Microbial community composition explains soil respiration responses to changing carbon inputs along an Andes-to-Amazon elevation gradient

Revealing bacterial and fungal communities of the untapped forest and alpine grassland zones of the Western-Himalayan region

The Western Himalayas offer diverse environments for investigating the diversity and distribution of microbial communities and their response to both the abiotic and biotic factors across the entire altitudinal gradient. Such investigations contribute significantly to our understanding of the complex ecological processes that shape microbial diversity. The proposed study focuses on the investigation of the bacterial and fungal communities in the forest and alpine grasslands of the Western Himalayan region, as well as their relationship with the physicochemical parameters of soil. A total of 185 isolates were obtained using the culture-based technique belonging to Bacillus (37%), Micrococcus (16%), and Staphylococcus (7%). Targeted metagenomics revealed the abundance of bacterial phyla Pseudomonadota (23%) followed by Acidobacteriota (20.2%), Chloroflexota (15%), and Bacillota (11.3%). At the genera level, CandidatusUdaeobacter (6%), Subgroup_2 (5.5%) of phylum Acidobacteriota, and uncultured Ktedonobacterales HSB_OF53-F07 (5.2%) of Choloroflexota phylum were found to be preponderant. Mycobiome predominantly comprised of phyla Ascomycota (54.1%), Basidiomycota (24%), and Mortierellomycota (19.1%) with Archaeorhizomyces (19.1%), Mortierella (19.1%), and Russula (5.4%) being the most abundant genera. Spearman's correlation revealed that the bacterial community was most influenced by total nitrogen in the soil followed by soil organic carbon as compared to other soil physicochemical factors. The study establishes a fundamental relationship between microbial communities and the physicochemical properties of soil. Furthermore, the study provides valuable insights into the complex interplay between biotic and abiotic factors that influence the microbial community composition of this unique region across various elevations.

Leafcutter ants enhance microbial drought resilience in tropical forest soil

We conducted a research campaign in a neotropical rainforest in Costa Rica throughout the drought phase of an El-Nino Southern Oscillation event to determine microbial community dynamics and soil C fluxes. Our study included nests of the leafcutter ant Atta cephalotes, as soil disturbances made by these ecosystem engineers may influence microbial drought response. Drought decreased the diversity of microbes and the abundance of core microbiome taxa, including Verrucomicrobial bacteria and Sordariomycete fungi. Despite initial responses of decreasing diversity and altered composition, 6 months post-drought the microbiomes were similar to pre-drought conditions, demonstrating the resilience of soil microbial communities to drought events. A. cephalotes nests altered fungal composition in the surrounding soil, and reduced both fungal mortality and growth of Acidobacteria post-drought. Drought increased CH4 consumption in soils due to lower soil moisture, and A. cephalotes nests decrease the variability of CH4 emissions in some soil types. CH4 emissions were tracked by the abundance of methanotrophic bacteria and fungal composition. These results characterize the microbiome of tropical soils across both time and space during drought and provide evidence for the importance of leafcutter ant nests in shaping soil microbiomes and enhancing microbial resilience during climatic perturbations.

The responses of CO2 emission to nitrogen application and earthworm addition in the soybean cropland

The effects of nitrogen application or earthworms on soil respiration in the Huang-Huai-Hai Plain of China have received increasing attention. However, the response of soil carbon dioxide (CO2) emission to nitrogen application and earthworm addition is still unclear. A field experiment with nitrogen application frequency and earthworm addition was conducted in the Huang-Huai-Hai Plain. Results showed nitrogen application frequency had a significant effect on soil respiration, but neither earthworms nor their interaction with nitrogen application frequency were significant. Low-frequency nitrogen application (NL) significantly increased soil respiration by 25%, while high-frequency nitrogen application (NH), earthworm addition (E), earthworm and high-frequency nitrogen application (E*NH), and earthworm and low-frequency nitrogen application (E*NL) also increased soil respiration by 21%, 21%, 12%, and 11%, respectively. The main reason for the rise in soil respiration was alterations in the bacterial richness and keystone taxa (Myxococcales). The NH resulted in higher soil nitrogen levels compared to NL, but NL had the highest bacterial richness. The abundance of Corynebacteriales and Gammaproteobacteria were positively connected with the CO2 emissions, while Myxococcales, Thermoleophilia, and Verrucomicrobia were negatively correlated. Our findings indicate the ecological importance of bacterial communities in regulating the carbon cycle in the Huang-Huai-Hai Plain.

