an additional polluted water source during dry periods could minimise system stress and eliminate the need to irrigate biofilters with potable water during dry spells. As such, the presented laboratory study tested the seasonal operation of biofilters, by switching from stormwater treatment in wet months to greywater treatment in dry months. Forty-five single planted biofilter columns, incorporating sedges, grasses, understory ornamentals and vines, were subjected to four months of stormwater inflows, followed by three months of greywater inflows. We also investigated the impact of including a carbon source in the saturated zone on treatment performance. The results showed plant species selection to be critical for nitrogen and phosphorus removal, with consistently effective species such as Carex appressa and Canna x generalis able to maintain low outflow concentrations (e.g. total nitrogen of 0.2-0.3 mg/L and 0.3-0.6 mg/L, respectively) across both water sources. Low outflow phosphorus concentrations were associated with plant species that had high filterable reactive phosphorus removal across both water sources. Similarly, higher removal of ammonia and oxidised nitrogen was associated with lower overall nitrogen concentrations. In contrast, high removal of total suspended sediment (>94%), biochemical oxygen demand (>98%) and some heavy metals (e.g. lead >98% and copper >93%) was reported across all designs. The results suggest that with the careful selection of plant species, biofilters can be operated seasonally as a feasible and practical solution to maintaining system health during extended dry periods.