Soil microbial responses to nitrogen addition in arid ecosystems

Coupling of soil methane emissions at different depths under typical coastal wetland vegetation types

As an important source of atmospheric methane, methane emissions from coastal wetlands are affected by many factors. However, the methane emission process and interrelated coupling mechanisms in coastal wetland soils of a variety of environments remain unclear owing to complex interactions between intensified anthropogenic activities and climate change in recent years. In this study, we investigated methane cycling processes and the response mechanisms of environmental and microbial factors in soils at different depths under four typical coastal wetland vegetation types of the Yellow River Delta, China, using laboratory culture and molecular biology techniques. Our results show that methane generation pathways differed among the different soil layers, and that the methane emission process has a special response to soil N compounds (NO3-, NH4+). We found that nitrogen can indirectly affect methane emission by impacting key physicochemical properties (pH, oxidation reduction potential, etc.) and some functional communities (mcrA, ANME-2d, sulfate-reducing bacteria (SRB), narG, nosZII). Methane production processes in shallow soils compete closely with sulfate reduction processes, while methane emissions facilitated in deeper soils due to denitrification processes. We believe that our results provide a reference for future research and wetland management practices that seek to mitigate the global greenhouse effect and climate change.

Microbial communities in terrestrial surface soils are not widely limited by carbon

Microbial communities in soils are generally considered to be limited by carbon (C), which could be a crucial control for basic soil functions and responses of microbial heterotrophic metabolism to climate change. However, global soil microbial C limitation (MCL) has rarely been estimated and is poorly understood. Here, we predicted MCL, defined as limited availability of substrate C relative to nitrogen and/or phosphorus to meet microbial metabolic requirements, based on the thresholds of extracellular enzyme activity across 847 sites (2476 observations) representing global natural ecosystems. Results showed that only about 22% of global sites in terrestrial surface soils show relative C limitation in microbial community. This finding challenges the conventional hypothesis of ubiquitous C limitation for soil microbial metabolism. The limited geographic extent of C limitation in our study was mainly attributed to plant litter, rather than soil organic matter that has been processed by microbes, serving as the dominant C source for microbial acquisition. We also identified a significant latitudinal pattern of predicted MCL with larger C limitation at mid- to high latitudes, whereas this limitation was generally absent in the tropics. Moreover, MCL significantly constrained the rates of soil heterotrophic respiration, suggesting a potentially larger relative increase in respiration at mid- to high latitudes than low latitudes, if climate change increases primary productivity that alleviates MCL at higher latitudes. Our study provides the first global estimates of MCL, advancing our understanding of terrestrial C cycling and microbial metabolic feedback under global climate change.

Effects of Short-Term Nitrogen Addition on Soil Fungal Community Increase with Nitrogen Addition Rate in an Alpine Steppe at the Source of Brahmaputra

The soil fungal community plays a crucial role in terrestrial decomposition and biogeochemical cycles. However, the responses of the soil fungal community to short-term nitrogen addition and its related dominant drivers still remain unclear. To address this gap, we conducted an experiment to explore how different levels of nitrogen addition (five levels: 0, 2.5, 5, 10, and 20 g N m-2 y-1) affected the soil fungal community in an alpine steppe at the source of Brahmaputra. Results showed that the reduced magnitudes of soil fungal species and phylogenetic α-diversity increased with the increasing nitrogen addition rate. Nitrogen addition significantly changed the community composition of species, and the dissimilarity of the soil fungal community increased with the increasing nitrogen addition rate, with a greater dissimilarity observed in the superficial soil (0-10 cm) compared to the subsurface soil (10-20 cm). Increases in the soil nitrogen availability were found to be the predominant factor in controlling the changes in the soil fungal community with the nitrogen addition gradient. Therefore, short-term nitrogen addition can still cause obvious changes in the soil fungal community in the alpine grassland at the source of Brahmaputra. We should not underestimate the potential influence of future nitrogen deposition on the soil fungal community in the high-altitude grassland of the Qinghai-Tibet Plateau. Adverse effects on the soil fungal community should be carefully considered when nitrogen fertilizer is used for ecosystem restoration of the alpine grassland of the Qinghai-Tibet Plateau.

