Microbial Respiration Research Articles

Microbe-Mineral Interactions between Asbestos and Thermophilic Chemolithoautotrophic Anaerobes.

The Fe content and the morphometry of asbestos are two major factors linked to its toxicity. This study explored the use of microbe-mineral interactions between asbestos (and asbestos-like) minerals and thermophilic chemolithoautotrophic microorganisms as possible mineral dissolution treatments targeting their toxic properties. The removal of Fe from crocidolite was tested through chemolithoautotrophic Fe(III) reduction activities at 60°C. Chrysotile and tremolite-actinolite were tested for dissolution and potential release of elements like Si and Mg through biosilicification processes at 75°C. Our results show that chemolithoautotrophic Fe(III) reduction activities by Deferrisoma palaeochoriense were supported with crocidolite as the sole source of Fe(III) used as a terminal electron acceptor during respiration. Microbial Fe(III) reduction activities resulted in higher Fe release rates from crocidolite in comparison to previous studies on Fe leaching from crocidolite through Fe assimilation activities by soil fungi. Evidence of biosilicification in Thermovibrio ammonificans did not correspond with increased Si and Mg release from chrysotile or tremolite-actinolite dissolution. However, overall Si and Mg release from chrysotile into our experimental medium outmatched previously reported capabilities for Si and Mg release from chrysotile by fungi. Differences in the profiles of elements released from chrysotile and tremolite-actinolite during microbe-mineral experiments with T. ammonificans underscored the relevance of underlying crystallochemical differences in driving mineral dissolution and elemental bioavailability. Experimental studies targeting the interactions between chemolithoautotrophs and asbestos (or asbestos-like) minerals offer new access to the mechanisms behind crystallochemical mineral alterations and their role in the development of tailored asbestos treatments. IMPORTANCE We explored the potential of chemosynthetic microorganisms growing at high temperatures to induce the release of key elements (mainly iron, silicon, and magnesium) involved in the known toxic properties (iron content and fibrous mineral shapes) of asbestos minerals. We show for the first time that the microbial respiration of iron from amphibole asbestos releases some of the iron contained in the mineral while supporting microbial growth. Another microorganism imposed on the two main types of asbestos minerals (serpentines and amphiboles) resulted in distinct elemental release profiles for each type of asbestos during mineral dissolution. Despite evidence of microbially mediated dissolution in all minerals, none of the microorganisms tested disrupted the structure of the asbestos mineral fibers. Further constraints on the relationships between elemental release rates, amount of starting asbestos, reaction volumes, and incubation times will be required to better compare asbestos dissolution treatments studied to date.

Shift from flooding to drying enhances the respiration of soil aggregates by changing microbial community composition and keystone taxa.

Changes in the water regime are among the crucial factors controlling soil carbon dynamics. However, at the aggregate scale, the microbial mechanisms that regulate soil respiration under flooding and drying conditions are obscure. In this research, we investigated how the shift from flooding to drying changes the microbial respiration of soil aggregates by affecting microbial community composition and their co-occurrence patterns. Soils collected from a riparian zone of the Three Gorges Reservoir, China, were subjected to a wet-and-dry incubation experiment. Our data illustrated that the shift from flooding to drying substantially enhanced soil respiration for all sizes of aggregate fractions. Moreover, soil respiration declined with aggregate size in both flooding and drying treatments. The keystone taxa in bacterial networks were found to be Acidobacteriales, Gemmatimonadales, Anaerolineales, and Cytophagales during the flooding treatment, and Rhizobiales, Gemmatimonadales, Sphingomonadales, and Solirubrobacterales during the drying treatment. For fungal networks, Hypocreales and Agaricalesin were the keystone taxa in the flooding and drying treatments, respectively. Furthermore, the shift from flooding to drying enhanced the microbial respiration of soil aggregates by changing keystone taxa. Notably, fungal community composition and network properties dominated the changes in the microbial respiration of soil aggregates during the shift from flooding to drying. Thus, our study highlighted that the shift from flooding to drying changes keystone taxa, hence increasing aggregate-scale soil respiration.

