Long-term N fertilization imbalances potential N acquisition and transformations by soil microbes

Microbiota recovery in a chronosquences of impoverished Cerrado soils with biosolids applications

Mining activities put the Brazilian savannas, a global biodiversity hotspot, in danger of species and soil carbon losses. Experiments employing biosolids have been applied to rejuvenate this degraded ecosystem, but a lingering question yet to be answered is whether the microbiota that inhabits these impoverished soils can be recovered towards its initial steady state after vegetation recovery. Here, we selected an 18-year-old restoration chronosequence of biosolids-treated, untreated mining and native soils to investigate the soil microbiota recovery based on composition, phylogeny, and diversity, as well as the potential factors responsible for ecosystem recovery. Our results revealed that the soil microbiota holds a considerable recovery potential in the degraded Cerrado biome. Biosolids application not only improved soil health, but also led to 41.7 % recovery of the whole microbial community, featuring significantly higher microbiota diversity and enriched groups (e.g., Firmicutes) that benefit carbon storage compared to untreated mining and native soils. The recovered community showed significant compositional distinctions from the untreated mining or native soils, rather than phylogenetic differences, with physiochemical properties explaining 55 % of the overall community changes. This study advances our understanding of soil microbiota dynamics in response to disturbance and restoration by shedding light on its recovery associated with biosolid application in a degraded biodiverse ecosystem.

Intensive N2 fixation accelerates microbial turnover in cropland soils

Biological nitrogen fixation (BNF) is strongly affected by the carbon (C) and nitrogen (N) stoichiometry in soil and depends on the input of organic C. Due to the high metabolic costs of nitrogenase activity, however, the response of BNF to organic C input and its impact on microbial turnover remain unclear. To address this knowledge gap, we combined 15N2 tracing with high-throughput sequencing by adding glucose or glucose plus mineral N fertilizer for a 12-day incubation in three cropland soils. Glucose addition alone strongly changed the BNF activity (0.76-2.51 mg N kg-1 d-1), while BNF was completely absent after mineral N fertilization. This switch-on of BNF by glucose addition supported equally high rates of microbial growth and organic C mineralization compared with the direct mineral N assimilation by microorganisms. Glucose-induced BNF was predominantly catalyzed by Azotobacter-affiliated free-living diazotrophs (>50 % of the total nifH genes), which increased with diverse nondiazotrophs such as Nitrososphaera, Bacillus and Pseudoxanthomonas. Structural equation models (SEMs) and random forest (RF) analyses consistently revealed that the soil C:N ratio and Azotobacter-affiliated diazotrophic abundances were the key factors affecting glucose-induced BNF. Our findings emphasize the importance of free-living diazotrophs for microbial turnover of organic C in soil.

Decrease of nitrogen cycle gene abundance and promotion of soil microbial-N saturation restrain increases in N2O emissions in a temperate forest with long-term nitrogen addition

Increases in soil available nitrogen (N) influence N-cycle gene abundances and emission of nitrous oxide (N2O), which is primarily due to N-induced soil acidification in forest. Moreover, the extent of microbial-N saturation could control microbial activity and N2O emission. The contributions of N-induced alterations of microbial-N saturation and N-cycle gene abundances to N2O emission have rarely been quantified. Here, the mechanism underlying N2O emission under N additions (three chemical forms of N, i.e., NO3--N, NH4+-N and NH4NO3-N, and each at two rates, 50 and 150 kg N ha-1 year-1, respectively) spanning 2011-2021 was investigated in a temperate forest in Beijing. Results showed N2O emissions increased at both low and high N rates of all the three forms compared with control during the whole experiment. However, N2O emissions were lower in high rate of NH4NO3-N and NH4+-N treatments than the corresponding low N rates in the recent three years. Effects of N on microbial-N saturation and abundances of N-cycle genes were dependent on the N rate and form as well as experimental time. Specifically, negative effects of N on N-cycle gene abundances and positive effects of N on microbial-N saturation were demonstrated in high N rate treatments, particularly with NH4+ addition during 2019-2021. Such effects were associated with soil acidification. A hump-backed trend between microbial-N saturation and N2O emissions was observed, suggesting N2O emissions decreased with increase of the microbial-N saturation. Furthermore, N-induced decreases in N-cycle gene abundances restrained N2O emissions. In particular, the nitrification process, dominated by ammonia-oxidize archaea, is critical to determination of N2O emissions in response to the N addition in the temperate forest. We confirmed N addition promoted soil microbial-N saturation and reduced N-cycle gene abundances, which restrained the continuous increase in N2O emissions. It is important for understanding the forest-N-microbe nexus under climate change.