Snow-cover loss attenuates the effects of N addition on desert nutrient cycling and microbial community

Desert ecosystems are sensitive to nitrogen (N) deposition. Considering snow is an important source of soil water, which is vital for plant growth and the biogeochemical cycle in desert areas. The effects of N deposition on biological soil crusts (BSCs) could be impacted by the removal of snow-cover. Here, we established a split-plot experiment in the Gurbantunggut Desert to examine the effects of snow-cover treatments on soil nutrients, enzyme activities, and the bacterial community under various N addition. The removal of snow-cover reduced the soil nutrients with light and moderate N addition, it also reduced the activities of urease (URE) and alkaline phosphatase (PHOS). The structural equation model (SEM) result indicated that low soil moisture (SMO) under snow-uncover inhibited the bacterial community, particularly suppressed bacterial diversity. Additionally, N addition indirectly affected the bacterial community via modifications to soil nutrients, and soil organic matter (SOM) (P < 0.001) was the crucial factor. Snow-uncover weakened soil nutrient and enzyme responses to N addition, indicating that snow-cover removal reduced the sensitivity of the desert ecosystem to N deposition. The study highlights the critical role of snow-cover in the desert ecosystem, raising our awareness of the ecological risks of BSCs in future global change.

Characterization of root-associated fungi and reduced plant growth in soils from a New Mexico uranium mine

Characterizing the diverse, root-associated fungi in mine wastes can accelerate the development of bioremediation strategies to stabilize heavy metals. Ascomycota fungi are well known for their mutualistic associations with plant roots and, separately, for roles in the accumulation of toxic compounds from the environment, such as heavy metals. We sampled soils and cultured root-associated fungi from blue grama grass (Bouteloua gracilis) collected from lands with a history of uranium (U) mining and contrasted against communities in nearby, off-mine sites. Plant root-associated fungal communities from mine sites were lower in taxonomic richness and diversity than root fungi from paired, off-mine sites. We assessed potential functional consequences of unique mine-associated soil microbial communities using plant bioassays, which revealed that plants grown in mine soils in the greenhouse had significantly lower germination, survival, and less total biomass than plants grown in off-mine soils but did not alter allocation patterns to roots versus shoots. We identified candidate culturable root-associated Ascomycota taxa for bioremediation and increased understanding of the biological impacts of heavy metals on microbial communities and plant growth.

Biocrust diazotrophs and bacteria rather than fungi are sensitive to chronic low N deposition

Anthropogenic long-term nitrogen (N) deposition may dramatically impact biocrusts due to the overarching N limitation of soil biota in deserts. Even low levels of N may reach a critical loading threshold altering biocrust constituents and function. To identify the impact of chronic and continuous low levels of N deposition on biocrusts, we created a realistic gradient mirroring anthropogenic N addition rate (2:1 NH₄ ⁺ : NO₃ ^- rates: 0.3, 0.5, 1.0, 1.5, 3 g N m^-2  yr^-1 ) and measured the response of bacteria and fungi within cyanobacterial-dominated biocrusts over 8 years in a temperate desert, the Gurbantunggut Desert, China. We found that once N deposition reached 1.5 g N m^-2  yr^-1 biocrust bacterial communities, including diazotrophs, were altered while no such tipping point existed for fungi. Above the threshold, bacterial richness was enhanced, the relative abundance of Chloroflexi, FBP and Gemmatimonadetes was elevated, and diazotrophs shifted from being dominated by Nostocaceae and Scytonemataceae (Cyanobacteria) to free-living Bradyrhizobiaceae (Alphaproteobacteria). Alternatively, the relative recovery of a few fungal species within the Lecanorales, Pleosporales and Verrucariales became either enriched or diminished due to N deposition. The chronic addition of N resulted in a dense and interconnected bacterial co-occurrence network that accentuated a functional shift from networks dominated by phototrophic species within the Nostocaceae, Xenococcaceae, Phormidiaceae and Scytonemataceae (Cyanobacteria) to ammonia-oxidizing species within the Nitrosomonadaceae (Betaproteobacteria) and nitrifying bacteria [i.e. Nitrospiraceae (Nitrospirae)]. Based on structural equation models, the effects of N additions on biocrust constituents were imposed through indirect effects on pH, soil electrical conductivity and ammonium concentrations. In summary, biocrust constituents are generally insensitive to chronic low levels of N depositions until rates reach above 1.5 g N m^-2  yr^-1 with diazotrophs being the most sensitive biocrust constituents followed by bacteria and finally fungi. Ultimately once the threshold is reached N deposition favours biocrust constituents utilizing inorganic N and other C sources over relying on phototrophic and/or N-fixing cyanobacteria for C and N.