Pulp mill biosolids mitigate soil greenhouse gas emissions from applied urea and improve soil fertility in a hybrid poplar plantation

Pulp mill biosolids (hereafter 'biosolids') could be used as an organic amendment to improve soil fertility and promote crop growth; however, it is unclear how the application of biosolids affects soil greenhouse gas emissions and the mechanisms underlying these effects. Here, we conducted a 2-year field experiment on a 6-year-old hybrid poplar plantation in northern Alberta, Canada, to compare the effects of biosolids, conventional mineral fertilizer (urea), and urea + biosolids on soil CO2, CH4 N2O emissions, as well as soil chemical and microbial properties. We found that the addition of biosolids increased soil CO2 and N2O emissions by 21 and 17%, respectively, while urea addition increased their emissions by 30 and 83%, respectively. However, the addition of urea did not affect soil CO2 emissions when biosolids were also applied. The addition of biosolids and biosolids + urea increased soil dissolved organic carbon (DOC) and microbial biomass C (MBC), while urea addition and biosolids + urea addition increased soil inorganic N, available P and denitrifying enzyme activity (DEA). Furthermore, the CO2 and N2O emissions were positively, while the CH4 emissions were negatively associated with soil DOC, inorganic N, available phosphorus, MBC, microbial biomass N, and DEA. In addition, soil CO2, CH4 and N2O emissions were also strongly associated with soil microbial community composition. We conclude that the application of the combination of biosolids and chemical N fertilizer (urea) could be a beneficial approach for both the disposal and use of pulp mill wastes, by reducing greenhouse gas emissions and improving soil fertility.

Responses of soil microbial communities and enzyme activities under nitrogen addition in fluvo-aquic and black soil of North China

This research investigates the impact of long-term nitrogen (N) addition on fluvo-aquic and black soils in north China, with a focus on soil microbial communities and enzyme activities. In each site, there were three N fertilization treatments, i.e., control, moderate-N, and high-N. Phospholipid Fatty Acid Analysis was employed to analyze the microbial community composition, and enzyme activities related to N, carbon (C), and phosphorus (P) cycling were assessed. The results showed that increasing N fertilization levels led to higher soil organic carbon (SOC) and total N (TN) concentrations, indicating enhanced nutrient availability. N fertilization reduced soil pH across both soils, with a more pronounced acidification effect observed in the black soil. Across both soils, N addition increased maize yield, but the higher crop yield was attained in moderate-N rate compared with high-N rate. Microbial community composition analysis revealed that N fertilization induced shifts in the relative abundances of specific microbial groups. The black soil exhibited pronounced shifts in the microbial groups compared to the fluvo-aquic soil, i.e., decreased fungal abundance and fungi: bacteria ratio in response to N input. In addition, the application of N fertilizer led to an elevated ratio of gram-positive to gram-negative (GP:GN) bacteria, but this effect was observed only in black soil. N fertilization had an impact on the enzyme activities related to C, N, and P cycling in both soil types, but black soil showed more pronounced changes in enzyme activities. Permutational multivariate analysis of variance indicated that soil types rather than N fertilization mediated the response of the soil microbial community and enzyme activities. Partial least square path modeling demonstrated that soil pH was the only key driver impacting soil microbial groups and enzyme activities in both soils. In conclusion, our findings highlighted that N fertilization exerted more pronounced impacts on soil biochemical properties, microbial community composition, and enzyme activities in black soil furthermore, moderate N rate resulted in higher crop productivity over high N rate.

Impacts of anthropogenic climate change on tropical montane forests: an appraisal of the evidence

In spite of their small global area and restricted distributions, tropical montane forests (TMFs) are biodiversity hotspots and important ecosystem services providers, but are also highly vulnerable to climate change. To protect and preserve these ecosystems better, it is crucial to inform the design and implementation of conservation policies with the best available scientific evidence, and to identify knowledge gaps and future research needs. We conducted a systematic review and an appraisal of evidence quality to assess the impacts of climate change on TMFs. We identified several skews and shortcomings. Experimental study designs with controls and long-term (≥10 years) data sets provide the most reliable evidence, but were rare and gave an incomplete understanding of climate change impacts on TMFs. Most studies were based on predictive modelling approaches, short-term (<10 years) and cross-sectional study designs. Although these methods provide moderate to circumstantial evidence, they can advance our understanding on climate change effects. Current evidence suggests that increasing temperatures and rising cloud levels have caused distributional shifts (mainly upslope) of montane biota, leading to alterations in biodiversity and ecological functions. Neotropical TMFs were the best studied, thus the knowledge derived there can serve as a proxy for climate change responses in under-studied regions elsewhere. Most studies focused on vascular plants, birds, amphibians and insects, with other taxonomic groups poorly represented. Most ecological studies were conducted at species or community levels, with a marked paucity of genetic studies, limiting understanding of the adaptive capacity of TMF biota. We thus highlight the long-term need to widen the methodological, thematic and geographical scope of studies on TMFs under climate change to address these uncertainties. In the short term, however, in-depth research in well-studied regions and advances in computer modelling approaches offer the most reliable sources of information for expeditious conservation action for these threatened forests.

