Denitrification and Biodiversity of Denitrifiers in a High-Mountain Mediterranean Lake

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

Simultaneous removal of ammonia nitrogen, recovery of phosphate, and immobilization of nickel in a polyester fiber with shell powder and iron carbon spheres bioreactor: Optimization and pathways mechanism

Composite pollutants are prevalent in wastewater, whereas, the simultaneous accomplishment of efficient nitrogen removal and resources recovery remains a challenge. In this study, a bioreactor was constructed to contain Pseudomonas sp. Y1 using polyester fiber wrapped with shell powder and iron carbon spheres, achieving ammonia nitrogen (NH₄⁺-N) removal, phosphate (PO₄^3--P) recovery, and nickel (Ni²⁺) immobilization. The optimal performance of bioreactor was average removal efficiencies of NH₄⁺-N, PO₄^3--P, calcium (Ca²⁺), and Ni²⁺ as 82.42, 96.67, 76.13, and 98.29% at a hydraulic retention time (HRT) of 6 h, pH of 7.0, and influent Ca²⁺ and Ni²⁺ concentrations of 100.0 and 3.0 mg L^-1, respectively. The bioreactor could remove PO₄^3--P, Ca²⁺, and Ni²⁺ by biomineralization, co-precipitation, adsorption, and lattice substitution. Moreover, microbial community analysis suggested that Pseudomonas was the predominant genus and had possessed tolerance to Ni²⁺ toxicity in wastewater. This study presented an effective method to synchronously remove NH₄⁺-N, recover PO₄^3--P, and fix heavy metals through microbially induced carbonate precipitation (MICP) and heterotrophic nitrification and aerobic denitrification (HNAD) technology.

Efficiency of reactive nitrogen removal in a model Mediterranean high-mountain lake and its downwater river ecosystem: Biotic and abiotic controls

High-mountain lakes and rivers are usually oligotrophic and strongly influenced by atmospheric transport processes. Thus, wet deposition of reactive N species (Nr), mainly in the form of nitrate (NO₃^-), is a major source of N input in these high-mountain ecosystems. Bacterial denitrifiers are thought to be largely responsible for reduction of NO₃^- to nitrous oxide (N₂O) and molecular dinitrogen (N₂) as main biological pathway of N removal in these ecosystems. Nitrifiers, through the oxidation of ammonium to NO₃^-, can also be a source of NO₃^- and N₂O. However, there is uncertainty regarding the abiotic and biotic factors controlling Nr elimination from aquatic ecosystems at different altitudes and seasons. We examined the efficiency of Nr removal as N₂O and N₂ (total removal) or N₂ only (clean removal) in a model lake and its downwater river ecosystem (Sierra Nevada, Spain) representative of Mediterranean high-mountain freshwater ecosystems along an altitudinal gradient during the warm period of the year. Denitrification activity and the abundance of nitrifiers and denitrifiers in sediments were measured at thaw, mid ice-free and late ice-free periods. We found the efficiency of total and clean removal of Nr increased from the downwater river to the high-mountain lake. Regardless of the location, the efficiency of total removal of Nr decreased over the ice-free period whereas that of clean removal of Nr peaked at mid ice-free period. The efficiency of total removal of Nr was mainly controlled by the abundance of archaeal nitrifiers and bacterial denitrifiers. Abiotic (ammonium and NO₃^- concentration) and biotic (mainly nosZI-type denitrifiers) factors drove changes in the efficiency of clean removal of Nr. Our results suggest that abiotic and biotic factors can control the efficiencies of Nr removal in Mediterranean high-mountain lakes and their downwater rivers, and that these efficiencies increase with altitude and vary over the ice-free period.

