Biogeochemical Cycles Of Nitrogen Research Articles

Periphytic biofilms-mediated microbial interactions and their impact on the nitrogen cycle in rice paddies

Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production. Periphytic biofilms (PBs) at the soil-water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency. PBs are composed of microbial aggregates, including a wide variety of microorganisms (algae, bacteria, fungi, protozoa, and metazoa), extracellular polymeric substances and minerals (iron, aluminum, and calcium), which form an integrated food web and energy flux within a relatively stable micro-ecosystem. PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization. Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated. We summarize the key functional importance of PBs, including the intricate and delicate community structure, microbial interactions among individual phylotypes, a wide diversity of self-produced organics, the active adaptation of PBs to constantly changing environments, and the intricate mechanisms by which PBs regulate the nitrogen cycle. We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability, optimizing nitrogen utilization and crop yields in rice paddies. ● Periphytic biofilms (PBs) are active microbial aggregates ubiquitously distributed in wetlands. ● PBs form a stable and intricate food web catalyzing biogeochemical cycling of soil nitrogen. ● PBs in rice paddies can improve nitrogen utilization efficiency by plants. ● PBs-mediated microbial interactions facilitate the nitrogen cycle cooperation among microorganisms, while self-produced organics and genomic adaptation are beneficial for the nitrogen cycle regulation by PBs.

Microbially mediated Fe-N coupled cycling at different hydrological regimes in riparian wetland

Although the significance of the coupled Fe- and N- cycling processes on biogeochemical transformation in riparian wetlands is well-known, the regulation associated with the changes on the microbiotas during different hydrological regimes remains unclear. This study performed field investigations on the bacterial community compositions (BCC) and specific genera associated to Fe- and N- cycling in the rhizosphere soil and sediments in a riparian wetland in Poyang lake, China. The predominant phyla Proteobacteria, Acidobacteria, and Nitrospirae from all the samples remarkably decreased after long-term continuous flooding, while Actinobacteria, Firmicutes and Bacteroidetes were enriched. For the family level, the relative abundances of iron-oxidizing bacteria (FeOB) Gallionellaceae, and N fixing bacteria Nitrospiraceae and Bradyrhizobiaceae significantly declined upon the long-term flooding and then increased with dewatering, which were consistent with the functional genes sequencing analysis. In which, the Bradyrhizobiaceae (RA 2.0 %–34.6 %) was the dominant nirS denitrifier and potential iron-reducing bacteria (FeRB), Sideroxydans lithotrophicus was one of the dominant FeOB (RA 1.7 %–23 %), which was also identified to be the nirS dentrifier (RA 0.2 %–4.3 %). The absolute quantification of the functional genes levels including nirS, nirK, FeRB (Geobacter spp.) showed their significant increases by 3–7 times upon desiccation compared to that under post-CF. The PCA and RDA results indicated the linkage between redox changes of N and Fe during inundation mediated by FeRB, NOB, and FeOB, which were closely related to hydrochemical indices NO3−, Fe2+ and SO42−. These evidences all implied the likely occurrence of nitrate reduction coupled to Fe(II) oxidation (NRFeOx) under oligotrophic conditions, which was potentially facilitated by metabolizers consisting of highly correlated Bradyrhizobiaceae and Sideroxydans (rho = 0.86, p < 0.01). These findings provide an interpretation of the biological reactions in the microbially mediated NRFeOx processes driven by hydrological change, which could assist the mechanistic understanding of the global biogeochemical cycles of iron and nitrogen in riparian wetlands.

Phylogenomics Uncovers Evolutionary Trajectory of Nitrogen Fixation in Cyanobacteria.