Improved Tolerance of Artemisia ordosica to Drought Stress via Dark Septate Endophyte (DSE) Symbiosis

Dark septate endophytes (DSEs) usually colonize plant roots, especially in stress environments. However, their relationship with plants ranges from beneficial to harmful and has remained largely uncharacterized. In the present study, 14 DSE species grouped into 11 genera were isolated from the roots of a desert plant, Artemisia ordosica, which is widely distributed in northwest China. Three dominant DSE species—Paraphoma chrysanthemicola (Pc), Alternaria chartarum (Ac), and Acrocalymma vagum (Av)—were selected and tested for their resistance to drought in vitro. Furthermore, we characterized the responses of A. ordosica under drought conditions in relation to the presence of these DSEs following inoculation. The results showed that all three strains grew well under in vitro drought stress, and the biomass of Ac and Av was significantly higher than that of the unstressed control. The effects of DSE inoculation on the growth of A. ordosica under drought stress varied according to the different DSE species but were generally beneficial. Under drought stress, Av and Pc promoted plant growth, antioxidant enzyme activity, and root development of the hosts. The Ac strain conferred obvious positive effects on the antioxidant enzyme activity of the hosts. In general, Av and Pc demonstrated better application potential for improving the drought resistance of A. ordosica.

Muted responses to chronic experimental nitrogen deposition on the Colorado Plateau

Anthropogenic nitrogen (N) deposition is significantly altering both community structure and ecosystem processes in terrestrial ecosystems across the globe. However, our understanding of the consequences of N deposition in dryland systems remains relatively poor, despite evidence that drylands may be particularly vulnerable to increasing N inputs. In this study, we investigated the influence of 7 years of multiple levels of simulated N deposition (0, 2, 5, and 8 kg N ha^-1 year^-1) on plant community structure and biological soil crust (biocrust) cover at three semi-arid grassland sites spanning a soil texture gradient. Biocrusts are a surface community of mosses, lichens, cyanobacteria, and/or algae, and have been shown to be sensitive to N inputs. We hypothesized that N additions would decrease plant diversity, increase abundance of the invasive annual grass Bromus tectorum, and decrease biocrust cover. Contrary to our expectations, we found that N additions did not affect plant diversity or B. tectorum abundance. In partial support of our hypotheses, N additions negatively affected biocrust cover in some years, perhaps driven in part by inter-annual differences in precipitation. Soil inorganic N concentrations showed rapid but ephemeral responses to N additions and plant foliar N concentrations showed no response, indicating that the magnitude of plant and biocrust responses to N fertilization may be buffered by endogenous N cycling. More work is needed to determine N critical load thresholds for plant community and biocrust dynamics in semi-arid systems and the factors that determine the fate of N inputs.

Assessment of cultured media for desert moss crust by physiological responses

The physiological responses of desert moss crusts under four artificial media (Beneck, Part, BG11, and Hogland) were investigated to evaluate the function of culture media during different culture periods. The results showed that the value of malondialdehyde (MDA) was at a maximum at 11d, on the contrary, chlorophyll-a, soluble protein, and soluble sugar were at a minimum. As the time increased, the value of MDA and soluble protein decreased faster in the Hogland, while the value of chlorophyll-a and soluble sugar increased. At the end of the culture period, the value of chlorophyll-a and soluble sugar was at a maximum in the Hogland, while the value of MDA and soluble protein was at a minimum. The results suggested that the Hogland medium had a promoting effect on the growth of desert moss crusts. The selected artificial cultivation medium towards wider and larger scale field applications of cultural desert biocrust was widely anticipated.

