Intermediate soil acidification induces highest nitrous oxide emissions.

Global potent greenhouse gas nitrous oxide (N2O) emissions from soil are accelerating, with increases in the proportion of reactive nitrogen emitted as N2O, i.e., N2O emission factor (EF). Yet, the primary controls and underlying mechanisms of EFs remain unresolved. Based on two independent but complementary global syntheses, and three field studies determining effects of acidity on N2O EFs and soil denitrifying microorganisms, we show that soil pH predominantly controls N2O EFs and emissions by affecting the denitrifier community composition. Analysis of 5438 paired data points of N2O emission fluxes revealed a hump-shaped relationship between soil pH and EFs, with the highest EFs occurring in moderately acidic soils that favored N2O-producing over N2O-consuming microorganisms, and induced high N2O emissions. Our results illustrate that soil pH has a unimodal relationship with soil denitrifiers and EFs, and the net N2O emission depends on both the N2O/(N2O + N2) ratio and overall denitrification rate. These findings can inform strategies to predict and mitigate soil N2O emissions under future nitrogen input scenarios.

Deciphering the biotic and abiotic drivers of coalescence asymmetry between soil and manure microbiomes.

Manure application improves soil fertility, yet its implications on the success of invasion of manure-borne microorganisms in the soil are poorly understood. Here, we assessed the importance of abiotic and biotic factors in modulating the extent to which manure-borne fungal and bacterial communities can invade resident soil microbial communities. For this purpose, we applied varying frequencies of two different amounts of manure to nine soils differing in physico-chemical properties, as well as in land-use history, over 180 days and monitored changes in bacterial and fungal communities. Variance partitioning revealed differential contributions of abiotic and biotic factors to invasion success, which together accounted for up to 82 % of the variance explained. We showed that the effects of interactions between biotic and abiotic factors increased with coalescence frequency and manure amount for the bacterial and fungal communities, respectively. Both abiotic and biotic factors were important for modulating coalescence asymmetry for the bacterial community, whereas abiotic factors had a greater effect on the fungal community. These results provide new insights into the drivers of coalescence events between manure and resident soil microbial communities. Moreover, our findings highlight the roles of the mixing ratio and frequency of coalescence events in modulating the survival of manure-borne microorganisms.

Climate warming suppresses abundant soil fungal taxa and reduces soil carbon efflux in a semi-arid grassland.

Soil microorganisms critically affect the ecosystem carbon (C) balance and C-climate feedback by directly controlling organic C decomposition and indirectly regulating nutrient availability for plant C fixation. However, the effects of climate change drivers such as warming, precipitation change on soil microbial communities, and C dynamics remain poorly understood. Using a long-term field warming and precipitation manipulation in a semi-arid grassland on the Loess Plateau and a complementary incubation experiment, here we show that warming and rainfall reduction differentially affect the abundance and composition of bacteria and fungi, and soil C efflux. Warming significantly reduced the abundance of fungi but not bacteria, increasing the relative dominance of bacteria in the soil microbial community. In particular, warming shifted the community composition of abundant fungi in favor of oligotrophic Capnodiales and Hypocreales over potential saprotroph Archaeorhizomycetales. Also, precipitation reduction increased soil total microbial biomass but did not significantly affect the abundance or diversity of bacteria. Furthermore, the community composition of abundant, but not rare, soil fungi was significantly correlated with soil CO2 efflux. Our findings suggest that alterations in the fungal community composition, in response to changes in soil C and moisture, dominate the microbial responses to climate change and thus control soil C dynamics in semi-arid grasslands.

Copiotrophic taxa in pig manure mitigate nitrogen limitation of soil microbial communities.