Biological nitrogen fixation (BNF) by cyanobacteria is of significant importance for the Earth’s biogeochemical nitrogen cycle but is restricted to a few genera that do not form monophyletic group. To explore the evolutionary trajectory of BNF and investigate the driving forces of its evolution, we analyze 650 cyanobacterial genomes and compile the database of diazotrophic cyanobacteria based on the presence of nitrogen fixation gene clusters (NFGCs). We report that 266 of 650 examined genomes are NFGC-carrying members, and these potentially diazotrophic cyanobacteria are unevenly distributed across the phylogeny of Cyanobacteria, that multiple independent losses shaped the scattered distribution. Among the diazotrophic cyanobacteria, two types of NFGC exist, with one being ancestral and abundant, which have descended from diazotrophic ancestors, and the other being anaerobe-like and sparse, possibly being acquired from anaerobic microbes through horizontal gene transfer. Interestingly, we illustrate that the origin of BNF in Cyanobacteria coincide with two major evolutionary events. One is the origin of multicellularity of cyanobacteria, and the other is concurrent genetic innovations with massive gene gains and expansions, implicating their key roles in triggering the evolutionary transition from nondiazotrophic to diazotrophic cyanobacteria. Additionally, we reveal that genes involved in accelerating respiratory electron transport (coxABC), anoxygenic photosynthetic electron transport (sqr), as well as anaerobic metabolisms (pfor, hemN, nrdG, adhE) are enriched in diazotrophic cyanobacteria, representing adaptive genetic signatures that underpin the diazotrophic lifestyle. Collectively, our study suggests that multicellularity, together with concurrent genetic adaptations contribute to the evolution of diazotrophic cyanobacteria.

The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil.

Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. IMPORTANCE In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrobacter winogradskyi play a central role in the global biogeochemical nitrogen cycle. In addition to this central role, the autotrophic nitrite-oxidizing bacteria also play a fundamental role in the global carbon cycle. They form the basis of heterotrophic food webs, in which the assimilated carbon is recycled. Little is known about the heterotrophic microorganisms that participate in these food webs, let alone their assembly in different ecosystems. This study showed that the assembly of microbial food webs by N. winogradskyi was a highly stochastic process and independent of the origin of the heterotrophic microorganisms, but the functional characteristics of the different food webs were similar.

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments.

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environments. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated data set of 33 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome-assembled genomes (MAGs), which we dereplicated into 55 unique, nearly complete medium- and high-quality MAGs spanning 12 bacterial and archaeal phyla. We also reconstructed 2,482 viral genomic contigs, which were dereplicated into 111 viral MAGs (vMAGs) of >10 kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovered new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. We show how these metabolic pathways, integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen, could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral MAGs to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling. IMPORTANCE Here we created HUM-V (hyporheic uncultured microbial and viral), an annotated microbial and viral MAG catalog that captures strain and functional diversity encoded in these Columbia River sediment samples. Demonstrating its utility, this genomic inventory encompasses multiple representatives of dominant microbial and archaeal phyla reported in other river sediments and provides novel viral MAGs that can putatively infect these. Furthermore, we used HUM-V to recruit gene expression data to decipher the functional activities of these MAGs and reconstruct their active roles in Columbia River sediment biogeochemical cycling. Ultimately, we show the power of MAG-resolved multi-omics to uncover interactions and chemical handoffs in river sediments that shape an intertwined carbon and nitrogen metabolic network. The accessible microbial and viral MAGs in HUM-V will serve as a community resource to further advance more untargeted, activity-based measurements in these, and related, freshwater terrestrial-aquatic ecosystems.

Biogeochemical Cycling of Carbon and Nitrogen in Rainfed Rice Production Under Conventional and Organic Rice Farming