Decreased Soil Microbial Nitrogen Under Vegetation ‘Shrubification’ in the Subarctic Forest–Tundra Ecotone: The Potential Role of Increasing Nutrient Competition Between Plants and Soil Microorganisms

The consequences of warming-induced ‘shrubification’ on Arctic soil carbon storage are receiving increased attention, as the majority of ecosystem carbon in these systems is stored in soils. Soil carbon cycles in these ecosystems are usually tightly coupled with nitrogen availability. Soil microbial responses to ‘shrubification’ may depend on the traits of the shrub species that increase in response to warming. Increase in deciduous shrubs such as Betula nana likely promotes a loss of soil carbon, whereas the opposite may be true if evergreen shrubs such as Empetrum hermaphroditum increase. We analyzed soil organic matter stocks and 13C NMR fractions, microbial CO2 respiration, biomass, extracellular enzyme activities (EEAs), and their association with shrub density in northern Sweden after 20 years of experimental warming using open top chambers (OTCs). Our study sites were located in a tundra heath that stores high soil carbon quantities and where the OTCs had increased deciduous shrubs, and in a mountain birch forest that stores lower soil carbon quantities and where the OTCs had increased evergreen shrubs. We predicted that organic matter stocks should be lower and respiration and EEAs higher inside the OTCs than untreated plots in the tundra, whereas no effect should be detected in the forest. Soil organic matter stocks and 13C NMR fractions remained unaffected at both sites. When expressed as per gram microbial biomass, respiration and EEAs for carbohydrate and chitin degradation were higher inside the OTCs, and contrasting our prediction, this effect was stronger in the forest. Unexpectedly, the OTCs also led to a substantially lower microbial biomass carbon and nitrogen irrespective of habitat. The decline in the microbial biomass counteracted increased activities resulting in no effect of the OTCs on respiration and a lower phenol oxidase activity per gram soil. Microbial biomass nitrogen correlated negatively with evergreen shrub density at both sites, indicating that ‘shrubification’ may have intensified nutrient competition between plants and soil microorganisms. Nutrient limitation could also underlie increased respiration per gram microbial biomass through limiting C assimilation into biomass. We hypothesize that increasing nutrient immobilization into long-lived evergreen shrubs could over time induce microbial nutrient limitation that contributes to a stability of accumulated soil organic matter stocks under climate warming.

Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers.

Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (Tmin) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.

On-Site Sensor Calibration Procedure for Quality Assurance of Barometric Process Separation (BaPS) Measurements

Barometric process separation (BaPS) is an automated laboratory system for the simultaneous measurement of microbial respiration and gross nitrification rates in soil samples. To ensure optimal functioning, the sensor system, consisting of a pressure sensor, an O2 sensor, a CO2 concentration sensor, and two temperature probes, must be accurately calibrated. For the regular on-site quality control of the sensors, we developed easy, inexpensive, and flexible calibration procedures. The pressure sensor was calibrated by means of a differential manometer. The O2 and CO2 sensors were simultaneously calibrated through their exposure to a sequence of O2 and CO2 concentrations obtained by sequentially exchanging O2/N2 and CO2/N2 calibration gases. Linear regression models were best suited for describing the recorded calibration data. The accuracy of O2 and CO2 calibration was mainly affected by the accuracy of the utilized gas mixtures. Because the applied measuring method is based on the O2 conductivity of ZrO2, the O2 sensor is particularly susceptible to aging and to consequent signal shifts. Sensor signals were characterized by high temporal stability over the years. Deviations in the calibration parameters affected the measured gross nitrification rate by up to 12.5% and affected the respiration rate by up to 5%. Overall, the proposed calibration procedures are valuable tools for ensuring the quality of BaPS measurements and for promptly identifying sensor malfunctions.

Soil microbial communities are sensitive to differences in fertilization intensity in organic and conventional farming systems.

Intensive agriculture has increased global food production, but also impaired ecosystem services and soil biodiversity. Organic fertilization, essential to organic and integrated farming, can provide numerous benefits for soil quality but also compromise the environment by polluting soils and producing greenhouse gases through animal husbandry. The need for reduced stocking density is inevitably accompanied by lower FYM inputs, but little research is available on the impact of these effects on the soil microbiome. We collected soil samples from winter wheat plots of a 42-year-old long-term trial comparing different farming systems receiving farmyard manure at two intensities and measured soil quality parameters and microbial community diversity through DNA metabarcoding. High-input fertilization, corresponding to 1.4 livestock units (LU) improved the soil's nutritional status and increased soil microbial biomass and respiration when compared to low-input at 0.7 LU. Bacterial and fungal α-diversity was largely unaffected by fertilization intensity, whereas their community structure changed consistently, accompanied by an increase in the bacterial copiotroph-to-oligotroph ratio in high-input systems and by more copiotrophic indicator OTUs associated with high than low-input. This study shows that reduced nutrient availability under low-input selects oligotrophic microbes efficiently obtaining nutrients from various carbon sources; a potentially beneficial trait considering future agroecosystems.