Disproportionate responses between free-living and particle-attached bacteria during the transition to oxygen-deficient zones in the Bohai Seawater

The Bohai Sea has recently suffered several seasonal oxygen-deficiency, even hypoxia events during the summer. To better understand effects of dissolved oxygen (DO) concentration on the bacterial composition in particle attached (PA) and free living (FL) fractions during the transition from oxic water to low oxygen conditions, the bacterial communities under three different oxygen levels, i.e., high oxygen (HO, close to 100% O₂ saturation), medium oxygen (MO, close to 75% O₂ saturation), and low oxygen (LO, close to 50% O₂ saturation) in the Bohai Sea were investigated using 16S rRNA amplicon sequencing. Fourteen water samples from 5 stations were collected during a cruise from August to September in 2018. The results showed that the sequences of Proteobacteria and Actinobacteriota jointly accounted for up to 74% across all 14 samples. The Shannon index in HO samples were significantly higher than in LO samples (P < 0.05), especially in PA communities. The composition of bacterial communities varied by oxygen concentration in all samples, and the effect was more pronounced in the PA fraction, which indicates that the PA fraction was more sensitive to the change in oxygen concentration, possibly due to the tighter interactions in this community than in the FL fraction. This study provides novel insights into the distribution of bacterial communities, and clues for understanding the responses of bacterial communities in the Bohai Sea during the transition from the oxic to oxygen-deficient zones.

The role and effectiveness of monoculture and polyculture phytoremediation systems in fish farm wastewater

Phytoremediation offers a sustainable solution to aquaculture pollution, but studies with critical evaluations of the treatment performances of macrophyte systems are limited. This study intended to evaluate the roles and treatment profiles of Spirodela polyrhiza (L.) Schleid. and Lemna sp. systems in terms of ammonia, nitrate, nitrite, phosphate (NH3-N, NO3 --N, NO2 --N, PO4 3-), chemical oxygen demand (COD), turbidity, and total suspended solids (TSS) on fish farm wastewater and to elucidate the rationale behind the removal of the pollutants and the changes in a raceway pond rig. The nitrogen and phosphorus removal in the Spirodela polyrhiza monoculture system outperformed the other configured systems. An 81% reduction in ammonia (to 3.90 mg of NH3-N/L), and sharp declines of up to 75%, 88%, and 71% in TSS, turbidity, and COD levels were recorded within two days, while significant decreases in nitrate, nitrite, and phosphate levels were observed. This indicated that the system could inhibit nitrate and nitrite spikes in waters (nitrification) via reducing the available ammonia and limiting subsequent nitrite and nitrate conversion, while reducing TSS in algal-bloom wastewater via shading. High biomass productivity and superior protein content were observed in the macrophyte systems (S. polyrhiza + Lemna sp. polyculture system), with up to 112% and 12% increases, respectively. This study demonstrated that the S. polyrhiza monoculture system is effective at treating fish farm wastewater, lowering the levels of relevant inorganic and organic pollutants, and it could be used as a biofilter for natural waters, preserving the existing ecology.

Housekeeping in the Hydrosphere: Microbial Cooking, Cleaning, and Control under Stress

Who's cooking, who's cleaning, and who's got the remote control within the waters blanketing Earth? Anatomically tiny, numerically dominant microbes are the crucial "homemakers" of the watery household. Phytoplankton's culinary abilities enable them to create food by absorbing sunlight to fix carbon and release oxygen, making microbial autotrophs top-chefs in the aquatic kitchen. However, they are not the only bioengineers that balance this complex household. Ubiquitous heterotrophic microbes including prokaryotic bacteria and archaea (both "bacteria" henceforth), eukaryotic protists, and viruses, recycle organic matter and make inorganic nutrients available to primary producers. Grazing protists compete with viruses for bacterial biomass, whereas mixotrophic protists produce new organic matter as well as consume microbial biomass. When viruses press remote-control buttons, by modifying host genomes or lysing them, the outcome can reverberate throughout the microbial community and beyond. Despite recognition of the vital role of microbes in biosphere housekeeping, impacts of anthropogenic stressors and climate change on their biodiversity, evolution, and ecological function remain poorly understood. How trillions of the smallest organisms in Earth's largest ecosystem respond will be hugely consequential. By making the study of ecology personal, the "housekeeping" perspective can provide better insights into changing ecosystem structure and function at all scales.