Dwindling carbon (C) and nitrogen (N) levels in paddy soils decreases rice production and threaten human food security globally. The efficient maintenance of C and N fluxes in soil-rice systems is a crucial prerequisite for agricultural and environmental sustainability. Herein, we examined the C and N fluxes from 63 rainfed rice paddy fields under conventional farming (CF) and organic farming (OF) systems in Thailand. The C and N fluxes were measured based on a detailed analysis of relevant influxes (fertilizer, manure, and biomass addition) and effluxes (biomass harvest and greenhouse gas emission). The results demonstrated that the harvested grain and straw contributed to the most abundant C and N effluxes for both farming systems. The CH4 effluxes were moderate, whereas the N2O effluxes were meager relative to their total effluxes. Stubble incorporation and animal manure addition to soil were the most extensive C influxes. However, the primary N influxes were stubble incorporation and animal manure addition for the OF system, and chemical-N fertilizers for the CF system. Net C depletions were observed in both the CF and OF systems. However, net N was depleted and accumulated in the CF and OF systems, respectively. Straw incorporation to soils could restore the net C accumulations for the CF and OF systems and elevate the net N accumulation for both systems. This study highlighted that complete straw removal has exacerbated the C and N stock in soil-rice systems, inducing insecurity for the environment and the agricultural systems. Effective straw management is a simple approach for sustaining paddy rice production.

Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench.

ABSTRACTThe unique geological features of hadal trenches are known to influence both the structure and ecological function of microbial communities. It is also well known that heterotrophs and chemoautotrophs dominate the hadal and abyssal pelagic zones, respectively. Here, a metagenomic investigation was conducted on sediment samples obtained from the abyssal-hadal transition zone in the Mariana Trench to gain a better understanding of the general diversity and potential function of the core microbiome in this zone. A high level of cosmopolitanism existed in the core microbiome referred from a high community similarity among different stations. Niche differentiation along the fine-scale of different sediment layers was observed, especially for major archaeal groups, largely due to sediment depth and the source of organic matter. A prevalence of nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation in the abyssal-hadal biosphere was also demonstrated. The predominance of heterotrophic over chemolithoautotrophic pathways in this transition zone was found, and a high abundance of genes related to respiration and carbon fixation (i.e., the intact Calvin and rTCA cycles) were detected as well, which might reflect the intensive microbial activities known to occur in this deep biosphere. The presence of those metabolic processes and associated microbes were reflected by functional and genetic markers generated from the metagenomic data in the current study. However, their roles and contributions to the nitrogen/carbon biogeochemical cycles and flux in the abyssal-hadal transition zone still need further analysis.IMPORTANCE The Mariana Trench is the deepest oceanic region on earth, its microbial ecological exploration has become feasible with the rapid progress of submersible and metagenomic sequencing. We investigated the community compositions and metabolic functions of the core microbiome along the abyssal-hadal transition zone of the Mariana Trench, although most studies by far were focused on the pelagic zone. We found a predominance of heterotrophic groups and related metabolic pathways, which were closely associated with nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation.

Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island.

Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with 15N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; therefore, this physical forcing should be considered in the future assessment of the global nitrogen budgets and biogeochemical nitrogen cycles.

Bacterial community response to chronic heavy metal contamination in marine sediments of the East China Sea

Marine sediments act as a sink for various heavy metals, which may have profound impact on sedimentary microbiota. However, our knowledge about the collaborative response of bacterial community to chronic heavy metal contamination remains little. In this study, concentrations of seven heavy metals (As, Cd, Cr, Cu, Hg, Pb, and Zn) in sediments collected from the East China Sea were analyzed and Illumina Miseq 16 S rRNA sequencing was applied to characterize the structure of bacterial community. Microbiota inhabiting sediments in the East China Sea polluted with heavy metals showed different community composition from relatively pristine sites. The response of bacterial community to heavy metal stress was further interrogated with weighted correlation network analysis (WGCNA). WGCNA revealed ten bacterial modules exhibiting distinct co-occurrence patterns and among them, five modules were related to heavy metal pollution. Three of them were positively correlated with an increase in at least one heavy metal concentration, hubs (more influential bacterial taxa) of which were previously reported to be involved in the geochemical cycling of heavy metals or possess tolerance to heavy metals, while another two modules showed opposite patterns. Our research suggested that ecological functional transition might have occurred in East China Sea sediments by shifts of community composition with sensitive modules majorly involved in the meaningful global biogeochemical cycling of carbon, sulfur, and nitrogen replaced by more tolerant groups of bacteria due to long-term exposure to low-concentration heavy metals. Hubs may serve as indicators of perturbations of benthic bacterial community caused by heavy metal pollution and support monitoring remediation of polluted sites in marine environments.