Effects of Land Cover Change on Vegetation Carbon Source/Sink in Arid Terrestrial Ecosystems of Northwest China, 2001–2018

The arid terrestrial ecosystem carbon cycle is one of the most important parts of the global carbon cycle, but it is vulnerable to external disturbances. As the most direct factor affecting the carbon cycle, how land cover change affects vegetation carbon sources/sinks in arid terrestrial ecosystems remains unclear. In this study, we chose the arid region of northwest China (ARNWC) as the study area and used net ecosystem productivity (NEP) as an indicator of vegetation carbon source/sink. Subsequently, we described the spatial distribution and temporal dynamics of vegetation carbon sources/sinks in the ARNWC from 2001–2018 by combining the Carnegie-Ames-Stanford Approach (CASA) and a soil microbial heterotrophic respiration (RH) model and assessed the effects of land cover change on them through modeling scenario design. We found that land cover change had an obvious positive impact on vegetation carbon sinks. Among them, the effect of land cover type conversion contributed to an increase in total NEP of approximately 1.77 Tg C (reaching 15.55% of the original value), and after simultaneously considering the effect of vegetation growth enhancement, it contributed to an increase in total NEP of approximately 14.75 Tg C (reaching 129.61% of the original value). For different land cover types, cropland consistently contributed the most to the increment of NEP, and the regeneration of young and middle-aged forests also led to a significant increase in forest carbon sinks. Thus, our findings provide a reference for assessing the effects of land cover change on vegetation carbon sinks, and they indicated that cropland expansion and anthropogenic management dominated the growth of vegetation carbon sequestration in the ARNWC, that afforestation also benefits the carbon sink capacity of terrestrial ecosystems, and that attention should be paid to restoring and protecting native vegetation in forestland and grassland regions in the future.

Contextualized response of carbon-use efficiency to warming at the plant and ecosystem levels

Carbon-use efficiency (CUE) has been widely used as a constant value in many earth system models to simulate how assimilated C is partitioned in ecosystems, to estimate ecosystem C budgets, and investigate C feedbacks to climate warming. Although correlative relationships from previous studies indicated that CUE could vary with temperature, and relying on a fixed CUE value could cause large uncertainty in model projections, however, due to the lack of manipulative experiment, it remains unclear how CUE at the plant (CUEp) and ecosystem (CUEe) levels respond to warming. Based on a 7-year manipulative warming experiment in an alpine meadow ecosystem on the Qinghai-Tibet Plateau, we quantitatively distinguished various C flux components of CUE, including gross ecosystem productivity, net primary productivity, net ecosystem productivity, ecosystem respiration, plant autotrophic respiration, and microbial heterotrophic respiration and explored how CUE at different levels responded to climate warming. We found large variations in both CUEp (0.60 to 0.77) and CUEe (from 0.38 to 0.59). The warming effect on CUEp was positively correlated with ambient soil water content (SWC) and the warming effect on CUEe was negatively correlated with ambient soil temperature (ST), but was positively correlated with warming-induced changes in ST. We also found that the direction and magnitude of the warming effects on different CUE components scaled differently with changes in the background environment, which explained the variation in CUE's warming response under environmental changes. Our new insights have important implications for reducing modelling uncertainty of ecosystem C budgets and improving our ability to predict ecosystem C-climate feedbacks under climate warming.

