The continuous increase of the greenhouse gas nitrous oxide (N2O) in the atmosphere due to increasing anthropogenic nitrogen input in agriculture has become a global concern. In recent years, ...identification of the microbial assemblages responsible for soil N2O production has substantially advanced with the development of molecular technologies and the discoveries of novel functional guilds and new types of metabolism. However, few practical tools are available to effectively reduce in situ soil N2O flux. Combating the negative impacts of increasing N2O fluxes poses considerable challenges and will be ineffective without successfully incorporating microbially regulated N2O processes into ecosystem modeling and mitigation strategies. Here, we synthesize the latest knowledge of (i) the key microbial pathways regulating N2O production and consumption processes in terrestrial ecosystems and the critical environmental factors influencing their occurrence, and (ii) the relative contributions of major biological pathways to soil N2O emissions by analyzing available natural isotopic signatures of N2O and by using stable isotope enrichment and inhibition techniques. We argue that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions. We further propose a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N2O emissions.
This review summarizes the major microbial pathways of soil N2O production, and key environmental factors modulating their relative contributions, and further proposes to use a combination of state-of-the-art approaches for better source partitioning and incorporation of microbial datasets to achieve better predictive ecosystem models.
Summary
Microbial elevational diversity patterns have been extensively studied, but their shaping mechanisms remain to be explored. Here, we examined soil bacterial and fungal diversity and community ...compositions across a 3.4 km elevational gradient (consists of five elevations) on Mt. Kilimanjaro located in East Africa. Bacteria and fungi had different diversity patterns across this extensive mountain gradient—bacterial diversity had a U shaped pattern while fungal diversity monotonically decreased. Random forest analysis revealed that pH (12.61% importance) was the most important factor affecting bacterial diversity, whereas mean annual temperature (9.84% importance) had the largest impact on fungal diversity, which was consistent with results obtained from mixed‐effects model. Meanwhile, the diversity patterns and drivers of those diversity patterns differ among taxonomic groups (phyla/classes) within bacterial or fungal communities. Taken together, our study demonstrated that bacterial and fungal diversity and community composition responded differently to climate and edaphic properties along an extensive mountain gradient, and suggests that the elevational diversity patterns across microbial groups are determined by distinct environmental variables. These findings enhanced our understanding of the formation and maintenance of microbial diversity along elevation, as well as microbial responses to climate change in montane ecosystems.
Purpose
Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, is a pivotal component of the biogeochemical nitrogen cycle. Nitrification was conventionally assumed as a two-step ...process in which ammonia oxidation was thought to be catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nitrite oxidation by nitrite-oxidizing bacteria (NOB). This long-held assumption of labour division between the two functional groups, however, was challenged by the recent unexpected discovery of complete ammonia oxidizers within the
Nitrospira
genus that are capable of converting ammonia to nitrate in a single organism (comammox). This breakthrough raised fundamental questions on the niche specialization and differentiation of comammox organisms with other canonical nitrifying prokaryotes in terrestrial ecosystems.
Materials and methods
This article provides an overview of the recent insights into the genomic analysis, physiological characterization and environmental investigation of the comammox organisms, which have dramatically changed our perspective on the aerobic nitrification process. By using quantitative PCR analysis, we also compared the abundances of comammox
Nitrospira
clade A and clade B, AOA, AOB and NOB in 300 forest soil samples from China spanning a wide range of soil pH.
Results and discussion
Comammox
Nitrospira
are environmentally widespread and numerically abundant in natural and engineered habitats. Physiological data, including ammonia oxidation kinetics and metabolic versatility, and comparative genomic analysis revealed that comammox organisms might functionally outcompete other canonical nitrifiers under highly oligotrophic conditions. These findings highlight the necessity in future studies to re-evaluate the niche differentiation between ammonia oxidizers and their relative contribution to nitrification in various terrestrial ecosystems by including comammox
Nitrospira
in such comparisons.
Conclusions
The discovery of comammox and their broad environmental distribution added a new dimension to our knowledge of the biochemistry and physiology of nitrification and has far-reaching implications for refined strategies to manipulate nitrification in terrestrial ecosystems and to maximize agricultural productivity and sustainability.
Summary
Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known.
Here we examined bacterial communities ...across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)‐wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites.
Our results demonstrate that microbiome assembly along the soil‐plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize.
Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.
Ammonium (NH4+) and ammonia (NH3) are notorious hard-to-treat pollutants, leading to serious deterioration of aquatic ecosystems and significant risks to human health. While adsorption is a promising ...method to tackle this problem, finding suitable adsorbent materials which are abundant, low-cost and efficient remains a constant challenge. Thus, this review summarizes recent development of important adsorbent materials implemented for NH3/NH4+ removal. Advantages and disadvantages of representative adsorbent materials including bentonite, zeolite, clay, biochar, activated carbon, metal organic framework and their modified forms are compared, and the nature of their adsorption processes are discussed in context of adsorption sites, isotherm models (e.g. Langmuir and Freundlich), kinetic equations (e.g. pseudo-first order, pseudo-second order and intra-particle diffusion) and thermodynamic analysis. Future perspective on the utilization of inexpensive lignite is also conferred. Although both conventional and nanostructured materials face challenges regarding economic cost, energy consumption, secondary pollution and adsorption efficiency, these can be tackled by adopting various of advanced options. Current research on adsorption mechanisms forms a solid basis for the design and development of novel adsorbent materials. We speculate that the pursuit of strategies for effective surface modification of natural abundant resources will lead to a bright future of removal processes suited to low NH3/NH4+ concentration conditions.