Insights into the deriving of rhizosphere microenvironments and its effects on the growth of authentic Angelica sinensis seedlings under continuous monoculture

Purpose

Continuous monoculture leads to deterioration of soil microenvironment, which can severely threat the quality and efficiency of Angelica sinensis (A. sinensis), especially for seedlings production. However, little attention has been paid to investigate how continuous monocropping affects the growth of A. sinensis seedling, rhizosphere microbial populations, and nutrient status.

Methods

A field experiment consisting of two different planting patterns — raising A. sinensis seedlings in reclamation alpine uncultivated meadow (RW) and 1-year continuous monoculture (CC), was carried out at Min County, Gansu province, China.

Result

The results showed that compared with RW, the growth rate and valid quantity of A. sinensis seedlings were significantly reduced by 195.4% and 36.7% in CC, respectively. Continuous monocropping significantly increased the rhizosphere soil pH value during the growing season, ranging from 6.18 to 7.10, while reducing the content of SOM, total N, and available P and K. Glomalin, AMF spore densities, and the number of actinomycetes, ammonifiers, and azotobacter were also decreased by CC. The CC treatment significantly increased the abundance of fungi. The diversity and richness of bacteria in CC were lower than RW. Furthermore, the composition and structure of bacterial and fungal flora also changed and that the abundance of beneficial bacteria decreased, while the abundance of pathogens increased in CC. Thus, CC appeared to completely upend the relationship between soil nutrient availability and microbial activity.

Conclusion

The results illustrated that continuous monoculture led the flora of bacteria and fungi to changed dramatically, with the abundance of beneficial bacteria decreased and the abundance of harmful microbes, such as Lasiosphaeriaceae, Vishniacozyma, Myrmecridium, and Hypocreales, increased. The function of microbial population has changed from “beneficial bacteria dominated” to “harmful microbes dominant.” We concluded that continuous monoculture significantly reduced the growth and the efficiency of A. sinensis seedlings and deteriorated the rhizosphere soil microenvironment by increasing pH and decreasing nutrient availability, as well as altering the function of interactions between soil nutrients and microbial populations, thereby resulting in an unsuitable microenvironment for A. sinensis seedlings growth.

Soil microbial nitrogen-cycling gene abundances in response to crop diversification: A meta-analysis

Single planting structure has a significant impact on the maintenance of nitrogen in managed ecosystems. Although the effect of crop diversity on soil nitrogen-cycling microbes is mainly related to the influence of environmental factors, there is a lack of quantitative research. This study aims to determine the effect of diversified cropping mode on the abundance of functional genes in the soil nitrogen cycle based on the quantitative integration of a meta-analysis database containing 189 observation data pairs. The results show that the soil nifH (nitrogenase coding gene), nirS and nirK (nitrite reductase coding gene), and narG (nitrate reductase coding gene) abundances are positively affected by the diversity of plant species, whereas the amoA (ammonia monooxygenase coding gene) and nosZ (nitrous oxide reductase coding gene) show no response. Diversification duration and ecosystem type are important factors that regulate soil nitrogen fixation and nitrification gene abundances. Denitrification genes are mainly affected by categorical variables such as the planting pattern, soil layer, application species, duration, and soil texture. Among them, the long-term continuous diversification is mainly manifested in the reduction of soil nifH and increase of nirK abundances. Soil organic carbon and nitrogen linearly affect the responses of nifH, amoA, nirS, and nirK. Therefore, to maintain the soil ecological function, diversity of planting patterns needs to be applied flexibly by regulating the abundance of nitrogen-cycling genes. Our study draws conclusions in order to provide theoretical references for the sustainability of nitrogen and improvement of management measures in the process of terrestrial managed ecosystem diversification.

Is Dairy Effluent an Alternative for Maize Crop Fertigation in Semiarid Regions? An Approach to Agronomic and Environmental Effects

Simple Summary

Dairy effluent can be an environmental problem if it is not properly managed. Several application technologies exist for its reuse as a source of nutrients in agricultural crops. Our study provides new information on GHG emissions after the application of dairy effluent through a subsurface drip irrigation system on a semiarid soil of the southern Pampean Region (Argentina). In addition, some edaphic properties are compared with conventional chemical fertilization on the yield of a corn crop, contributing as a proposal for an improvement in agricultural sustainability.

