Biogeochemical Cycles Of Nitrogen Research Articles

Temporal variations of biological nitrogen fixation and diazotrophic communities associated with artificial seaweed farms

Diazotrophic communities contribute inorganic nitrogen for the primary productivity of the marine environment by biological nitrogen fixation (BNF). They play a vital role in the biogeochemical cycle of nitrogen in the marine ecological environment. However, there is still an incomplete understanding of BNF and diazotrophs in artificial seaweed farms. Therefore, this study comprehensively investigated the temporal variations of BNF associated with Gracilariopsis lemaneiformis, as well as the diazotrophic communities associated with macroalgae and its surrounding seawater. Our results revealed that a total of 13 strains belonging to Proteobacteria and Bacteroidetes were identified as N2-fixing bacteria using azotobacter selective solid medium and nifH gene cloning. Subsequently, BNF and diazotrophic communities were characterized using the acetylene reduction method and high-throughput sequencing of the nifH gene, respectively. The results showed that nitrogenase activity and nifH gene abundance of epiphytic bacteria on G. lemaneiformis varied significantly among four different cultivation periods, i.e., Cultivation Jan. (CJ), Cultivation Feb. (CF), Cultivation Mar. (CM), Cultivation Apr. (CA). Among them, the nitrogenase activity and nifH gene abundance of epiphytic bacteria on G. lemaneiformis in CM were significantly higher than those in CJ, CF, and CA, indicating that the BNF of eiphytic bacteria on G. lemaneiformis was markedly enhanced. Combined with the data on environmental factors, it was found that the low concentration of nitrogen and phosphorus in CM might considerably boost the BNF of epiphytic bacteria in G. lemaneiformis. The sequencing results of the nifH gene showed that the α-diversity of diazotrophic communities associated with G. lemaneiformis and seawater in CM was higher than that in other cultivation periods. In addition, the diazotrophic communities on G. lemaneiformis were significantly different in CJ, CF, CM, and CA, and they were significantly diverse from diazotrophic communities in seawater. LEfSe analysis indicated that Rhodobacterales, Hyphomonadaceae, Robiginitomaculum, and Robiginitomaculum antarcticum within α-proteobacteria played a remarkable role in BNF in response to nitrogen nutrient deficiency. Taken together, these results provide a unique insight into the interaction between macroalgae and its epiphytic bacteria and lay a foundation for further research on the mechanism of action of nitrogen-cycling microorganisms associated with macroalgae.

Conception and parameterization of field-scale models for simulating ammonia loss from fertilized lands: a review

Conception and parameterization of field-scale models for simulating ammonia loss from fertilized lands: a review

Historical development, impact mechanism and future trends of nitrogen footprint in Wuxi City, China

Human activities have changed the biogeochemical cycle of nitrogen, leading to a large amount of reactive nitrogen (Nr) into the environment, aggravating a series of environmental problems, affecting human and ecosystem health. Cities are the core areas driving nitrogen cycling in terrestrial ecosystems, however, there are numerous influencing factors and their contributions are unclear. The nitrogen footprint is an important index to understand the impact of human activities on the environment, however, the calculation of urban nitrogen footprint needs a simplified and accurate system method. Here we use a nitrogen footprint calculation model at the urban system level based on system nitrogen balance, and a multi-factor extended STIRPAT (stochastic impact by regression on population, affluence, and technology) model suitable for analyzing the impact mechanism of nitrogen footprint to estimate nitrogen footprint of Wuxi City during 1990–2050. We find that: (1) from 1990 to 2020, the total nitrogen footprint of Wuxi City was in an increasing trend, but the per capita nitrogen footprint was in a decreasing trend. The per capita nitrogen footprint of 22.36 kg capita−1 in 2020 was at a lower level globally. (2) Nr discharge from fossil fuel combustion and Haber-Bosch nitrogen fixation accounted for the main proportion of nitrogen footprint. (3) Dietary choice (Ad), GDP per capita (Ag), urbanization rate (Au), population (P), and fossil energy productivity (Te) were the key factors contributing to the increase of the nitrogen footprint, which resulted in an annual increase of 1.39 %. While nitrogen footprint productivity (Tn), nitrogen use efficiency in crop farming (Tc), and nitrogen use efficiency in animal breeding (Ta) were the key inhibit factors that inhibit the increase of nitrogen footprint, and these factors slow down the annual growth rate of nitrogen footprint by 0.39 %. (4) The continuous growth of nitrogen footprint in the baseline and population growth scenarios will bring more environmental problems and greater environmental governance pressure to Wuxi City, while the sustainable scenario that includes comprehensive means such as economic adaptation and technological improvement is more in line with the requirements of high-quality development in China. Several mitigation measures are then proposed by considering Wuxi's realities from both key impact factors and potential for nitrogen footprint reduction in different scenarios, which can provide valuable policy insights to other cities, especially lakeside cities to mitigate nitrogen footprint.