Nitrate with enriched heavy oxygen isotope linked to changes in nitrogen source and transformation as groundwater table rises

Nitrate is a significant constituent of the total nitrogen pool in shallow aquifers and poses an escalating threat to groundwater resources, making it crucial to comprehend the source, conversion, and elimination of nitrogen using appropriate techniques. Although dual-isotope dynamics in nitrate have been widely used, uncertainties remain regarding the asynchronously temporal changes in δ18O-NO3- and δ15N-NO3- observed in hypoxic aquifers. This study aimed to investigate changes in nitrogen sources and transformations using temporal changes in field-based NO3- isotopic composition, hydro-chemical variables, and environmental DNA profiling, as the groundwater table varied. The results showed that the larger enrichment in δ18O-NO3- (+13‰) compared with δ15N-NO3- (−2‰) on average during groundwater table rise was due to a combination of factors, including high 18O-based atmospheric N deposition, canopies nitrification, and soil nitrification transported vertically by rainfalls, and 18O-enriched O2 produced through microbial and root respiration within denitrification. The strong association between functional gene abundance and nitrogen-related indicators suggests that anammox was actively processed with nitrification but in small bacterial population during groundwater table rise. Furthermore, bacterial species associated with nitrogen-associated gradients provided insight into subsurface nitrogen transformation, with Burkholderiaceae species and Pseudorhodobacter potentially serving as bioindicators of denitrification, while Candidatus Nitrotogn represents soil nitrification. Fluctuating groundwater tables can cause shifts in hydro-chemical and isotopic composition, which in turn can indicate changes in nitrogen sources and transformations. These changes can be used to improve input sources for mixture models and aid in microbial remediation of nitrate.

Dead bamboo culms promote litter mass, carbon and nitrogen loss, but do not modulate the effect of soil fauna on litter decomposition

Bamboos contribute significantly to carbon cycling in many (sub)tropical and temperate forests. In East Asia, unmanaged Moso bamboo stands accumulate large amounts of dead culms. However, very little is known about the indirect effects of dead culms on biogeochemical cycling through changes in soil conditions and decomposer communities. We evaluated the interactive effects of dead culms and soil fauna on litter decomposition in an unmanaged Moso bamboo stand. We placed leaf litter beneath the dead culms and on the forest floor (control) and used litterbags with different mesh sizes (1 mm and 42 μm) to control the access of soil mesofauna to the litter. We hypothesized that dead culms and soil fauna synergistically accelerate litter decomposition mainly because dead culms influence soil conditions and alter the litter fauna assemblage. We found that litter decomposing under the dead culms had greater litter mass, carbon and nitrogen loss, and microbial respiration rates than the control. The presence of soil mesofauna decreased litter mass, carbon and nitrogen loss but had no effect on the microbial respiration rate. Soil moisture was consistently higher under the dead culms, but their effect on soil temperature was dependent on the season. The litter decomposing below the dead culms had relatively higher mesofauna abundance and order richness. However, the contribution of the mesofauna to litter mass and nutrient loss was not modulated by the dead culms, suggesting that soil fauna had essentially the same effect on litter decomposition irrespective of the presence of dead culms. We showed that dead bamboo culms influence litter nutrient dynamics and promote habitat heterogeneity for soil microarthropods. Our results further highlight the ecological role played by dead culms and have implications for Moso bamboo management. The removal of dead culms from the forest floor could have substantial impact on the soil biota and ecosystem processes in managed stands.

Different behaviors of organic matter under physical-biological controls in the eastern Indian Ocean

Marine organic matter (OM) pools are the key to understanding biogeochemical cycles and carbon storage, especially under ongoing ocean warming. The tropical eastern Indian Ocean (IO) is ideal for unraveling marine OM pools for being one of the least understood ocean basins in terms of its complex physical and biogeochemical dynamics. So far, OM transformation and export remain underexplored and enigmatic in the IO. Here, we integrated in situ observations and incubation experiments in the Central IO (CIO) and Bay of Bengal (BoB). A large OM pool was found in the CIO, where we emphasized the prominent contribution of production in the deep euphotic layer, with physical forcing seasonally playing a supporting role. The dissolved organic matter (DOM)-degradation experiment results revealed high efficiency of in situ DOM consumption in the BoB, whereas dark carbon fixation by ammonia-oxidizing microorganisms was considered an alternative strategy in the euphotic CIO. Water mixing was found to highly influence the OM pools in the mesopelagic waters in the tropical eastern IO, but active microbial respiration could also regulate the OM degradation in the CIO. Our results emphasized the heterogeneity of OM pools between the BoB and CIO, and stated their different regulators of carbon reservoir considering an ocean warming scenario.