Contrasting responses of soil microbial biomass and extracellular enzyme activity along an elevation gradient on the eastern Qinghai-Tibetan Plateau

Soil microbial community composition and extracellular enzyme activity are two main drivers of biogeochemical cycling. Knowledge about their elevational patterns is of great importance for predicting ecosystem functioning in response to climate change. Nevertheless, there is no consensus on how soil microbial community composition and extracellular enzyme activity vary with elevation, and little is known about their elevational variations on the eastern Qinghai-Tibetan Plateau, a region sensitive to global change. We therefore investigated the soil microbial community composition using phospholipid fatty acids (PLFAs) analysis, and enzyme activities at 2,820 m (coniferous and broadleaved mixed forest), 3,160 m (dark coniferous forest), 3,420 m (alpine dwarf forest), and 4,280 m (alpine shrubland) above sea level. Our results showed that soil microbial community composition and extracellular enzyme activities changed significantly along the elevational gradient. Biomass of total microbes, bacteria, and arbuscular mycorrhizal fungi at the highest elevation were the significantly lowest among the four elevations. In contrast, extracellular enzyme activities involved in carbon (C)-, nitrogen (N)-, and phosphorus (P)- acquiring exhibited the maximum values at the highest elevation. Total nutrients and available nutrients, especially P availability jointly explained the elevational pattern of soil microbial community, while the elevational variation of extracellular enzyme activities was dependent on total nutrients. Microbial metabolism was mainly C- and P-limited with an increasing C limitation but a decreasing P limitation along the elevational gradient, which was related significantly to mean annual temperature and total P. These results indicated a vital role of soil P in driving the elevational patterns of soil microbial community and metabolism. Overall, the study highlighted the contrasting responses of soil microbial biomass and extracellular enzyme activities to elevation, possibly suggesting the differences in adaption strategy between population growth and resource acquisition responding to elevation. The results provide essential information for understanding and predicting the response of belowground community and function to climate change on the eastern Qinghai-Tibetan Plateau.

Land use intensification in a dry-hot valley reduced the constraints of water content on soil microbial diversity and multifunctionality but increased CO2 production

Conversion of abandoned land (mainly savanna) into cropland generally occurs in fragile ecosystems such as dry-hot valleys (DHVs) in southwest China, with the intent of increasing land productivity and conducting ecological restoration. However, the effects of conversion on soil microbial communities and carbon turnover of savanna ecosystems remain unclear, since savannas could be a vital but overlooked carbon sink. To illustrate the ecological consequences of land-use change (LUC) for savanna ecosystems, a 1-year field experiment was conducted in DHVs of southwest China. The soil properties, microbial respiration, and metagenomics from two different land-use types (grassland and mango plantation) were examined to reveal the effects of regional LUC on soil C turnover and microbial traits. Conversion from degraded grassland into cropland increased the contribution of soil microclimate to the microbial community composition, reduced the constraints of soil water content (SWC), and further decreased nutrient availability. LUC reshaped the composition and structure of soil bacterial communities. Specifically, soil dominant microbes that belonged to Actinobacteria and Proteobacteria were significantly enriched by conversion, while rare microbes that belonged to a wider range of phyla were generally depleted, leading to an overall decrease in community diversity. In addition, LUC-induced changes in soil characteristics and microbial communities further decreased soil multifunctionality as well as the carbon use efficiency of microbes. Intensified microbial respiration and a significant increase in the soil CO₂ efflux were observed following LUC, which could drive changes in soil microbial community composition and functions (such as growth and regeneration). In summary, through simultaneously reducing constraints on SWC and decreasing nutrient availability, conversion from degraded grassland to cropland in a DHV decreased soil microbial diversity and multifunctionality, and increased microbial respiration and soil CO₂ efflux. Our study provides new insights for understanding the role and mechanisms of LUC in soil carbon turnover in ecologically fragile areas such as DHVs.

Seasonal Influence of Biodiversity on Soil Respiration in a Temperate Forest

Soil respiration in forests contributes to significant carbon dioxide emissions from terrestrial ecosystems but it varies both spatially and seasonally. Both abiotic and biotic factors influence soil respiration but their relative contribution to spatial and seasonal variability remains poorly understood, which leads to uncertainty in models of global C cycling and predictions of future climate change. Here, we hypothesize that tree diversity, soil diversity, and soil properties contribute to local-scale variability of soil respiration but their relative importance changes in different seasons. To test our hypothesis, we conducted seasonal soil respiration measurements along a local-scale environmental gradient in a temperate forest in Northeast China, analyzed spatial variability of soil respiration and tested the relationships between soil respiration and a variety of abiotic and biotic factors including topography, soil chemical properties, and plant and soil diversity. We found that soil respiration varied substantially across the study site, with spatial coefficients of variation (CV) of 29.1%, 27.3% and 30.8% in spring, summer, and autumn, respectively. Soil respiration was consistently lower at high soil water content, but the influence of other factors was seasonal. In spring, soil respiration increased with tree diversity and biomass but decreased with soil fungal diversity. In summer, soil respiration increased with soil temperature, whereas in autumn, soil respiration increased with tree diversity but decreased with increasing soil nutrient content. However, soil nutrient content indirectly enhanced soil respiration via its effect on tree diversity across seasons, and forest stand structure indirectly enhanced soil respiration via tree diversity in spring. Our results highlight that substantial differences in soil respiration at local scales was jointly explained by soil properties (soil water content and soil nutrients), tree diversity, and soil fungal diversity but the relative importance of these drivers varied seasonally in our temperate forest.