Guanidine production by plant homoarginine-6-hydroxylases.

Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.

Guanidine production by plant homoarginine-6-hydroxylases

Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.

Deciphering the functional importance of comammox vs. canonical ammonia oxidisers in nitrification and N2O emissions in acidic agricultural soils

The discovery of comammox Nitrospira has altered our perception of the nitrogen biogeochemical cycle. However, their functional importance compared to canonical ammonia oxidisers (i.e., ammonia-oxidising bacteria (AOB) and archaea (AOA)) in agricultural soils remains elusive, especially in acidic soils. Here, we assessed the functional importance of these functional guilds in nitrification and nitrous oxide (N2O) emissions in three acidic agricultural soils by using a range of nitrification inhibitors (acetylene, 3,4-dimethylpyrazole phosphate (DMPP) and different concentrations of 1-octyne) and monitored their community assemblage and population dynamics. The sensitivity of comammox Nitrospira clade A to 1-octyne varied across soils, highlighting that the inappropriate use of 1-octyne can lead to misestimation of comammox activity. AOA were key NH3 oxidisers in the three soils, while AOB also contributed significantly to nitrification in one soil. In contrast, comammox Nitrospira always played a minor role in ammonia oxidation and N2O emissions, likely due to their low abundances, restricted cellular kinetic properties and N2O production mechanisms. Together, this study demonstrates that comammox Nitrospira play a less important role in ammonia oxidation and N2O production in acidic agricultural soils than AOA and AOB, thereby providing important novel insights into the mitigation of nitrogen fertiliser loss and N2O emissions.

Dynamic stratification and biogeochemical cycling response of microbial communities in east indian ocean ridge

Marine harbors a diverse and intricate microbial ecosystem crucial for driving biogeochemical and nutrient cycles. To gain insights into the ecological functions of microbial communities in deep-sea sediments and their responses to biogeochemical cycling, this study investigated microbial dynamics within the East Indian Ocean (EIO) ridge, focusing on vertical stratification of sediment communities. Notably, depth-related microbial patterns surpassed regional stratification effects. Environmental factors, such as TN and NO2–-N, significantly shaped community structures, while stochastic processes, particularly homogenizing dispersal, contributed to spatial similarity and structural stability. In this challenging environment, bacterial and archaeal communities established symbiotic relationships for enhanced survival, and dominated carbon and nitrogen biogeochemical cycling processes, respectively. Key bacterial genera acted as bridging agents, orchestrating intricate interactions, while archaeal communities displayed greater dispersion. Metabolic pathways analyses revealed that bacterial community was characterized by denitrification and DNRA processes, while archaea were dominated by the nirK-encoded denitrification pathway. Ultimately, this study shed light on nuanced interactions and ecological roles of microbial communities, contributed to broader understanding of biogeochemical processes and global carbon/nitrogen sinks.