Abstract

The reuse of effluents from intensive dairy farms combined with localized irrigation techniques (fertigation) has become a promising alternative to increase crop productivity while reducing the environmental impact of waste accumulation and industrial fertilizers production. Currently, the reuse of dairy effluents through fertigation by subsurface drip irrigation (SDI) systems is of vital importance for arid regions but it has been poorly studied. The present study aimed to assess the greenhouse gas (GHG) emissions, soil properties, and crop yield of a maize crop fertigated with either treated dairy effluent or dissolved granulated urea applied through an SDI system at a normalized N application rate of 200 kg N ha⁻¹. Fertilizer application was divided into six fertigation events. GHG fluxes were measured during fertigation (62-day) using static chambers. Soil properties were measured previous to fertilizer applications and at the harvest coinciding with crop yield estimation. A slight increase in soil organic matter was observed in both treatments for the 20–60 cm soil depth. Both treatments also showed similar maize yields, but the dairy effluent increased net GHG emissions more than urea during the fertigation period. Nevertheless, the net GHG emissions from the dairy effluent were lower than the theoretical CO₂eq emission that would have been emitted during urea manufacturing or the longer storage of the effluent if it had not been used, showing the need for life-cycle assessments. Local-specific emission factors for N₂O were determined (0.07%), which were substantially lower than the default value (0.5%) of IPCC 2019. Thus, the subsurface drip irrigation systems can lead to low GHG emissions, although further studies are needed.

Limited Impacts of Cover Cropping on Soil N-Cycling Microbial Communities of Long-Term Corn Monocultures

Cover cropping (CC) is a promising in-field practice to mitigate soil health degradation and nitrogen (N) losses from excessive N fertilization. Soil N-cycling microbial communities are the fundamental drivers of these processes, but how they respond to CC under field conditions is poorly documented for typical agricultural systems. Our objective was to investigate this relationship for a long-term (36 years) corn [Zea mays L.] monocultures under three N fertilizer rates (N0, N202, and N269; kg N/ha), where a mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth.] was introduced for two consecutive years, using winter fallows as controls (BF). A 3 × 2 split-plot arrangement of N rates and CC treatments in a randomized complete block design with three replications was deployed. Soil chemical and physical properties and potential nitrification (PNR) and denitrification (PDR) rates were measured along with functional genes, including nifH, archaeal and bacterial amoA, nirK, nirS, and nosZ-I, sequenced in Illumina MiSeq system and quantified in high-throughput quantitative polymerase chain reaction (qPCR). The abundances of nifH, archaeal amoA, and nirS decreased with N fertilization (by 7.9, 4.8, and 38.9 times, respectively), and correlated positively with soil pH. Bacterial amoA increased by 2.4 times with CC within N269 and correlated positively with soil nitrate. CC increased the abundance of nirK by 1.5 times when fertilized. For both bacterial amoA and nirK, N202 and N269 did not differ from N0 within BF. Treatments had no significant effects on nosZ-I. The reported changes did not translate into differences in functionality as PNR and PDR did not respond to treatments. These results suggested that N fertilization disrupts the soil N-cycling communities of this system primarily through soil acidification and high nutrient availability. Two years of CC may not be enough to change the N-cycling communities that adapted to decades of disruption from N fertilization in corn monoculture. This is valuable primary information to understand the potentials and limitations of CC when introduced into long-term agricultural systems.

Contribution of ammonia-oxidizing archaea and bacteria to nitrification under different biogeochemical factors in acidic soils

Nitrification in soils is an essential process that involves archaeal and bacterial ammonia-oxidizers. Despite its importance, the relative contributions of soil factors to the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their nitrification performances are seldom discussed. The aim of this study was to determine the effects of AOA and AOB abundance and different environmental conditions (pH, TC, TN, moisture, and temperature) on nitrification performance. The soils of the long-term fertilized tea orchards and forests were sampled in the field, and nitrification experiments were conducted in the laboratory. The acid soils were collected from the field and used in laboratory incubation experiments to calculate the nitrification rate, including the net nitrification rate (NN rate), nitrification potential (NP), and nitrification kinetics. The basic parameters, different forms of nitrogen content, and AOA and AOB amoA gene copies were also analyzed. Compared with the forest soil, the tea orchard soil had a lower pH and higher nitrogen content (p < 0.05). The AOA and AOB abundance in the soils of the forests and tea orchards were pH-dependent. The NN rate and NP had good relationships with AOA or AOB in the forest soil; however, poor relationships were observed in the tea orchard soil. When pH < 4, the performances of AOA and AOB were restricted by pH and the environment, especially in long-term fertilized farmlands. Long-term fertilization can cause soil acidification, which regulates the abundance of AOA and AOB and their nitrifying ability. The soil environment rather than AOA or AOB could control nitrification in long-term fertilized farmlands with a pH below 4. These findings could improve fertilization efficiency and control nutrient runoff in hilly agricultural ecosystems.