Alfalfa-grass mixtures reduce greenhouse gas emissions and net global warming potential while maintaining yield advantages over monocultures

Improving forage productivity with lower greenhouse gas (GHG) emissions from limited grassland has been a hotspot of interest in global agricultural production. In this study, we analyzed the effects of grasses (tall fescue, smooth bromegrass), legume (alfalfa), and alfalfa-grass (alfalfa + smooth bromegrass and alfalfa + tall fescue) mixtures on GHG emissions, net global warming potential (Net GWP), yield-based greenhouse gas intensity (GHGI), soil chemical properties and forage productivity in cultivated grassland in northwest China during 2020-2021. Our results demonstrated that alfalfa-grass mixtures significantly improved forage productivity. The highest total dry matter yield (DMY) during 2020 and 2021 was obtained from alfalfa-tall fescue (11,311 and 13,338 kg ha^-1) and alfalfa-smooth bromegrass mixtures (10,781 and 12,467 kg ha^-1). The annual cumulative GHG emissions from mixtures were lower than alfalfa monoculture. Alfalfa-grass mixtures significantly reduced GHGI compared with the grass or alfalfa monocultures. Furthermore, results indicated that grass, alfalfa and alfalfa-grass mixtures differentially affected soil chemical properties. Lower soil pH and C/N ratio were recorded in alfalfa monoculture. Alfalfa and mixtures increased soil organic carbon (SOC) and soil total nitrogen (STN) contents. Importantly, alfalfa-grass mixtures are necessary for improving forage productivity and mitigating the GHG emissions in this region. In conclusion, the alfalfa-tall fescue mixture lowered net GWP and GHGI in cultivated grassland while maintaining high forage productivity. These advanced agricultural practices could contribute to the development of climate-sustainable grassland production in China.

Root associated fungal lineages of a tropical montane forest show contrasting sensitivities to the long-term addition of nitrogen and phosphorus

Root associated fungal (RAF) communities can exert strong effects on plant communities and are potentially sensitive to shifts in soil fertility. As increased atmospheric nitrogen (N) and phosphorus (P) deposition can alter the nutrient balance in natural ecosystems, we assessed the response of RAF communities to a fertilization experiment deployed on a highly diverse Andean forest. The stand level fine root fraction was sampled after 7 years of systematic N and P additions and RAF communities were characterized by a deep sequencing approach. We expected that fertilization will enhance competition of fungal taxa for limiting nutrients, thus eliciting diversity reductions and alterations in the structure of RAF communities. Fertilization treatments did not reduce RAF richness but affected community composition. At the phylum level fertilization reduced richness exclusively among Glomeromycota. In contrast, N and P additions (alone or in combination) altered the composition of several fungal phyla. The lack of a generalized response to long-term fertilization among RAF lineages suggests that most of these lineages will not be directly and immediately affected by the increasing rates of atmospheric N and P deposition expected for this region by 2050.

Effects of simulated acid rain on rhizosphere microorganisms of invasive Alternanthera philoxeroides and native Alternanthera sessilis

Acid rain not only has serious harm to the environment, but also has the same threat to plants, but the invasive plant Alternanthera philoxeroides still grows well compared to the native plant Alternanthera sessilis under acid rain stress. However, the underlying mechanism of resistance to the acid rain environment in invasive Alternanthera philoxeroides remains unclear. In the current study, we comparatively analyzed the plant physiological characteristics, soil physicochemical properties, and rhizosphere microbial communities of invasive A. philoxeroides and native A. sessilis under different pH condition. The simulated acid rain had a significant inhibitory effect on the morphological and physiological traits of A. philoxeroides and A. sessilis and reduced the soil nutrient content. However, A. philoxeroides was more tolerant of acid rain. Compared with CK, simulated acid rain treatment at pH 2.5 significantly increased the Chao1, ACE, and Shannon indexes of A. philoxeroides microorganisms. Under simulated acid rain treatment at pH 2.5, the fungal flora Chao1, ACE and Shannon index were significantly higher than those of CK by 14.5%, 12.4%, and 30.4%, respectively. The dominant bacterial phyla of soil bacteria were Proteobacteria, Actinobacteria, Bacteroidota, Actinobacteria, Firmicutes, Myxococcota, Chloroflexi, Patescibacteria, Gemmatimonadota, Verrucomicrobiota, and Armatimonadota. The dominant fungi were Ascomycota, Basidiomycota, Rozellomycota, and Olpidiomycota. The bacterial and fungal diversity and structure of A. philoxeroides and A. sessilis showed the greatest difference between the pH 2.5 treatment and CK. Redundancy analysis showed that electrical conductivity (EC) and total phosphorus (TP) were the main factors changing the bacterial communities, and available phosphorus (AP), organic matter (OM), EC, and pH were the main factors changing the fungal communities. This study contributes to the microbial community structure of the invasive plant A. philoxeroides and provides a theoretical basis for studying the invasion mechanism of invasive plants under acid rain.