Life cycle assessment of ammonium sulfate recovery from urban wastewater

ABSTRACT Anthropogenic nitrogen fluxes are profoundly altering the global biogeochemical nitrogen cycle. Better management of these nitrogen fluxes is essential. Recovering nitrogen from urban wastewater reduces both the energy and resources required to produce nitrogen-based fertilizer and to remove nitrogen from wastewater collected. Nitrogen can be recovered from wastewater in the form of ammonium sulfate, a common nitrogen-based fertilizer. In the urban setting, the technology can be applied to target source-separated urine or municipal wastewater. To assess the environmental sustainability of this approach, this study compared the life cycle environmental impacts of ammonium sulfate recovered from urban wastewater (through eight different recovery technology trains) and ammonium sulfate produced by six different industrial processes. The results show that wastewater-derived ammonium sulfate generally has lower potential environmental impacts than industrially produced ammonium sulfate in most of the impact categories assessed. The impact for the source-separated urine centralized recovery train is the smallest. The contribution analysis shows that energy, sulfuric acid and sodium hydroxide use are the major contributors, while the background inventory analysis shows that the results can be sensitive to the choice of region-specific background inventory. In the future, nitrogen recovery from urban wastewater is promising for the circular economy in cities.

Effects of biodegradable microplastics on arsenic migration and transformation in paddy soils: a comparative analysis with conventional microplastics

The combined pollution of microplastics (MPs) and arsenic (As) in paddy soils has attracted more attention worldwide. However, there are few comparative studies on the effects of biodegradable and conventional MPs on As migration and transformation. Therefore, conventional (polystyrene, polyethylene, polyvinyl chloride) and biodegradable (polybutadiene styrene, polylactic acid, polybutylene adipate terephthalate) MPs were selected to explore and demonstrate their influences and mechanism on As migration from paddy soils to overlying water and As speciation transformation through microcosmic experiment with measuring the changes of As chemical distribution, physicochemical indexes and microbial community in paddy soils. The results showed that biodegradable MPs enhanced As migration and transformation more effective than conventional MPs during 60 d. Biodegradable MPs indirectly increased the content of As(Ⅲ) and bioavailable As by changing the microbial community structure and affecting the biogeochemical cycles of carbon, nitrogen, sulfur and iron in soils, and promoted the As migration and transformation. PBS showed the strongest promoting effect, transforming to more As(Ⅲ) (11.43%) and bioavailable As (4.28%) than control. This helps to a better understanding of the effects of MPs on As biogeochemical cycle and to clarify the ecological and food safety risks of their combined pollution in soils.

Experimental simulation of thermal evolution of nitrogen content and isotopes in source rocks: Implications for nitrogen cycling characterization and oil-source correlation