Bioengineering remediation of former industrial sites contaminated with chemical mixtures

Former gasworks sites are known to be contaminated with complex chemical mixtures that require remediation before redevelopment. Bioamendments such as biochar and spent mushroom compost (SMC) offer a green and sustainable remediation approach to help tackle this issue. However, the effectiveness of different biochar types and their interactions with the soil microbial community is still not well understood. To address this, a full factorial microcosm experiment was carried out using biochar derived from rice husk (RHB) and wheat straw (WSB) mixed with soil from a former gasworks site at varying concentrations (0%, 2.5%, and 5%), with and without SMC. The experiment aimed to evaluate the fate of contaminants including alkanes, PAHs, and metals, and their effect on the soil microbial community, as well as the implications for remediation endpoints. The results showed that the bioamendments had an average TPH reduction of 92%, with SMC and WSB-SMC having the highest degradation rates at 93%. While the bioamendments did not significantly affect the extent of TPH removal compared to the control, they did improve the degradation of high molecular weight (HMW) PAHs, particularly in RHB-SMC for EC17-20 (60%) and EC21-35 (62%) of total PAH concentration, and in WSB-SMC for HMW bioavailable PAH concentration (89%). The bioamendments also affected the partitioning and distribution of metals after 120 days of treatment, leading to decreased available phase fractions. The treatments increased microbial abundance in the soil, with Gram positives, Gram negatives, and fungi increasing by 4%, 8%, and 38%, respectively, after 120 days, particularly in SMC and mixed treatments. This was mirrored in increased microbial soil respiration. After 120 days, low metal (178 ± 5 mg/kg) and TPH (21 ± 7 mg/kg) bioavailability translated into higher EC50 (10624 ± 710 mg/L), indicating lower toxicity. There was a strong correlation between bioavailability and toxicity of TPH and metals with microbial relative abundance and activity. In summary, while green and sustainable remediation may accelerate the remediation process, monitored natural attenuation may be sufficient for site reclamation. However, this strategy, as demonstrated here, can reduce metal bioavailability, and promote the biodegradation of HMW PAHs.

Comparing effects of microplastic exposure, FPOM resource quality, and consumer density on the response of a freshwater particle feeder and associated ecosystem processes

Fine particulate organic matter (FPOM) is an important basal resource in stream ecosystems for deposit- and filter-feeding macroinvertebrates (collectively ‘particle feeders’). Microplastics (MP) share many characteristics with FPOM (e.g. size range, surface area to volume ratios) and are potentially consumed by particle feeders. Accordingly, MP contamination of natural FPOM pools might affect particle feeder growth and survival, particularly when background FPOM resource quality is low, or intraspecific competition is high. We conducted a microcosm experiment to evaluate how a realistic (1400 particles/kg sediment) polyethylene MP (ø = 45–53 µm) concentration interacts with FPOM (ø = 63–250 µm) resource quality (low versus high nutrient content) and consumer density (10 versus 20 individuals per microcosm) to affect growth and survival of larval Chironomus riparius (Diptera: Chironomidae), a model particle feeder. We additionally quantified community respiration, based on three hour measurements of oxygen consumption in the microcosms at the end of the experiment. MP exposure reduced larval body lengths by 26.7%, but only under the low consumer density treatment. MPs reduced community respiration by 26.2%, but only in the absence of chironomids, indicating an impact on microbial respiration. In comparison, low resource quality and high consumer density were associated with 53.5–70.2% reductions in community respiration, chironomid body length and/or body mass. These results suggest that effects of contamination of FPOM with MPs at environmentally realistic concentrations on the life histories of particle feeders such as C. riparius might be limited, especially relative to the effects of resource quality and consumer density. However, the reduction in microbial respiration when MPs were present highlights the need for further research addressing MP impacts on microbes, given their key roles in ecosystem functioning.

Plant influences on soil microbial carbon pump efficiency.

Microbe-mediated carbon transformation plays an important role in soil carbon sequestration, which is considered to be one of the key strategies to achieve carbon neutrality in the long term. Assessing the efficiency of microbial necromass accumulation relative to plant carbon input or microbial respiration will help to identify ways to promote soil carbon sequestration from an ecosystem perspective.