Denitrification rates in lake sediments of mountains affected by high atmospheric nitrogen deposition

During the last decades, atmospheric nitrogen loading in mountain ranges of the Northern Hemisphere has increased substantially, resulting in high nitrate concentrations in many lakes. Yet, how increased nitrogen has affected denitrification, a key process for nitrogen removal, is poorly understood. We measured actual and potential (nitrate and carbon amended) denitrification rates in sediments of several lake types and habitats in the Pyrenees during the ice-free season. Actual denitrification rates ranged from 0 to 9 μmol N₂O m⁻² h⁻¹ (mean, 1.5 ± 1.6 SD), whereas potential rates were about 10-times higher. The highest actual rates occurred in warmer sediments with more nitrate available in the overlying water. Consequently, littoral habitats showed, on average, 3-fold higher rates than the deep zone. The highest denitrification potentials were found in more productive lakes located at relatively low altitude and small catchments, with warmer sediments, high relative abundance of denitrification nitrite reductase genes, and sulphate-rich waters. We conclude that increased nitrogen deposition has resulted in elevated denitrification rates, but not sufficiently to compensate for the atmospheric nitrogen loading in most of the highly oligotrophic lakes. However, there is potential for high rates, especially in the more productive lakes and landscape features largely govern this.

Quantification of denitrifier genes population size and its relationship with environmental factors

The objectives of this study were to use real-time PCR for culture-independent quantification of the copy numbers of 16S rRNA and denitrification functional genes, and also the relationships between gene copy numbers and soil physicochemical properties. In this study, qPCR analysis of the soil samples showed 16S rRNA, nirS, nirK, nosZI and nosZII average densities of 3.0 × 10⁸, 2.25 × 10⁷, 2.9 × 10⁵, 4.0 × 10⁶ and 1.75 × 10⁷ copies per gram of dry soil, respectively. In addition, the abundances of (nirS + nirK), nosZI and nosZII relative to 16S rRNA genes were 1.4-34.1%, 0.06-3.95% and 1.3-39%, respectively, confirming the low proportion of denitrifiers to total bacteria in soil. This showed that the non-denitrifying nosZII-type bacteria may contribute significantly to N₂O consumption in the soil. Furthermore, the shifts in abundance and diversity of the total bacteria and denitrification functional gene copy numbers correlated significantly with the various soil factors. It is the first study in Turkey about the population size of denitrification functional genes in different soil samples. It also aims to draw attention to nitrous oxide-associated global warming.

The DNRA-Denitrification Dichotomy Differentiates Nitrogen Transformation Pathways in Mountain Lake Benthic Habitats

Effects of nitrogen (N) deposition on microbially-driven processes in oligotrophic freshwater ecosystems are poorly understood. We quantified guilds in the main N-transformation pathways in benthic habitats of 11 mountain lakes along a dissolved inorganic nitrogen gradient. The genes involved in denitrification (nirS, nirK, nosZ), nitrification (archaeal and bacterial amoA), dissimilatory nitrate reduction to ammonium (DNRA, nrfA) and anaerobic ammonium oxidation (anammox, hdh) were quantified, and the bacterial 16S rRNA gene was sequenced. The dominant pathways and associated bacterial communities defined four main N-transforming clusters that differed across habitat types. DNRA dominated in the sediments, except in the upper layers of more productive lakes where nirS denitrifiers prevailed with potential N₂O release. Loss as N₂ was more likely in lithic biofilms, as indicated by the higher hdh and nosZ abundances. Archaeal ammonia oxidisers predominated in the isoetid rhizosphere and rocky littoral sediments, suggesting nitrifying hotspots. Overall, we observed a change in potential for reactive N recycling via DNRA to N losses via denitrification as lake productivity increases in oligotrophic mountain lakes. Thus, N deposition results in a shift in genetic potential from an internal N accumulation to an atmospheric release in the respective lake systems, with increased risk for N₂O emissions from productive lakes.