Microbial functional assemblages predicted by the FAPROTAX analysis are impacted by physicochemical properties, but C, N and S cycling genes are not in mangrove soil in the Beibu Gulf, China

Mangroves and their global significance in climate change based on the storage of blue carbon and release of CO2, CH4, and N2O have attracted great attention. Microbial communities and their functions are essential for the biogeochemical cycle of carbon (C), nitrogen (N), and sulfur (S). Therefore, the assessment of microbial functions in mangrove habitats, which suffer from different external environments, is necessary to evaluate their unique ecological service functions. In the present work, the functional profiles of microbial communities in four mangrove reserves (one sandy and three muddy, in Beibu Gulf, China) were detected by 16 s RNA gene amplicon-based Functional Annotation of Procaryotic Taxa (FAPROTAX) analysis as well as C, N, and S gene q-PCR chips. The FAPROTAX analysis showed that the metabolic potential in C, N, and S cycling indicated a difference in the four mangrove regions. Moreover, some functional groups involved in N, C, and S cycling were significantly correlated with physicochemical characteristics. However, N, C, and S metabolic genes detected by q-PCR chip did not present the same changes following the variation of environmental conditions as those predicted by the FAPROTAX analysis. Most of the N, C, and S cycling genes were equally distributed in the four mangroves. Several genes involved in N cycling (amoA, amoB, nirK, and nosZ), carbon degradation (amyA, apu, mnp, lig, and chiA), carbon fixation (aclB), and oxidation of H2S (SoxY) were significantly higher in sampling site in Beihai City (Bei), which was the only site with sandy soils. We hypothesized that soil texture (sandy or muddy) rather than physicochemical elements contributes more significantly to the abundance of N, S, and C metabolic genes in mangrove sediment. Our study demonstrated that the change of physicochemical property in mangrove soil was easier to modify the functional microbial groups than functional genes. We should pay attention to the functional redundancy of soil microbiota when using microorganisms as ecological indicator to access the soil activity in mangrove habitats.

Suspended particulate matter drives the spatial segregation of nitrogen turnover along the hyper-turbid Ems estuary

Abstract. Estuaries are nutrient filters and change riverine nutrient loads before they reach coastal oceans. Their morphology have been extensively changed by anthropogenic activities like draining, deepening and dredging to meet economic and social demand, causing significant regime changes like tidal amplifications and in some cases to hyper-turbid conditions. Furthermore, increased nutrient loads, especially nitrogen, mainly by agriculture cause coastal eutrophication. Estuaries can either act as a sink or as a source of nitrate, depending on environmental and geomorphological conditions. These factors vary along an estuary, and change nitrogen turnover in the system. Here, we investigate the factors controlling nitrogen turnover in the hyper-turbid Ems estuary (Northern Germany), which has been strongly impacted by human activities. During two research cruises in August 2014 and June 2020, we measured water column properties, dissolved inorganic nitrogen, dual stable isotopes of nitrate and dissolved nitrous oxide concentration along the estuary. We found that three distinct biogeochemical zones exist along the estuary. A strong fractionation (∼26 ‰) of nitrate stable isotopes points towards nitrate removal via water column denitrification in the hyper-turbid tidal river, driven by anoxic conditions in deeper water layers. In the middle reaches of the estuary nitrification gains importance, turning this section into a net nitrate source. The outer reaches are dominated by mixing, with nitrate uptake in 2020. We find that the overarching control on biogeochemical nitrogen cycling, zonation and nitrous oxide production in the Ems estuary is exerted by suspended particulate matter concentrations and the linked oxygen deficits.