Pharmaceutical Attenuation Differs within Woodchip-Based Lignocellulose Bioreactors across Nitrate- and Sulfate-Reducing Conditions

Lignocellulosic bioreactors use solid-phase substrates such as woodchips to sustain microbial respiration and have been applied to treat agricultural runoff, stormwater, and other impaired waters. Here, we query how respiration of different soluble electron acceptors impacts the degradation of environmentally relevant pharmaceuticals associated with treated municipal wastewater discharge. Laboratory-scale columns containing a mixture of woodchips and alfalfa were manipulated across nitrate- and sulfate-reducing conditions using residence time and influent composition. Under steady-state conditions, bioreactors dominated by nitrate reduction harbored a distinct phylogenetic profile containing the genera Denitratisoma and increases in the denitrification gene nirS. In contrast, bioreactors where sulfate reduction dominated exhibited increased relative abundance of fermenters (e.g., Obscuribacteriales) and putative sulfate reducers (e.g., Desulfobulbus). Atenolol attenuation and biotransformation to carboxy-metoprolol accelerated under nitrate-reducing conditions; in contrast, trimethoprim attenuation and biotransformation to desmethyl trimethoprim was nearly an order of magnitude faster under sulfate-reducing conditions. Modest sulfamethoxazole attenuation occurred under all tested conditions. Denitrification-associated rate constants for atenolol were comparable to those reported in constructed wetlands and aquifer recharge, suggesting commonality in biotransformation mechanisms. Collectively, results suggest that manipulation of biogeochemical gradients during nature-based treatment can be applied to attenuate nitrate and trace quantities of pharmaceuticals.

Stenotrophomonas pavanii DJL-M3 inoculated biochar stabilizes the rhizosphere soil homeostasis of carbendazim-stressed rice

Plant–microbe interactions have been effectively used in phytoremediation to reduce agrochemical contamination of crops and soils, but little information is available regarding the general effect of such association on rhizosphere soil homeostasis. In this study, we immobilized Stenotrophomonas pavanii DJL-M3, a carbendazim (CBZ)-degrading endophyte, in rice husk-derived biochar to control fungicide residue in the rice microenvironment. The influence of biochar inoculated with strain DJL-M3 on rhizobacterial communities was also investigated, including activity and fundamental function predictions. An adsorption kinetics test showed that strain DJL-M3 slowed the adsorption rate slightly without sacrificing the adsorption capacity of rice-husk biochar on CBZ. Immobilization in biochar helped S. pavanii DJL-M3 to establish an ecological niche in rhizosphere soils. This process significantly reduced CBZ levels in rice and rhizosphere soil while maintaining stable heterotrophic microbial respiration and carbon (C) metabolic activity. Soil amendment with the strain DJL-M3–biochar composite resulted in relatively little disturbance of fundamental soil functions, such as nitrogen (N) and sulfur (S) cycling, which explained the better plant growth and higher soil fertility observed with CBZ contamination. Overall, the combination of biochar and S. pavanii DJL-M3 demonstrated the potential to safeguard the microbiological environment of rice.

Short-Term Effects of Bamboo Biochar and Oyster Shell Powder on Soil Organic Carbon Fraction, Microbial Respiration, and Enzymatic Stoichiometry in a Lei Bamboo Plantation

Both biochar and oyster shell powder have been known as promising amendments to ameliorate soil acidity and enhance soil fertility. However, it is still unclear how their application alone and in combination affect the soil organic carbon (C) fraction and microbial activity in subtropical bamboo plantations. Therefore, to investigate the effects of biochar and oyster shell powder on soil microbial respiration, organic C fractions, microbial biomass, and enzyme activities related to C, N and P cycling, topsoil samples were collected from plots in a bamboo (Phyllostachys praecox) plantation that has been amended with oyster shell powder at 4 t ha−1 (T), bamboo biochar at 10 t ha−1 (B), and their combination (TB, with 4 t ha−1 T and 10 t ha−1 B) for 8 months. Our results showed that T alone significantly increased soil microbial respiration by 21.5%, whereas B alone and TB significantly decreased soil microbial respiration and metabolic quotient compared with T. T alone also increased soil pH, the size of labile C pool and the activities of β−glucosidase and cellobiosidase, whereas TB rather than B increased soil pH, the recalcitrant C pool size and declined these enzyme activities relative to T. T alone significantly enhanced microbial C limitation by 28.6% and decreased P limitation by 13.0%, while TB decreased microbial C limitation and increased microbial C use efficiency (CUE). Structural equation modeling indicated that T enhanced soil microbial respiration through increasing soil pH and enzyme activity, while biochar co-addition weakened the stimulation of T on microbial respiration by increasing soil recalcitrant C pool size and microbial metabolic quotient. Our study suggests that adding bamboo biochar together with oyster shell powder could be a better strategy to decrease soil C loss and ameliorate soil acidity in bamboo plantations compared with the application of oyster shell powder alone.