Multifarious Responses of Forest Soil Microbial Community Toward Climate Change

Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO₂, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.

Soil Enzyme Activity Regulates the Response of Soil C Fluxes to N Fertilization in a Temperate Cultivated Grassland

Exogenous nitrogen (N) inputs greatly change the emission and uptake of carbon dioxide (CO2) and methane (CH4) from temperate grassland soils, thereby affecting the carbon (C) budget of regional terrestrial ecosystems. Relevant research focused on natural grassland, but the effects of N fertilization on C exchange fluxes from different forage soils and the driving mechanisms were poorly understood. Here, a three-year N addition experiment was conducted on cultivated grassland planted with alfalfa (Medicago sativa) and bromegrass (Bromus inermis) in Inner Mongolia. The fluxes of soil-atmospheric CO2 and CH4; the content of the total dissolved N (TDN); the dissolved organic N (DON); the dissolved organic C (DOC); NH4+–N and NO3−–N in soil; enzyme activity; and auxiliary variables (soil temperature and moisture) were simultaneously measured. The results showed that N fertilization (>75 kg N ha−1 year−1) caused more serious soil acidification for alfalfa planting than for brome planting. N fertilization stimulated P-acquiring hydrolase (AP) in soil for growing Bromus inermis but did not affect C- and N-acquiring hydrolases (AG, BG, CBH, BX, LAP, and NAG). The oxidase activities (PHO and PER) of soil for planting Bromus inermis were higher than soil for planting Medicago sativa, regardless of N, whether fertilization was applied or not. Forage species and N fertilization did not affect soil CO2 flux, whereas a high rate of N fertilization (150 kg N ha−1 year−1) significantly inhibited CH4 uptake in soil for planting Medicago sativa. A synergistic effect between CO2 emission and CH4 uptake in soil was found over the short term. Our findings highlight that forage species affect soil enzyme activity in response to N fertilization. Soil enzyme activity may be an important regulatory factor for C exchange from temperate artificial grassland soil in response to N fertilization.

Microbial assemblies associated with temperature sensitivity of soil respiration along an altitudinal gradient

Identifying the drivers of the response of soil microbial respiration to warming is integral to accurately forecasting the carbon-climate feedbacks in terrestrial ecosystems. Microorganisms are the fundamental drivers of soil microbial respiration and its response to warming; however, the specific microbial communities and properties involved in the process remain largely undetermined. Here, we identified the associations between microbial community and temperature sensitivity (Q₁₀) of soil microbial respiration in alpine forests along an altitudinal gradient (from 2974 to 3558 m) from the climate-sensitive Tibetan Plateau. Our results showed that changes in microbial community composition accounted for more variations of Q₁₀ values than a wide range of other factors, including soil pH, moisture, substrate quantity and quality, microbial biomass, diversity and enzyme activities. Specifically, co-occurring microbial assemblies (i.e., ecological clusters or modules) targeting labile carbon consumption were negatively correlated with Q₁₀ of soil microbial respiration, whereas microbial assemblies associated with recalcitrant carbon decomposition were positively correlated with Q₁₀ of soil microbial respiration. Furthermore, there were progressive shifts of microbial assemblies from labile to recalcitrant carbon consumption along the altitudinal gradient, supporting relatively high Q₁₀ values in high-altitude regions. Our results provide new insights into the link between changes in major microbial assemblies with different trophic strategies and Q₁₀ of soil microbial respiration along an altitudinal gradient, highlighting that warming could have stronger effects on microbially-mediated soil organic matter decomposition in high-altitude regions than previously thought.

Depth-resolved microbial diversity and functional profiles of trichloroethylene-contaminated soils for Biolog EcoPlate-based biostimulation strategy

This study explores the toxic effect of TCE at different depths of sub-surface soil and underpins microbial community-level suitable carbon (C)-sources that provided directionality to the in situ biostimulation effort via augmentation strategy for effective TCE remediation in soil. The impacts on resident microbial communities and their functional profiles that govern the TCE biodegradation process were identified. Highly contaminated PW01 soil (9 m depth) had severely limited microbial diversity and was enriched in Proteobacteria and Firmicutes. The abundance of TCE degradation-associated genera was observed in all contaminated samples, and the abundance of TCE-degradation-related taxa were positively correlated with soil TCE contamination levels. Community-level metabolic activity associated with the utilization of diverse external C-sources was directly influenced by TCE concentration and soil depth. Multivariate data analysis revealed that the functional genus, TCE concentration, and selected available C substrate uptake capacity correlated in soil samples. Pearson's correlation tests revealed that C sources such as L-arginine, phenylethylamine and γ-hydroxybutyric acid utilization trait exhibited significant positive correlations with chloroalkane and chloroalkene degradation pathway abundance. Ultimately, depth and TCE contamination level-associated soil microbiota and their most preferred C-source understanding could add to facilitate effective biostimulation via external nutrient amendment for efficient in situ TCE degradation.