A potential linkage between excess silicate-bound nitrogen and N2-rich natural gas in sedimentary reservoirs

Molecular nitrogen (N2) released from sedimentary rocks during metamorphism is an important component of the biogeochemical nitrogen cycles. However, the importance and variability of this metamorphic N2 flux from rock nitrogen to Earth's surface environment remains largely unexplored. Here we present a comprehensive bulk rock C-N and N2 concentration dataset from the lower Cambrian shale across the Yangtze Block. The results reveal a spatial trend of excess silicate-bound nitrogen in the lower Cambrian shale throughout the Yangtze Block, which is interpreted as partial assimilation of ammonium (NH4+) with high concentrations of NH4+ accumulating in the euxinic water column and in sediment pore waters at shelf and slope environments during sedimentation. The remarkable spatial coupling between silicate-bound nitrogen in bulk rock shale and N2 concentration in modern shale reservoirs indicates that the high proportion of silicate-bound nitrogen may act as an important control on the formation of N2-rich gas in shale reservoirs during metamorphism. These N2-rich reservoir rocks may have affected the surface environment through tectonic movement over Earth's history. Our results therefore identify a novel linkage in the nitrogen cycle and provide evidence for the importance of metamorphism on the return of rock nitrogen back to the surface environment. We further reveal that the metamorphic N2 gas flux from the geosphere to the atmosphere is dependent on environmental conditions during sediment deposition.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems.

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.

Hydrazines as Substrates and Inhibitors of the Archaeal Ammonia Oxidation Pathway.

ABSTRACTAmmonia-oxidizing archaea (AOA) and bacteria (AOB) perform key steps in the global nitrogen cycle, the oxidation of ammonia to nitrite. While the ammonia oxidation pathway is well characterized in AOB, many knowledge gaps remain about the metabolism of AOA. Hydroxylamine is an intermediate in both AOB and AOA, but homologues of hydroxylamine dehydrogenase (HAO), catalyzing bacterial hydroxylamine oxidation, are absent in AOA. Hydrazine is a substrate for bacterial HAO, while phenylhydrazine is a suicide inhibitor of HAO. Here, we examine the effect of hydrazines in AOA to gain insights into the archaeal ammonia oxidation pathway. We show that hydrazine is both a substrate and an inhibitor for AOA and that phenylhydrazine irreversibly inhibits archaeal hydroxylamine oxidation. Both hydrazine and phenylhydrazine interfered with ammonia and hydroxylamine oxidation in AOA. Furthermore, the AOA “Candidatus Nitrosocosmicus franklandus” C13 oxidized hydrazine into dinitrogen (N2), coupling this reaction to ATP production and O2 uptake. This study expands the known substrates of AOA and suggests that despite differences in enzymology, the ammonia oxidation pathways of AOB and AOA are functionally surprisingly similar. These results demonstrate that hydrazines are valuable tools for studying the archaeal ammonia oxidation pathway.IMPORTANCE Ammonia-oxidizing archaea (AOA) are among the most numerous living organisms on Earth, and they play a pivotal role in the global biogeochemical nitrogen cycle. Despite this, little is known about the physiology and metabolism of AOA. We demonstrate in this study that hydrazines are inhibitors of AOA. Furthermore, we demonstrate that the model soil AOA “Ca. Nitrosocosmicus franklandus” C13 oxidizes hydrazine to dinitrogen gas, and this reaction yields ATP. This provides an important advance in our understanding of the metabolism of AOA and expands the short list of energy-yielding compounds that AOA can use. This study also provides evidence that hydrazines can be useful tools for studying the metabolism of AOA, as they have been for the bacterial ammonia oxidizers.

Bacterial communities in surface and basal ice of a glacier terminus in the headwaters of Yangtze River on the Qinghai\u2013Tibet Plateau