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Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of ...the dominant role of ammonia-oxidizing bacteria (AOB) in nitrification. We investigated AOB and AOA growth and nitrification rate in two different layers of three grassland soils treated with animal urine substrate and a nitrification inhibitor dicyandiamide (DCD). We show that AOB were more abundant in the topsoils than in the subsoils, whereas AOA were more abundant in one of the subsoils. AOB grew substantially when supplied with a high dose of urine substrate, whereas AOA only grew in the Controls without the urine-N substrate. AOB growth and the amoA gene transcription activity were significantly inhibited by DCD. Nitrification rates were much higher in the topsoils than in the subsoils and were significantly related to AOB abundance, but not to AOA abundance. These results suggest that AOB and AOA prefer different soil N conditions to grow: AOB under high ammonia (NH₃) substrate and AOA under low NH₃ substrate conditions.
Summary
Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling ...processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8‐year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant–soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top‐down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop‐associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.
Summary
Bacterial resistance to antibiotics and heavy metals are frequently linked, suggesting that exposure to heavy metals might select for bacterial assemblages conferring resistance to ...antibiotics. However, there is a lack of clear evidence for the heavy metal‐induced changes of antibiotic resistance in a long‐term basis. Here, we used high‐capacity quantitative PCR array to investigate the responses of a broad spectrum of antibiotic resistance genes (ARGs) to 4–5 year copper contamination (0–800 mg kg−1) in two contrasting agricultural soils. In total, 157 and 149 unique ARGs were detected in the red and fluvo‐aquic soil, respectively, with multidrug and β‐lactam as the most dominant ARG types. The highest diversity and abundance of ARGs were observed in medium copper concentrations (100–200 mg kg−1) of the red soil and in high copper concentrations (400–800 mg kg−1) of the fluvo‐aquic soil. The abundances of total ARGs and several ARG types had significantly positive correlations with mobile genetic elements (MGEs), suggesting mobility potential of ARGs in copper‐contaminated soils. Network analysis revealed significant co‐occurrence patterns between ARGs and microbial taxa, indicating strong associations between ARGs and bacterial communities. Structural equation models showed that the significant impacts of copper contamination on ARG patterns were mainly driven by changes in bacterial community compositions and MGEs. Our results provide field‐based evidence that long‐term Cu contamination significantly changed the diversity, abundance and mobility potential of environmental antibiotic resistance, and caution the un‐perceived risk of the ARG dissemination in heavy metal polluted environments.
The recent discovery of comammox Nitrospira capable of converting ammonia to nitrate in a single organism radically challenged our century-long perception of the classic two-step nitrification ...performed by ammonia oxidizers and nitrite oxidizers. However, our understanding of the niche separation of comammox Nitrospira and canonical nitrifiers in forest ecosystems remains limited, especially under a global scenario of elevated nitrogen (N) deposition. Here we evaluated the impacts of six-year N deposition on the dynamics of comammox Nitrospira, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a subtropical forest soil. Soil inorganic N concentrations significantly increased under the six-year simulation of N deposition, while soil pH, available phosphorus, total carbon (C), C/N ratio and microbial biomass significantly decreased. Quantitative PCR showed that the amoA gene abundances of comammox Nitrospira clade B and AOA substantially increased under the increasing rates of N deposition. By contrast, the AOB amoA gene abundance significantly decreased with the higher levels of N deposition (100 and 150 kg N ha−1 yr−1). Increased 13CO2 incorporation into the AOA communities, rather than comammox Nitrospira or AOB, was demonstrated in a DNA-stable isotope probing microcosm, indicative of the capacity of AOA to assimilate 13CO2 through autotrophic nitrification in the investigated subtropical forest soil under long-term N deposition. Phylogenetic analysis revealed that the autotrophic AOA assemblages belonged to the Nitrosotalea cluster, and their capacity for assimilating CO2 through autotrophic nitrification was not affected by the long-term N deposition. Taken together, we provided new evidence for the niche separation of comammox Nitrospira and canonical ammonia oxidizers in soil nitrification under the long-term N deposition in the acidic subtropical forest soil.
•The abundances of comammox Nitrospira clade B and AOA increased with N input.•The abundance of AOB decreased with N input rates higher than 100 kg N ha−1 yr−1.•Increased 13CO2 was only incorporated into soil AOA through autotrophic pathway.•N input showed no effect on autotrophic AOA within the Nitrosotalea cluster.
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