Sedimentary nitrogen isotopes have been widely used to reconstruct the nitrogen cycling and redox characteristics of ancient oceans, but they also have important value in the study of oil genesis, such as oil classification. However, the thermal evolution of nitrogen isotopes in the source rock and associated oil is currently unclear. In this study, the thermal evolution (from the oil generation to the dry gas stage) of three types of low-maturity source rock was simulated. And the content and isotope composition of total organic carbon (TOC) and total nitrogen (TN) of the pyrolyzed source rock, expelled oil and retained oil were measured. In combination with weight-quantitative analyses, the following conclusions can be drawn: (1) During the main oil and gas generation stage, the pyrolyzed source rocks lost 15.1–28.3% of TN, which is much lower than the loss of TOC (26.2–46.1%). This difference may be related to the fact that the TOC content of the generated oil and gas is two orders of magnitude higher than the TN. In addition, TOC loss occurred mainly within the oil generation-expulsion stage, whereas TN loss occurred mainly in the dry gas stage and higher maturity stage. (2) The nitrogen isotope compositions of three types of source rocks and associated kerogens became heavier by 0.5–1.5‰ as thermal maturity increased, which is similar to the change of organic carbon isotope compositions. The δ15N values of pyrolyzed source rocks generally have poor relationships with either the amount of expelled oil and gas or the TN loss, which is different from the δ13Corg values. The δ15N fluctuations may be attributed to three processes: oil generation-expulsion, N2 gas generation-expulsion, and inorganic N (like NH4+) expulsion. The bulk nitrogen isotope composition of source rocks is only slightly affected by thermal maturity and can be used to indicate the nitrogen biogeochemical cycle and water redox conditions during the deposition. (3) Similar to δ13Corg values, δ15N values of both expelled oil and retained oil increased gradually with enhanced thermal maturity, implying a control of kinetic isotope effect. Among the three types of source rock, two of them having relatively light nitrogen isotope compositions (δ15N value of ∼2.5‰) generated and expelled oils with similar nitrogen isotope compositions, while the third type, which has heavy nitrogen isotope composition (δ15N value of ∼13.0‰), generated and expelled oils with much lighter nitrogen isotope compositions (by 3–6‰). This finding shows that there may be significant nitrogen isotope fractionation during the generation and primary migration of oil from source rocks. The nitrogen isotopes should be used in oil-source correlation with caution, even though related mechanisms need to be further studied. Nevertheless, using a combination of organic carbon and nitrogen isotopes, the oil generated and expelled by the three types of source rocks could be distinguished. Therefore, the use of nitrogen isotopes for oil-source correlation under geological conditions should be combined with other isotope and molecular indicators.

Uptake patterns for nitrogen and sulfur source by aquatic plants and various nitrogen acquisition strategies: Affected by mining activities

Understanding the nitrogen and sulfur uptake strategies of mine plants, including sources and preferences for nitrogen forms (ammonium nitrogen (NH4+) vs nitrate nitrogen (NO3−)), is critical to improving understanding of the role of plants in participating in the biogeochemical cycles of nitrogen and sulfur in mining areas. In this study, the stable N and S isotopic compositions of two species of aquatic plants (calamus and reed) in Linhuan mining area were analyzed to determine their absorption strategies for different nitrogen and sulfur sources. The results showed that river water was the largest source of nitrogen and sulfur, contributing 54.6% and 53.9% respectively. NO3− is the main form of nitrogen uptake by reed and calamus, followed by NH4+. In order to adapt to the change of nitrogen form in the environment, reed and calamus tend to absorb and utilize NO3− to maintain their absorption of nitrogen. Mine effluents from mining activities provide at least 12.9% and 16.8% sulfate to reed and calamus respectively, and the effect of mine effluents on reed and calamus sulfur has been underestimated. This study reveals the key factors controlling plant isotope composition, and the use of nitrogen and sulfur isotope composition of aquatic plants can help quantify the level of influence of mining activities, and understand the biogeochemical cycle of nitrogen and sulfur in mining areas.

Improved Method for Extracting Nitrites in Soil

Soil nitrite (NO2−) is an important reactive intermediate in many nitrogen transformation processes, but it is unstable under acidic conditions and may be lost as gaseous N. The canonical extraction method of soil NO2− using a potassium chloride (KCl) solution greatly underestimates its concentration. To reflect the concentration more accurately, we optimized the extraction method of soil NO2− for three agricultural soils differing in soil texture and pH, an alkalic fluvo-aquic soil and acidic Mollisol and Ultisol soils, respectively. Both extractable soil ammonium (NH4+) and nitrate (NO3−) were systematically investigated to optimize the simultaneous extraction of soil inorganic nitrogen. The effects of different extractants (deionized water (DIW), un-buffered 2 mol L−1 KCl, and pH-buffered 2 mol L−1 KCl), shaking time (10 and 30 min), and storage duration of the extracts (stored at −20 °C for 1 day, and at 4 °C for 1, 3, and 6 days) on the determination of soil inorganic nitrogen were investigated. The results showed that the un-buffered KCl extractant significantly underestimated soil NO2− concentration compared to DIW. The highest recovery of NO2− was obtained by extracting with DIW at 10 min of shaking for all three soils. Compared with DIW, the concentration of NH4+ and NO3− in soil extracted from the KCl solution increased significantly. Furthermore, the soil inorganic nitrogen content of extracts stored at 4 °C for one day was closer to the direct measurements of fresh samples than with the other storage methods. Overall, the recommended analysis method for soil NO2− was extraction by DIW, shaking for 10 min, and filtering with a 0.45 µm filter, while soil NH4+ and NO3− were extracted with a KCl solution and shaken for 30 min. The extract should be stored at 4 °C and analyzed within 24 h. Our study provides an efficient extraction method for soil NO2− and supports studies on the biogeochemical nitrogen cycle, e.g., in the investigation of soil nitrous acid (HONO) and nitric oxide (NO) emissions.

Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen.

Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.

Precipitation fuels dissolved greenhouse gas (CO2, CH4, N2O) dynamics in a peatland-dominated headwater stream: results from a continuous monitoring setup

Stream ecosystems are actively involved in the biogeochemical cycling of carbon (C) and nitrogen (N) from terrestrial and aquatic sources. Streams hydrologically connected to peatland soils are suggested to receive significant quantities of particulate, dissolved, and gaseous C and N species, which directly enhance losses of greenhouse gases (GHGs), i.e., carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), and fuel in-stream GHG production. However, riverine GHG concentrations and emissions are highly dynamic due to temporally and spatially variable hydrological, meteorological, and biogeochemical conditions. In this study, we present a complete GHG monitoring system in a peatland stream, which can continuously measure dissolved GHG concentrations and allows to infer gaseous fluxes between the stream and the atmosphere and discuss the results from March 31 to August 25 at variable hydrological conditions during a cool spring and warm summer period. Stream water was continuously pumped into a water-air equilibration chamber, with the equilibrated and actively dried gas phase being measured with two GHG analyzers for CO2 and N2O and CH4 based on Off-Axis Integrated Cavity Output Spectroscopy (OA-ICOS) and Non-Dispersive Infra-Red (NDIR) spectroscopy, respectively. GHG measurements were performed continuously with only shorter measurement interruptions, mostly following a regular maintenance program. The results showed strong dynamics of GHGs with hourly mean concentrations up to 9959.1, 1478.6, and 9.9 parts per million (ppm) and emissions up to 313.89, 1.17, and 0.40 mg C or N m−2h−1 for CO2, CH4, and N2O, respectively. Significantly higher GHG concentrations and emissions were observed shortly after intense precipitation events at increasing stream water levels, contributing 59% to the total GHG budget of 762.2 g m−2 CO2-equivalents (CO2-eq). The GHG data indicated a constantly strong terrestrial signal from peatland pore waters, with high concentrations of dissolved GHGs being flushed into the stream water after precipitation. During drier periods, CO2 and CH4 dynamics were strongly influenced by in-stream metabolism. Continuous and high-frequency GHG data are needed to assess short- and long-term dynamics in stream ecosystems and for improved source partitioning between in-situ and ex-situ production.

High niche specificity and host genetic diversity of groundwater viruses.

Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.

Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria.

Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.

Coupling of nitrogen biogeochemical cycling and phytoplankton community structure before and after the Late Ordovician mass extinction in South China