Soil prokaryotic community shows no response to 2 years of simulated nitrogen deposition in an arid ecosystem in northwestern China

An arid ecosystem might be sensitive to nitrogen (N) deposition, but the associated ecosystem-specific response of soil microbes is not well studied. To assess the N enrichment effects on plant and prokaryotic community diversity, we performed a two-year NH₄ NO₃ treatment in a desert steppe in northwestern China. Results showed that N addition increased plant aboveground biomass and decreased plant Shannon diversity. A C₄ herb (Salsola collina) became dominant, and loss of legume species was observed. The concentrations of soil NH₄ ⁺ -N, NO₃ ^- -N, microbial biomass N, and the plant aboveground biomass N pool increased in contrast to total N, suggesting that the N input into the arid ecosystem might mainly be assimilated by plants and exit the ecosystem. Remarkably, the α-diversity and structure of the soil prokaryotic community did not vary even at the highest N addition rate. Structural equation modelling further found that the plant aboveground N pool counteracted the acidification effect of N deposition and maintained soil pH thus partially stabilizing the composition of prokaryotic communities in a desert steppe. These findings suggested that the plants and N loss might contribute to the lack of responsiveness of soil prokaryotic community to N deposition in a desert steppe.

Salt stress alters the short-term responses of nitrous oxide emissions to the nitrogen addition in salt-affected coastal soils

Increasing nitrogen deposition has become one of major environmental concerns in coastal wetlands. However, little is known about the response of soil nitrous oxide (N₂O) emissions, a powerful greenhouse gas, to the different levels and forms of nitrogen addition, in salt-affected coastal soils. To close the knowledge gap, a laboratory factorial incubation experiment with four nitrogen addition levels (0, no N addition; low-N, 45; medium-N, 90; high-N, 270 mg N kg^-1), three forms (NO₃^- (KN); NH₄⁺ (NH); DN, NH₄NO₃ (DN)), and three levels of salt addition (0, no salt addition; 12 ppt, low-salt; 35 ppt, high-salt) was carried out in two coastal soils with different initial salinity levels (LW: lower salinity wetlands; HW: higher salinity wetlands) in the Yellow River Delta, China. Results showed that, in no salt addition treatments, the cumulative N₂O emissions were linearly related to nitrogen addition, and high nitrogen addition significantly promoted N₂O emissions by 213% in LW soils and 848% in HW soils (p < 0.05), indicating that the mitigate effects of nitrogen addition to the deleterious salt stress were stronger in HW soils. Meanwhile, the promoting effects of DN and KN treatments were more obvious than NH treatments, suggesting that denitrification was responsible for the N₂O emission. However, with salt addition, the nonlinear response pattern and reduced response sizes were observed for KN and DN treatments (p < 0.05), suggesting the alteration in responses of N₂O emission to nitrogen addition by salt stress. In addition, the reduction and modification of response pattern was more obvious in soil with lower initial salinity. The findings of this work suggest the uniqueness and complexity of N₂O emission responses to nitrogen inputs related to the salinity levels in coastal wetlands.

Differences in substrate use linked to divergent carbon flow during litter decomposition

Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

Influence of enhanced ultraviolet-B radiation during rice plant growth on rice straw decomposition with nitrogen deposition

Although straw decomposition is important for ecosystem fertility and carbon balance, influence of ultraviolet-B (UV-B) radiation and nitrogen (N) deposition on this process is unclear. In this study, UV-B-exposed rice straw was decomposed under different N addition treatments for 15 months to investigate the indirect effects of UV-B radiation on straw chemistry and direct effects of N deposition on decomposition. UV-B exposure during rice plant growth changed the rice straw chemical composition, increasing the concentrations of acid-insoluble fraction (AIF), acid-soluble fraction, and UV-B-absorbing compounds. High N content had a negative effect on decomposition of rice straw exposed to enhanced and ambient UV-B radiation. Both AIF concentration and FTIR peak intensities indicated that lignin in rice straw was selectively preserved following N addition and UV-B radiation, reducing straw decomposition rate, which corresponded to lower activities of lignin-degrading enzymes in the later stage of decomposition. Thus, enhanced UV-B radiation during rice plant growth produced more recalcitrant substrates (lignin) and N reacted with lignin to produce more resistant compounds, further decreasing straw decomposition rate. UV-B radiation during plant growth and N deposition inhibit litter decomposition in agroecosystem, and their effects should be considered when establishing biogeochemical models in response to global changes.