BackgroundOn the front lines of climate change, glacier termini play crucial roles in linking glaciers and downstream ecosystems during glacier retreat. However, we lack a clear understanding of biological processes that occur in surface and basal ice at glacier termini.MethodsHere, we studied the bacterial communities in surface ice and basal ice (the bottom layer) of a glacier terminus in the Yangtze River Source, Qinghai–Tibet Plateau.ResultsSurface and basal ice harbored distinct bacterial communities but shared some core taxa. Surface ice communities had a higher α-diversity than those in basal ice and were dominated by Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Cyanobacteria while basal ice was dominated by Firmicutes and Proteobacteria. The bacterial communities were also substantially different in functional potential. Genes associated with functional categories of cellular processes and metabolism were significantly enriched in surface ice, while genes connected to environmental information processing were enriched in basal ice. In terms of biogeochemical cycles of carbon, nitrogen, phosphorus, and sulfur, bacterial communities in surface ice were enriched for genes connected to aerobic carbon fixation, aerobic respiration, denitrification, nitrogen assimilation, nitrogen mineralization, sulfur mineralization, alkaline phosphatase, and polyphosphate kinase. In contrast, bacterial communities in basal ice were enriched for genes involved in anaerobic carbon fixation, fermentation, nitrate reduction, 2-aminoethylphosphonic acid pathway, G3P transporter, glycerophosphodiester phosphodiesterase, and exopolyphosphatase. Structural equation modeling showed that total nitrogen and environmental carbon:phosphorus were positively while environmental nitrogen:phosphorus was negatively associated with taxonomic β-diversity which itself was strongly associated with functional β-diversity of bacterial communities.ConclusionsThis study furthers our understanding of biogeochemical cycling of the mountain cryosphere by revealing the genetic potential of the bacterial communities in surface and basal ice at the glacier terminus, providing new insights into glacial ecology as well as the influences of glacier retreat on downstream systems.

Biochar application affects Nitrobacter rather than Nitrospira in plastic greenhouse vegetable soil

Nitrite oxidation, driven by nitrite-oxidizing bacteria, is an important step of nitrification and thus plays a vital role in biogeochemical nitrogen cycling in agricultural ecosystems. Although biochar has been widely recognized as a promising material for use in vegetable fields to slowly release nutrients, the current understanding of how nitrite oxidizers respond to the application of biochar in a plastic greenhouse vegetable field is very limited. A soil incubation experiment showed that soil nitrite oxidation was increased by 13.0%, 35.0% and 64.2% (P < 0.05) with the application of 0.5% (C0.5), 1.5% (C1.5), and 4.0% (C4.0) biochar (mass ratio), respectively. Methods including qPCR and Illumina MiSeq sequencing were also used to explore the impact of biochar on functional communities involved in nitrite oxidation. Nitrobacter and Nitrospira were the main genera of the nitrite-oxidizing bacteria and were assumed to be very important in the soil environment. Moreover, the increases in soil nitrite oxidation were positively correlated with the abundance of Nitrobacter-like NOB (P < 0.05) but not the Nitrospira-like NOB gene abundance. Furthermore, biochar application combined with nitrogen fertilizer had a significant effect on the Nitrobacter community composition, with lineages such as Nitrobacter alkalicus and Nitrobacter vulgaris being significantly enriched. Redundancy analysis indicated that the observed variations in the Nitrobacter community structure were associated with changes in soil microbial biomass nitrogen and nitrate nitrogen induced by biochar. These results implied that Nitrobacter rather than Nitrospira was significantly improved by biochar added to the soil for vegetable production.

Cultivation of ammonia-oxidising archaea on solid medium

Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: ‘Candidatus Nitrosocosmicus franklandus C13’, Nitrososphaera viennensis EN76 and ‘Candidatus Nitrosotalea sinensis Nd2’. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both ‘Ca. N. franklandus C13’ and N. viennensis EN76 tolerated Phytagel™ while the acidophilic ‘Ca. N. sinensis Nd2’ was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel™ and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from ‘Ca. N. franklandus C13’ and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.