The Ordovician–Silurian transition (OST) is a crucial geological interval in Earth history, coinciding with the first of the ‘Big Five’ Phanerozoic mass extinction events (ca. 445 Ma). In addition to the dramatic loss of biodiversity, significant environmental change course such as redox conditions and nutrient availability have been the focus of debate. Previous studies have used isotopes of nitrogen (N) to reconstruct the redox evolution of the paleo-ocean and have identified biological nitrogen fixation as the main mode of nitrogen cycling during the OST. However, low δ15N values, ranging from −2‰ to +1‰, possibly correspond to four different redox conditions. The precise roles of these redox conditions and the spatial distributions of phytoplankton communities under different nitrogen cycles remain elusive. Here we present high-resolution nitrogen isotope, carbon isotope and lipid biomarker datasets from two drilled sections located on a submerged high of the Yangtze Basin to unravel the coupling between nitrogen biogeochemical cycling and phytoplankton community structure across the OST. The results suggest that there was a dominantly biological nitrogen fixation with local aerobic nitrogen cycling in the Yangtze Sea, and the nitrate inventory during the OST was smaller than that in the modern ocean. Particularly, before the Late Ordovician mass extinction (LOME), N-fixing cyanobacteria were likely extensively developed in the photic zone, while eukaryotic algae were limited. After the LOME, sea levels rose and the chemocline was higher than before the LOME. There was probably some NO3− that did not undergo denitrification in the surface ocean, favoring the development of eukaryotic algae. The ecological diversification from prokaryotic cyanobacteria to eukaryotic phytoplankton to eukaryotic zooplankton is likely to be a response to the enhanced biological pump, which generates positive feedbacks among the evolution of eukaryotic phytoplankton, organic matter enrichment, ocean oxygenation and atmospheric oxygen levels.

Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments

Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade’s ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.

Uncovering the Prokaryotic Diversity of the Bathyal Waters above the Kuril–Kamchatka Trench

The Kuril–Kamchatka Trench (North-West Pacific Ocean) is included in the deepest trenches (>9000 m). This study is the first that aims at uncovering the bathyal prokaryotic diversity (1000–2000 m) of this fascinating extreme environment. The analysis of α-diversity revealed that bacterial communities showed greater diversity than archaeal communities and that both communities were characterized by poor evenness (indicative of the presence of few dominant OTUs). The metabarcoding analysis showed that Proteobacteria (65.5–90.7%), Bacteroidetes (2.4–10.7%), and Actinobacteria (2.5–9.6%) were the highly represented phyla of bacteria, with Acinetobacter (21.5–62.5%) as the most abundant genus. Moreover, the recently described Pseudofrancisella genus, which has been isolated from estuarine environments, has been found among the major bacterial taxa. This work represents the first report stating the presence of this genus in bathyal waters. The archaeal communities were dominated by the phylum Thaumarchaeota (53.6–94.0%), with Nitrosopumilus (53.6–94%) as its representative genus. The functional diversity analysis revealed that overall, the bacterial communities had a higher involvement in the carbon and nitrogen biogeochemical cycles, with chemoheterotrophy (mostly aerobic), aromatic compound degradation, and nitrate reduction as the most represented functions. In the archaeal communities, the most represented ecological function was the aerobic oxidation of ammonia (first stage of nitrification), a functional feature characteristic of Nitrosopumilus.

Effects and mechanism of microplastics on organic carbon and nitrogen cycling in agricultural soil: A review

AbstractAt present, microplastics (MPs) are a kind of emerging pollutants of concern in the environment, and have a wide and far‐reaching impact on terrestrial ecosystems. This article summarizes the latest research progress of the impact of MPs pollution on the biogeochemical cycle of carbon (C) and nitrogen (N), and summarizes the current situation of MPs pollution in agricultural soil. On the basis of summarizing the effects of MPs on soil physicochemical properties, soil microorganisms and soil plants and animals, this article focuses on how soil MPs affect the C and N cycles by changing these factors. MPs can alter organic matter degradation and C and N cycles by changing the soil physicochemical properties, as well as the soil microbial and enzymatic activities. MPs may alter plants' nutrient uptake processes, which in turn affects the ability of plants to photosynthesize and absorb C and N elements. MPs can affect the survival rate, the growth rate and intestinal injury of soil animals, therefore indirectly affecting the soil C and N cycles. At the same time, this article compares the different effects of conventional plastics and biodegradable plastics on soil, and looks forward to the current research deficiencies and the future research directions of ecotoxicology of MPs on C and N cycle.