Increasing acid rain frequency promotes the microbial community dissimilarities of forest soil rather than agricultural soil in southern China

Soil microbial community drives the terrestrial carbon (C) cycling by C sources metabolism (i.e., organic C decomposition), however, the microbial response to changing acid rain frequency remains less studied, thus hampering global warming projection. Here, we manipulated a simulated experiment to decipher the impact of acid rain frequency (0, 30%, and 100%) on microbial community and C sources metabolism in the agricultural and forest soils of southern China, based on the phospholipid fatty acids (PLFAs) analysis and BIOLOG method, respectively. We found that changing acid rain frequency did not affect the microbial biomass and community structure of agricultural soil during the whole experiment period, while the 30% and 100% acid rain frequencies significantly decreased the microbial biomass, and altered the microbial community structure of forest soil at the early stage. However, changing acid rain frequency did not influence the microbial C sources metabolism in the agricultural soil, but 30% acid rain frequency significantly reduced the microbial utilization of carboxylic acids in the forest soil. Moreover, increasing acid rain frequency promoted the microbial community dissimilarities of forest soil. The microbial community structure and C sources utilization of agricultural soil were significantly related to soil available phosphorus content, while that of forest soil correlated with the soil available potassium content and temperature. Changes in soil environmental condition, soil acidification parameters and soil nutrients explained most of the variance of microbial community and C sources utilization (81% and 57%, respectively) in the forest soil, whereas great uncertainties of microbial community and C sources utilization existed in the agricultural soil with the explanatory proportion being 20% and 10%, respectively. Our findings suggest that the microbial community of forest soil is more sensitive to changing acid rain frequency than that of agricultural soil in a short term. These results support the prediction of microbes-driven C cycling dynamics in specific soil ecosystems in the context of changing acid rain frequency.

Seasonal dynamics of soil microbial diversity and functions along elevations across the treeline

Although microbial diversity patterns along elevations have been extensively studied, little is known about whether the patterns are influenced by seasonality. To test the seasonal and elevational effects on microbial communities and functions, we collected soil samples across a mountain gradient above and below the treeline in three seasons (spring, summer and autumn). Microbial diversity based on the sequencing of 16S rRNA, 18S rRNA and nifH genes was measured, and microbial functions represented by soil basal respiration and microbial biomass were analyzed. As expected, we found significant seasonal and elevational effects on microbial α- and β-diversity and functions, and the effects of elevations were greater than seasonal effects. Elevational patterns of microbial β-diversity and functions were not influenced by seasonality. However, the elevational α-diversity patterns showed by specific groups (bacteria, protist and metazoa) changed among seasons. Further, we identified key soil properties (i.e. moisture, total carbon, total nitrogen and nitrate) which had higher seasonal and elevational variations, mainly contributing to the spatiotemporal variations of microbial diversity and functions. The findings of higher soil nutrients, archaeal and metazoan richness, and microbial functions at the treeline elevation, imply a strong edge effect of treeline on microbial diversity and functions. Together, our study highlights that seasonality influences the elevational patterns of soil microbial α-diversity, rather than that of β-diversity and functions, thus provides new insights into the seasonal and elevational effects on microbial communities and functions.

Plant Growth-Promoting Rhizobacteria as a Green Alternative for Sustainable Agriculture

Environmental stress is a major challenge for sustainable food production as it reduces yield by generating reactive oxygen species (ROS) which pose a threat to cell organelles and biomolecules such as proteins, DNA, enzymes, and others, leading to apoptosis. Plant growth-promoting rhizobacteria (PGPR) offers an eco-friendly and green alternative to synthetic agrochemicals and conventional agricultural practices in accomplishing sustainable agriculture by boosting growth and stress tolerance in plants. PGPR inhabit the rhizosphere of soil and exhibit positive interaction with plant roots. These organisms render multifaceted benefits to plants by several mechanisms such as the release of phytohormones, nitrogen fixation, solubilization of mineral phosphates, siderophore production for iron sequestration, protection against various pathogens, and stress. PGPR has the potential to curb the adverse effects of various stresses such as salinity, drought, heavy metals, floods, and other stresses on plants by inducing the production of antioxidant enzymes such as catalase, peroxidase, and superoxide dismutase. Genetically engineered PGPR strains play significant roles to alleviate the abiotic stress to improve crop productivity. Thus, the present review will focus on the impact of PGPR on stress resistance, plant growth promotion, and induction of antioxidant systems in plants.