Effect of Nitrogen Addition on Soil Microbial Functional Gene Abundance and Community Diversity in Permafrost Peatland

Nitrogen is the limiting nutrient for plant growth in peatland ecosystems. Nitrogen addition significantly affects the plant biomass, diversity and community structure in peatlands. However, the response of belowground microbe to nitrogen addition in peatland ecosystems remains largely unknown. In this study, we performed long-term nitrogen addition experiments in a permafrost peatland in the northwest slope of the Great Xing'an Mountains. The four nitrogen addition treatments applied in this study were 0 g N·m-2·year-1 (CK), 6 g N·m-2·year-1 (N1), 12 g N·m-2·year-1 (N2), and 24 g N·m-2·year-1 (N3). Effects of nitrogen addition over a period of nine growing seasons on the soil microbial abundance and community diversity in permafrost peatland were analyzed. The results showed that the abundances of soil bacteria, fungi, archaea, nitrogen-cycling genes (nifH and b-amoA), and mcrA increased in N1, N2, and N3 treatments compared to CK. This indicated that nitrogen addition promoted microbial decomposition of soil organic matter, nitrogen fixation, ammonia oxidation, nitrification, and methane production. Moreover, nitrogen addition altered the microbial community composition. At the phylum level, the relative abundance of Proteobacteria increased significantly in the N2 treatment. However, the relative abundances of Actinobacteria and Verrucifera in the N2 treatment and Patescibacteria in the N1 treatment decreased significantly. The heatmap showed that the dominant order composition of soil bacteria in N1, N2, and N3 treatments and the CK treatment were different, and the dominant order composition of soil fungi in CK and N3 treatments were different. The N1 treatment showed a significant increase in the Ace and Chao indices of bacteria and Simpson index of fungi. The outcomes of this study suggest that nitrogen addition altered the soil microbial abundance, community structure, and diversity, affecting the soil microbial carbon and nitrogen cycling in permafrost peatland. The results are helpful to understand the microbial mediation on ecological processes in response to N addition.

Enrichment of nosZ-type denitrifiers by arbuscular mycorrhizal fungi mitigates N2 O emissions from soybean stubbles

Hotspots of N2 O emissions are generated from legume residues during decomposition. Arbuscular mycorrhizal fungi (AMF) from co-cultivated intercropped plants may proliferate into the microsites and interact with soil microbes to reduce N2 O emissions. Yet, the mechanisms by which or how mycorrhizal hyphae affect nitrifiers and denitrifiers in the legume residues remain ambiguous. Here, a split-microcosm experiment was conducted to assess hyphae of Rhizophagus aggregatus from neighbouring maize on overall N2 O emissions from stubbles of nodulated or non-nodulated soybean. Soil microbes from fields intercropped with maize/soybean amended with fertilizer nitrogen (SS-N1) or unamended (SS-N0) were added to the soybean chamber only. AMF hyphae consistently reduced N2 O emissions by 20.8%-61.5%. Generally, AMF hyphae promoted the abundance of N2 O-consuming (nosZ-type) denitrifiers and altered their community composition. The effects were partly associated with increasing MBC and DOC. By contrast, AMF reduced the abundance of nirK-type denitrifiers in the nodulated SS-N0 treatment only and that of AOB in the non-nodulated SS-N1 treatment. Taken together, our results show that AMF reduced N2 O emissions from soybean stubbles, mainly through the promotion of N2 O-consuming denitrifiers. This holds promise for mitigating N2 O emissions by manipulating the efficacious AMF and their associated microbes in cereal/legume intercropping systems.

Soil Microbial Indicators within Rotations and Tillage Systems

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.

Build Your Own Mushroom Soil: Microbiota Succession and Nutritional Accumulation in Semi-Synthetic Substratum Drive the Fructification of a Soil-Saprotrophic Morel

Black morel, a widely prized culinary delicacy, was once an uncultivable soil-saprotrophic ascomycete mushroom that can now be cultivated routinely in farmland soils. It acquires carbon nutrients from an aboveground nutritional supplementation, while it remains unknown how the morel mycelium together with associated microbiota in the substratum metabolizes and accumulates specific nutrients to support the fructification. In this study, a semi-synthetic substratum of quartz particles mixed with compost was used as a replacement and mimic of the soil. Two types of composts (C1 and C2) were used, respectively, plus a bare-quartz substratum (NC) as a blank reference. Microbiota succession, substrate transformation as well as the activity level of key enzymes were compared between the three types of substrata that produced quite divergent yields of morel fruiting bodies. The C1 substratum, with the highest yield, possessed higher abundances of Actinobacteria and Chloroflexi. In comparison with C2 and NC, the microbiota in C1 could limit over-expansion of microorganisms harboring N-fixing genes, such as Cyanobacteria, during the fructification period. Driven by the microbiota, the C1 substratum had advantages in accumulating lipids to supply morel fructification and maintaining appropriate forms of nitrogenous substances. Our findings contribute to an increasingly detailed portrait of microbial ecological mechanisms triggering morel fructification.