Effects of anthropogenic nitrogen deposition on soil nitrogen mineralization and immobilization in grassland soil under semiarid climatic conditions

Earlier studies by the authors on English soils under grassland strongly supported their hypothesis that soil/plant systems have naturally evolved to conserve nitrogen (N) by having a close match between the dynamics of mineral-N production in soils and the dynamics of plant N requirements. Thus, maximum mineral-N production in soils occurred in spring when plant N requirements were greatest and were very low in mid to late summer. Low temperature and a high C:N ratio of senescing material helped to conserve N in winter, but mobile N was associated with pollution inputs. We test the hypothesis that under the much more arid conditions of Pakistan, soil/plant systems naturally have evolved to conserve mineral-N, especially over the very dry and cooler months between October and February. When soils from a grassland site were incubated at ambient temperatures after removal of plant roots and exclusion of atmospheric N inputs, there was consistent evidence of immobilization of nitrate and immobilization and possibly volatilization of ammonia/ammonium. In the wetter months of July and August, the soil at 0-10 cm depth showed no evidence of significant ammonium-N production in July and only small ammonium production at 10-20 cm depth in August, but was associated with significant nitrate-N immobilization in August. Nitrate leaching only appeared likely towards the end of the rainy season in September. The results strongly suggest that, under grass, the retention of atmospheric N inputs over the long dry periods is regulating the pools of available N in the soils, rather than the N produced by mineralization of soil organic matter.

Chronic nitrogen addition induces a cascade of plant community responses with both seasonal and progressive dynamics

Short-lived herbaceous plants provide a useful model to rapidly reveal how multiple generations of plants in natural plant communities of sensitive desert ecosystems will be affected by N deposition. We monitored dynamic responses of community structure, richness, evenness, density and biomass of herbaceous plants to experimental N addition (2:1 NH₄⁺:NO₃^- added at 0, 0.5, 1, 3, 6 and 24gNm^-2a^-1) in three seasons in each of three years in the Gurbantunggut desert, a typical temperate desert of central Asia. We found clear rate-dependent and season-dependent effects of N deposition on each of these variables, in most cases becoming more obvious through time. N addition reduced plant richness, leading to a loss of about half of the species after three generations in the highest N application level. Evenness and density were relatively insensitive to all but the greatest levels of N addition for two generations, but negative effects emerged in the third generation. Biomass, both above and below ground, was non-linearly affected by N deposition. Low and intermediate levels of N deposition often increased biomass, whereas the highest level suppressed biomass. Stimulatory effects of intermediate N addition disappeared in the third generation. All of these responses are strongly interrelated in a cascade of changes. Notably, changes in biomass due to N deposition were mediated by declines in richness and evenness, and other changes in community structure, rather than solely being the direct outcome of release from limitation. The interrelationships between N deposition and the different plant community attributes change not only seasonally, but also progressively change through time. These temporal changes appear to be largely independent of interannual or seasonal climatic conditions.

Stimulation of long-term ammonium nitrogen deposition on methanogenesis by Methanocellaceae in a coastal wetland

Atmospheric nitrogen deposition caused by human activities has been receiving much attention. Here, after long-term simulated ammonium and nitrate nitrogen deposition (NH₄Cl, KNO₃, and NH₄NO₃) in the Yellow River Delta (YRD), a sensitive coastal wetland ecosystem typified by a distinct wet and dry season, methane fluxes were measured, by adopting a closed static chamber technique. The results showed that deposition of ammonium nitrogen accelerated methane emissions all year round. Ammonium nitrogen deposition transformed the YRD from a methane sink into a source during the dry season. Methanocellaceae is the only methanogen with increased abundance after the application of NH₄Cl and NH₄NO₃, which promoted methane emissions, during the wet season. The findings suggested that Methanocellaceae may facilitate methane emissions in response to increased ammonium nitrogen deposition. Other methanogens might have profited from ammonium supplementation, such as Methanosarcinaceae. Deposition of nitrate nitrogen did not affect methane flux significantly. To the best of our knowledge, this study is the first to show that Methanocellaceae may be responsible for methane production in coastal wetland system. This study highlights the significant effect of ammonium nitrogen and slight effect of nitrate nitrogen on methane emission in the YRD and it will be helpful to understand the microbial mechanism responding to increased nitrogen deposition in the sensitive coastal wetland ecosystem.

Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0-0.5 or 0-10 cm) across the N-amendment gradient (0, 7, and 15 kg ha(-1) yr(-1)). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.