Microbial nitrogen (N) limitation is a common problem in terrestrial ecosystems. Pig manure, a type of solid waste, is increasingly applied to improve soil N availability in agriculture through inputs of organic matter and inorganic N. Pig manure application also introduces a lot of exogenous microorganisms, which have distinctly different N requirements and metabolic properties, into the resident soil microbial community. However, the impacts of these manure-borne microorganisms on soil N cycling have not been well determined. Here, we investigated effects of manure-borne microorganisms on the N limitation of soil microorganisms using an ecoenzymatic stoichiometry analysis. We monitored microbial communities over a 90-day period in a laboratory-controlled experiment with four treatments: (1) non-sterilized soil mixed with non-sterilized manure (S-M), (2) non-sterilized soil mixed with sterilized manure (S-sM), (3) sterilized soil mixed with non-sterilized manure (sS-M), and (4) non-sterilized soil without manure addition (S, the control). The microbial N limitations were significantly mitigated in both S-M and sS-M. By contrast, the S-sM and S showed high levels of microbial N limitation, likely stemming from differences in the microbial functional composition. We found chitin-degrading bacteria were the dominant copiotrophic manure-borne bacteria associated with N mineralization, and they may improve soil N availability. We further identified several copiotrophic manure-borne bacteria in S-M and sS-M, and their abundances had significantly negative correlation with the level of N limitation and significantly positive correlation with the stoichiometric homeostasis. As these copiotrophic taxa can maintain homeostasis through regulating enzymatic activities, our results indicate that copiotrophic taxa in pig manure contribute to the mitigation of soil microbial N limitation. Our study also highlights the invasiveness capacity of manure-borne microorganisms in soil and evaluates the biotic effects of manure application on soil N cycling.

Warming and elevated ozone induce tradeoffs between fine roots and mycorrhizal fungi and stimulate organic carbon decomposition.

Climate warming and elevated ozone (eO3) are important climate change components that can affect plant growth and plant-microbe interactions. However, the resulting impact on soil carbon (C) dynamics, as well as the underlying mechanisms, remains unclear. Here, we show that warming, eO3, and their combination induce tradeoffs between roots and their symbiotic arbuscular mycorrhizal fungi (AMF) and stimulate organic C decomposition in a nontilled soybean agroecosystem. While warming and eO3 reduced root biomass, tissue density, and AMF colonization, they increased specific root length and promoted decomposition of both native and newly added organic C. Also, they shifted AMF community composition in favor of the genus Paraglomus with high nutrient-absorbing hyphal surface over the genus Glomus prone to protection of soil organic C. Our findings provide deep insights into plant-microbial interactive responses to warming and eO3 and how these responses may modulate soil organic C dynamics under future climate change scenarios.

Caenorhabditis elegans Extracts Stimulate IAA Biosynthesis in Arthrobacter pascens ZZ21 via the Indole-3-pyruvic Acid Pathway.

Inter-organismal metabolites play important roles in regulating organism behavior and the communication between organisms. Nematodes, the most abundant animals on earth, are crucial participants in soil ecosystems through their interactions with microbes. For example, bacterial-feeding nematodes increase the activity of indole-3-acetic acid (IAA)-producing bacteria and the IAA content in soil. However, the way in which these nematodes interact with bacteria and affect IAA biosynthesis is not well understood. Here, using the model nematode Caenorhabditis elegans and the plant-beneficial bacterium Arthrobacter pascens ZZ21, we examined the effects of nematode excretions or extracts on bacterial IAA biosynthesis. To explore the underlying regulatory mechanism in more detail, we performed transcriptome sequencing and metabolomic analysis. Our findings suggest that C. elegans extracts promote IAA biosynthesis in A. pascens ZZ21 by increasing the expression of genes and the abundance of intermediates involved in the indole-3-pyruvic acid (IPyA) pathway. C. elegans extracts also significantly influenced biosynthetic and metabolic activity in A. pascens ZZ21. Treatment with C. elegans extracts promoted pyruvate metabolism, the citrate cycle (TCA) cycle and the production of some TCA-cycle-related amino acids and inhibited oxidative phosphorylation, which induced the accumulation of reduced nicotinamide adenine dinucleotide (NADH). We propose that the extracts altered the metabolism of A. pascens ZZ21 to help the bacteria resist stress caused by their predator. Our findings indicate that bacterial-feeding nematodes mediate the interaction between nematodes and bacteria via their extracts, providing insights into the ecological function of C. elegans in soil.

Simulated warming enhances the responses of microbial N transformations to reactive N input in a Tibetan alpine meadow.