Hemp Seed Production: Environmental Impacts of Cannabis sativa L. Agronomic Practices by Life Cycle Assessment (LCA) and Carbon Footprint Methodologies

This paper evaluated the environmental impacts of different agronomic practices for a hemp seed crop grown in Mediterranean environment. The following agricultural variables have been considered: seven monoecious hemp varieties(Epsilon68 (E68), Fedora17 (F17), Felina32 (F32), Ferimon (Fe), Futura75 (F75), Santhica27 (S27), Uso31 (U31)), three plant densities (40, 80, and 120 plants m−2), and two levels of nitrogen (N) fertilization (50 and 100 kg ha−1 of N). Life cycle assessment (LCA) and carbon footprint (CF) methodologies have been applied to evaluate impacts. In all hemp genotypes, the impacts grew by decreasing both N fertilizer and plants densities. The scenario most impacting was E68/F75/S27 genotypes cultivated with 50 kg ha−1 of N fertilizer and 40 plants m−2, while the lowest one was Fe with 100 kg ha−1 of N fertilizer and 120 plants m−2. The highest CF was found for E68/F75/S27 cultivated with 50 kg ha−1 of N fertilizer and 40 plants m−2 (18.720 kg CO2 eq). This study highlighted the most environmentally sustainable agronomic practices to support farmer and decision maker in Cannabis sativa L. cultivation for seed production.

Acidification in corn monocultures favor fungi, ammonia oxidizing bacteria, and nirK-denitrifier groups

Agricultural practices of no-till and crop rotations are critical to counteract the detrimental effects of monocultures and tillage operations on ecosystem services related to soil health such as microbial N cycling. The present study explored the main steps of the microbial N cycle, using targeted gene abundance as a proxy, and concerning soil properties, following 19 and 20 years of crop monocultures and rotations of corn (Zea mays L.), and soybean [Glycine max (L.) Merr.], either under no-till or chisel tillage. Real-time quantitative polymerase chain reaction (qPCR) was implemented to estimate phylogenetic groups and functional genes related to the microbial N cycle: nifH (N₂ fixation), amoA (nitrification) and nirK, nirS, and nosZ (denitrification). Our results indicate that long-term crop rotation and tillage decisions affect soil health as it relates to soil properties and microbial parameters. No-till management increased soil organic matter (SOM), decreased soil pH, and increased copy numbers of AOB (ammonia oxidizing bacteria). Crop rotations with more corn increased SOM, reduced soil pH, reduced AOA (ammonia oxidizing archaea) copy numbers, and increased AOB and fungal ITS copy numbers. NirK denitrifier groups were also enhanced under continuous corn. Altogether, the more corn years included in a crop rotation multiplies the amount of N needed to sustain yield levels, thereby intensifying the N cycle in these systems, potentially leading to acidification, enhanced bacterial nitrification, and creating an environment primed for N losses and increased N₂O emissions.

Long-Term N Fertilization Decreased Diversity and Altered the Composition of Soil Bacterial and Archaeal Communities

Soil microbial communities are essential in the cycling of nutrients that affect crop production. Our goal was to characterize the microbial community structure following 34 years of nitrogen (N) fertilization treatments in continuous maize production in highly fertile soils. Using 16S rRNA gene-based analysis of the V4 region via Illumina HiSeq2500 technology with downstream bioinformatics processing and analysis with QIIME 2.0, we aimed to characterize the prokaryotic communities under three increasing N fertilization rates. Factor analyses indicated that a high N level decreased the diversity of soil bacterial and archaeal communities and altered the relative abundance (RA) of the dominant (>1% RA) and minor (<1% RA) phyla. Among the 12 major phyla, we determined increases in Gemmatimonadetes, Proteobacteria, and Euryarchaeota, accompanied by reductions in Cyanobacteria, Chloroflexi, Firmicutes, and Planctomycetes with increasing N. Within the 29 minor phyla, N fertilization led to increases in Aquificae, WPS2, Parvarchaeota, AD3, FCPU426, Armatimonadetes, TM7, Chlamydiae, and OD1, along with reductions of Nitrospirae, WS3, Tenericutes, Lentisphaerae, OP3, Synergistetes, Thermotogae, and prokaryotes that could not be reliably assigned to a phylum (classified as Other).