Seasonality regulates the effects of acid rain on microbial community in a subtropical agricultural soil of Southern China

Acid rain alters soil carbon (C) cycling by influencing the soil microbial community structure and functions. However, the response of soil microbial communities to acid rain with time and underlying mechanisms are still poorly understood. Herein, we conducted a one-year intact soil core experiment to investigate the temporal changes of soil microbial community composition and C sources metabolism under acid rain (pH 5.0, pH 4.0, and pH 3.0) in an agricultural soil of southern China. We found that pH 3.0 acid rain increased the total, bacterial, gram-positive bacterial, and actinomycetal PLFAs at the early stage, but this effect diminished with time. Conversely, the gram-negative bacterial PLFAs contents were reduced under pH 3.0 acid rain at the later stage. Interestingly, pH 5.0 acid rain increased the total, bacterial, gram-positive bacterial, and actinomycetal PLFAs contents at the later stage. In addition, pH 3.0 and pH 5.0 acid rain treatments accordingly altered the soil microbial community structure at the early and later stage. However, acid rain did not change the microbial C sources utilization pattern. The principal response curve analysis revealed that the seasonal variation exerted a greater effect on the overall variance of soil microbial community structure than the acidity of acid rain. Our results demonstrate the asynchronous response of soil microbial community structure and function, which implies that the microbial functional redundancy may exist in the subtropical agricultural soil under acid rain.

Microbial seasonality promotes soil respiratory carbon emission in natural ecosystems: A modeling study

Seasonality is a key feature of the biosphere and the seasonal dynamics of soil carbon (C) emissions represent a fundamental mechanism regulating the terrestrial-climate interaction. We applied a microbial explicit model-CLM-Microbe-to evaluate the impacts of microbial seasonality on soil C cycling in terrestrial ecosystems. The CLM-Microbe model was validated in simulating belowground respiratory fluxes, that is, microbial respiration, root respiration, and soil respiration at the site level. On average, the CLM-Microbe model explained 72% (n = 19, p < 0.0001), 65% (n = 19, p < 0.0001), and 71% (n = 18, p < 0.0001) of the variation in microbial respiration, root respiration, and soil respiration, respectively. We then compared the model simulations of soil respiratory fluxes and soil organic C content in top 1 m between the CLM-Microbe model with (CLM-Microbe) and without (CLM-Microbe_wos) seasonal dynamics of soil microbial biomass in natural biomes. Removing soil microbial seasonality reduced model performance in simulating microbial respiration and soil respiration, but led to slight differences in simulating root respiration. Compared with the CLM-Microbe, the CLM-Microbe_wos underestimated the annual flux of microbial respiration by 0.6%-32% and annual flux of soil respiration by 0.4%-29% in natural biomes. Correspondingly, the CLM-Microbe_wos estimated higher soil organic C content in top 1 m (0.2%-7%) except for the sites in Arctic and boreal regions. Our findings suggest that soil microbial seasonality enhances soil respiratory C emissions, leading to a decline in SOC storage. An explicit representation of soil microbial seasonality represents a critical improvement for projecting soil C decomposition and reducing the uncertainties in global C cycle projection under the changing climate.

Quarry restoration treatments from recycled waste modify the physicochemical soil properties, composition and activity of bacterial communities and priming effect in semi-arid areas

The selection of a suitable organic amendment for recovery of semi-arid soils degraded by mining is key to the success of an ecological restoration. The aim of this research is to study the short-term responses of physicochemical, biochemical and biological properties, as well as the changes of a soil bacterial community at the genus level after application of five types of organic amendments in a limestone quarry in Almería (SE, Spain). The relationship among bacterial taxa with biochemical and physicochemical properties and priming effect from restored soils was also analysed. Six months after the application of organic amendments, the values of different soil status, such as total organic carbon, total nitrogen, assimilable phosphorus and labile organic matter forms (carbohydrates and polyphenols), basal respiration (BR) and enzymatic activities increased significantly with respect to unrestored soils. Similarly, a positive priming effect of soil organic matter mineralisation was produced by all organic amendments, being significantly higher (p < 0.05) in sewage sludge-treated soils. Bacterial diversity was higher in restored than in control soils. The restoration caused changes in soil bacterial communities' composition at the phylum and genus levels. It was observed that soil bacterial communities were significantly related to several physical, chemical and biochemical soil properties, establishing two different co-occurrence patterns between restored and unrestored soils. A first bacterial co-occurrence pattern showed significant positive correlations to pH and C/N ratio and negativity with the rest of the soil properties. The second bacterial pattern was positively correlated with carbohydrates, μg of C, priming effect, BR, β-glucosidase and phosphatase and negatively with pH and C/N ratio. It was concluded that soil bacterial communities are clearly influenced by the types of organic amendments applied. Bacterial taxa such as Taibaiella or Pseudomonas could perform key functions in the carbon cycle in restored soils.

Plant community composition alters moisture and temperature sensitivity of soil respiration in semi-arid shrubland

Soil respiration (Rs) is the second largest carbon (C) flux to the atmosphere and our understanding of how Rs and its components shift with plant-community composition remains an important question. We used high-frequency soil respiration measurements and root exclusion to evaluate how Rs, autotrophic respiration (Ra) and heterotrophic respiration (Rh) vary between a semi-arid perennial shrub community and annual invasive community. Over two growing seasons, total Rs was 40% higher under annual vegetation compared to shrubs. Partitioning revealed consistently higher Ra under annual vegetation which accounted for most of the difference in Rs. Under annual vegetation, Ra increased soon after the first rain events and remained high despite cooling temperatures while shrub Ra increased only when soil temperature began to warm up. The Rh rates were similar between vegetation types when daily soil temperatures were lower than 20 °C. As soil temperatures increased and soil moisture dropped below 10%, Rh was consistently higher under annual vegetation than shrubs. Seasonal dynamics of Rs and Rh were best modeled with an interaction term between soil moisture and temperature with significantly different model parameters for each vegetation type. Differences in the timing and magnitude of Rs and Ra between vegetation types are consistent with phenological differences between shrubs and annuals. Under annuals, larger Rh at high temperatures suggests that expansion of annual vegetation and future hotter and drier conditions could lead to greater C losses from this semi-arid shrub system.