Density functional theory calculations of nitrogen and oxygen equilibrium isotope fractionations in NO3−–NO2−–H2O aqueous system reveal inverse kinetic isotope effects during nitrite oxidation

Nitrate and nitrite play key roles in the nitrogen cycle on Earth's surface. The isotope fractionation during nitrate reduction on enzymatic level involves multiple steps, including transfer of free NO3− to the activate site on nitrate reductase and NO2− equilibration with ambient water. However, the isotope fractionation factors of 15N and 18O among NO3−, NO2−, and H2O molecules in aqueous phases are poorly constrained. It strongly impedes the understanding of the involved processes and using stable isotopes to quantitatively examine the biogeochemical nitrogen cycle. In this contribution, we employ the density functional theory method with the Urey-Bigeleisen-Goeppert-Mayer model to predict the nitrogen and oxygen equilibrium isotope fractionation factors of NO3−, NO2−, and H2O molecules in gaseous and aqueous phases. Our calculation results show that the solvent effect has a large influence on equilibrium isotope fractionation for oxygen in water (+10.1‰ between liquid and vapor water at 25 °C), which is different to the little solvent effects on both oxygen and nitrogen in nitrate and nitrite. The calculated temperature-dependent equilibrium isotope fractionations between nitrogen of NO3− and NO2−, and oxygen of H2O and NO2− are consistent with previous laboratory experiments. Our results confirm that the oxygen equilibrium isotope fractionations between NO3− and NO2− should be +9.4‰ at 25 °C. Integrating the new results and previously reported kinetic isotope effects of nitrate reduction, we demonstrate inverse kinetic isotope effects for both nitrogen (+15.4‰) and oxygen (+5.2‰) during nitrite oxidation, which falls in the range of previous experiments. The new results enable us to use both nitrogen and oxygen isotopes as a bonded isotope tool to quantitatively assess the nitrogen cycle in low-temperature environments.

MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes.

Methane is a critical greenhouse gas with significant impacts on environmental and global change. However, CH4 cycling processes and coupling mechanisms with the biogeochemical cycling of carbon, nitrogen, sulfur and metals in the environment remain elusive. To fill such knowledge gaps, we constructed a manually curated methane cycling database (MCycDB) for comprehensive and accurate analysis of methane cycling microbial communities. MCycDB contains 298methane cycling gene families covering 10methane metabolism pathways with 610,208 representative sequences, and associated reference sequences from the NCBI RefSeq database with 48 phyla and 2,197genera, and five phyla and 100genera for bacteria and archaea, respectively. Also, homologous groups from public orthology databases were identified and included in MCycDB to reduce false positive assignments. We applied MCycDB to profile methane cycling gene families and associated taxonomic groups from various environments. Gene families involved in methanogenesis were abundant in hot spring sediment and less abundant in freshwater, whereas the ones involved in aerobic oxidation of methane were abundant in permafrost and peatland. This study demonstrates that MCycDB is a useful tool for studying microbially-driven methane cycling processes with high specificity, coverage and accuracy.

Linkages between nitrogen cycling, nitrogen isotopes, and environmental properties in paleo-lake basins

AbstractThe linkages between nitrogen cycling, nitrogen isotopes, and environmental properties are fundamental for reconstructing nitrogen biogeochemistry. While the impact of ocean redox changes on nitrogen isotopes is relatively well understood, it is poorly known how nitrogen responds to changes in pH and salinity. To fill the knowledge gap, we explore the effects of these environmental parameters using a well-controlled set of samples from Carboniferous–Paleogene lake sediments in China. Our results show that the threshold of 10–12‰ in δ15N works to distinguish alkaline (pH &amp;gt; 9) from circum-neutral conditions. Elevated Mo levels in the alkaline samples support the idea of NH3 volatilization from a reducing water column in an alkaline setting. For non-alkaline lakes, δ15N values tend to be higher (up to +10‰) in more saline, anoxic settings, which is attributed to either the expansion of stagnant anoxic waters spurring water-column denitrification or a shift from plant-based toward more microbially dominated ecosystems or both. Our results imply that salinity-induced redox stratification and basicity can alter nitrogen biogeochemical cycling beyond what is shown by the marine nitrogen isotope record alone. This finding will result in an improved understanding of the dynamic controls of δ15N in sediments and lead to better biogeochemical interpretations of paleo-environmental conditions from unknown environmental settings on Earth and beyond Earth.