Alpine ecosystems worldwide are characterized with high soil organic carbon (C) and low mineral nitrogen (N). Climate warming has been predicted to stimulate microbial decomposition and N mineralization in these systems. However, experimental results are highly variable, and the underlying mechanisms remain unclear. We examined the effects of warming, N input, and their combination on soil N pools and N-cycling microbes in a field manipulation experiment. Special attention was directed to the ammonia-oxidizing bacteria and archaea, and their mediated N-cycling processes (transformation rates and N2O emissions) in the third plant growing season after the treatments were initiated. Nitrogen input (12 g m-2 y-1) alone significantly increased soil mineral N pools and plant N uptake, and stimulated the growth of AOB and N2O emissions in the late growing season. While warming (by 1.4 °C air temperature) alone did not have significant effects on most parameters, it amplified the effects of N input on soil N concentrations and AOB abundance, eliciting a chain reaction that increased nitrification potential (+83%), soil NO3--N (+200%), and N2O emissions (+412%) across the whole season. Also, N input reduced AOB diversity but increased the dominance of genus Nitrosospira within the AOB community, corresponding to the increased N2O emissions. These results showed that a small temperature increase in soil may significantly enhance N losses through NO3- leaching and N2O emissions when mineral N becomes available. These findings suggest that interactions among global change factors may predominantly affect ammonia-oxidizing microbes and their mediated N-cycling processes in alpine ecosystems under future climate change scenarios.

Cadmium immobilization in aqueous solution by Aspergillus niger and geological fluorapatite.

This study investigated the application of fungus Aspergillus niger and geological fluorapatite (FAp) to cadmium (Cd) immobilization in aqueous solution. The initial Cd concentrations were set at 100, 50, 25, and 10 mg L-1. The mineralogy of the products was investigated by using scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and attenuated total reflection-infrared spectroscopy (ATR-IR). In both A. niger + FAp + Cd and A. niger + Cd treatments, A. niger secreted abundant oxalic acid, then dissolved the FAp, and reacted with Cd2+ cations to produce relatively insoluble Cd oxalate. Meanwhile, FAp can provide P source to improve microbial growth. The fungal tolerance to Cd2+ was identified at around 100 mg L-1. The final Cd concentrations of 13.7, 3.2, and 0.2 mg L-1 were recorded for A. niger + FAp + Cd treatments with initial Cd concentrations of 50, 25, and 10 mg L-1 respectively. Meanwhile, it was observed that the Cd concentration at 25 mg L-1 stimulated higher bioactivities of A. niger, which further enhanced Cd bioremediation. The immobilization efficiency (%) of the treatments at low to medium Cd concentrations was in the order: Asp + FAp > Asp > FAp, while FAp alone was most efficient at the high Cd concentration of 100 mg L-1. This research provides insights into the mechanisms of combining fungus and FAp as a composite to Cd contamination at various Cd levels.

Combination of warming and N inputs increases the temperature sensitivity of soil N2O emission in a Tibetan alpine meadow.

Many high-elevation alpine ecosystems have been experiencing significant increases in air temperature and, to a lesser extent, nitrogen (N) deposition. These changes may affect N-cycling microbes and enhance emissions of nitrous oxide (N2O, a potent greenhouse gas) from soil. However, few studies have investigated whether and how the resulting changes in N-cycling microbes may affect the temperature sensitivity (Q10) of N2O emission and in turn feed back to N2O emissions. We conducted two incubation experiments to examine N2O emissions and their temperature sensitivities in soils that had experienced 3-yr field treatments of warming, N inputs and their combination in a Tibetan alpine meadow. Our results showed that neither N inputs nor warming alone affected the rate or Q10 of soil N2O emission, but combining the two significantly increased both parameters. Also, combined N and warming significantly increased the abundance of ammonia-oxidizing bacteria (AOB), corresponding with high soil N2O emission. In addition, N2O emission from nitrification accounted for 60-80% of total emissions in all soils, indicating that nitrifying microbes dominated the N2O production and its temperature sensitivity. Using random forest (RF) and structural equation model (SEM) analyses, we further evaluated the effects of various soil characteristics on soil N2O emissions and Q10. We identified soil moisture, pH, N mineralization and AOB abundance as the main predictors of the Q10 of N2O emissions. Together, these findings suggest that alterations in soil moisture, pH and ammonia-oxidizing bacteria induced by long-term N inputs and warming may increase temperature sensitivity of soil N2O emissions, leading to a positive climate feedback in this high-altitude alpine ecosystem.