Spatially-explicit estimate of nitrogen effects on soil respiration across the globe.

Soil respiration (Rs), as the second largest flux of carbon dioxide (CO2 ) between terrestrial ecosystems and the atmosphere, is vulnerable to global nitrogen (N) enrichment. However, the global distribution of the N effects on Rs remains uncertain. Here, we compiled a new database containing 1282 observations of Rs and its heterotrophic component (Rh) in field N manipulative experiments from 317 published papers. Using this up-to-date database, we first performed a formal meta-analysis to explore the responses of Rs and Rh to N addition, and then presented a global spatially-explicit quantification of the N effects using a Random Forest model. Our results showed that experimental N addition significantly increased Rs but had a minimal impact on Rh, not supporting the prevailing view that N enrichment inhibits soil microbial respiration. For the major biomes, the magnitude of N input was the main determinant of the spatial variation in Rs response, while the most important predictors for Rh response were biome-specific. Based on the key predictors, global mapping visually demonstrated a positive N effect in the regions with higher anthropogenic N inputs (i.e., atmospheric N deposition and agricultural fertilization). Overall, our analysis not only provides novel insight into the N effects on soil CO2 fluxes, but also presents a spatially-explicit assessment of the N effects at the global scale, which are pivotal for understanding ecosystem carbon dynamics in future scenarios with more frequent anthropogenic activities.

Experimental warming causes mismatches in alpine plant-microbe-fauna phenology

Long-term observations have shown that many plants and aboveground animals have changed their phenology patterns due to warmer temperatures over the past decades. However, empirical evidence for phenological shifts in alpine organisms, particularly belowground organisms, is scarce. Here, we investigate how the activities and phenology of plants, soil microbes, and soil fauna will respond to warming in an alpine meadow on the Tibetan Plateau, and whether their potential phenological changes will be synchronized. We experimentally simulate an increase in soil temperature by 2–4 °C according to future projections for this region. We find that warming promotes plant growth, soil microbial respiration, and soil fauna feeding by 8%, 57%, and 20%, respectively, but causes dissimilar changes in their phenology during the growing season. Specifically, warming advances soil faunal feeding activity in spring and delays it in autumn, while their peak activity does not change; whereas warming increases the peak activity of plant growth and soil microbial respiration but with only minor shifts in their phenology. Such phenological asynchrony in alpine organisms may alter ecosystem functioning and stability.

Responses of soil microbial communities to vegetation restoration on the Loess Plateau of China: A meta-analysis

Vegetation restoration has been implemented to prevent ecosystem degradation worldwide. However, the general response of soil microbial communities to vegetation restoration remains highly controversial. Herein, 417 paired observations from 74 studies on the Loess Plateau of China were selected to investigate the effects of vegetation restoration on the soil microbial community and to determine the factors that affected their variation. The results showed that vegetation restoration significantly increased microbial biomass (phospholipid fatty acid and microbial biomass C, N, and P) and enzyme activities (invertase, urease, phosphatase, catalase and glucosidase) but decreased the fungi to bacteria ratio (F:B). Specifically, microbial biomass was mainly affected by slope gradient, pH, and available nitrogen. Enzyme activities were mainly affected by available nitrogen, pH, and soil water content. F:B was mainly affected by available phosphorus. However, the variations in Oligotroph:Copiotroph ratio, gram-positive bacteria to gram-negative bacteria ratio, microbial diversity (Shannon index and OTU richness), and microbial activity (microbial respiration, metabolic quotient, and microbial entropy carbon) were nonsignificant. Our study also showed that the effects of vegetation restoration on the soil microbial community were substantially dependent on vegetation type (restoration type, leaf form, mycorrhizal type) and restoration year. For example, greater microbial biomass was found in soils of trees (sites that had been restored to forest), higher enzyme activity was found in soils of broadleaf tree species, and a lower F:B was found in soils of arbuscular mycorrhizal species.