Impact of simulated acid rain on the composition of soil microbial communities and soil respiration in typical subtropical forests in Southwest China

The relationship between soil respiration (SR) and microbial community structure (MCS) is relevant to changes in forest soil ecosystem stability and chemical cycling under acid rain. Simulated acid rain treatments of pH 4.5 (control), 4.0, 3.25 and 2.5 were applied to two forest stands in the Three Gorges Reservoir Area of Jinyun Mountain, Chongqing. We used phospholipid fatty acid (PLFA) analysis to observe the MCS in the 0-10 cm soil layer and measured SR in situ from January 2016 to December 2017. Additionally, we determined the effects of soil properties on the MCS and SR. Acid rain simulation significantly increased the fungal PLFA abundance and decreased the bacterial PLFA abundance in the mixed coniferous and broad-leaved forest (CF). However, in the evergreen broad-leaved forest (BF), the abundance of bacterial and fungal PLFAs did not differ significantly among treatments. Redundancy analysis (RDA) showed that significant changes in the MSC were mainly due to the C/N ratio, hydrolysable N content, content, fine root biomass and sucrase activity. Acid rain simulation in the CF and BF significantly inhibited SR, but the SR sensitivity to simulated acid rain differed among forests. In 2017, the annual mean SR in the CF under the pH 4.0, 3.25 and 2.5 treatments decreased significantly by 6.1%, 19.2% and 28.9%, but in the BF, SR decreased significantly by 25.6% only under pH 2.5. The structural equation model showed that the relationship between the MCS and the variation in SR was closer and more direct than that with soil nutrients. The microbial community structure was an important factor driving the response of soil respiration to acid rain.

Resuscitation of the microbial seed bank alters plant-soil interactions

While microorganisms are recognized for driving belowground processes that influence the productivity and fitness of plant populations, the vast majority of bacteria and fungi in soil belong to a seed bank consisting of dormant individuals. However, plant performance may be affected by microbial dormancy through its effects on the activity, abundance, and diversity of soil microorganisms. To test how microbial seed banks influence plant-soil interactions, we purified recombinant resuscitation promoting factor (Rpf), a bacterial protein that terminates dormancy. In a factorially designed experiment, we then applied the Rpf to soil containing field mustard (Brassica rapa), an agronomically important plant species. Plant biomass was ~33% lower in the Rpf treatment compared to plants grown with an unmanipulated microbial seed bank. In addition, Rpf reduced soil respiration, decreased bacterial abundance, and increased fungal abundance. These effects of Rpf on plant performance were accompanied by shifts in bacterial community composition, which may have diluted mutualists or resuscitated pathogens. Our findings suggest that changes in microbial seed banks may influence the magnitude and direction of plant-soil feedbacks in ways that affect above- and belowground biodiversity and function.

Composition of soil bacterial and fungal communities in relation to vegetation composition and soil characteristics along an altitudinal gradient

The objective of the present study was to evaluate how altitudinal gradients shape the composition of soil bacterial and fungal communities, humus forms and soil properties across six altitude levels in Hyrcanian forests. Soil microbiomes were characterized by sequencing amplicons of selected molecular markers. Soil chemistry and plant mycorrhizal type were the two dominant factors explaining variations in bacterial and fungal diversity, respectively. The lowest altitude level had more favorable conditions for the formation of mull humus and exhibited higher N and Ca contents. These conditions were also associated with a higher proportion of Betaproteobacteria, Acidimicrobia, Acidobacteria and Nitrospirae. Low soil and forest floor quality as well as lower bacterial and fungal diversity characterized higher altitude levels, along with a high proportion of shared bacterial (Thermoleophilia, Actinobacteria and Bacilli) and fungal (Eurotiomycetes and Mortierellomycota) taxa. Beech-dominated sites showed moderate soil quality and high bacterial (Alphaproteobacteria, Acidobacteria, Planctomycetes and Bacteroidetes) and fungal (Basidiomycota) diversity. Particularly, the Basidiomycota were well represented in pure beech forests at an altitude of 1500 m. In fertile and nitrogen rich soils with neutral pH, soil quality decreased along the altitudinal gradient, indicating that microbial diversity and forest floor decomposition were likely constrained by climatic conditions.

Response of carbon and microbial properties to risk elements pollution in arctic soils

A 180-day incubation study was conducted to evaluate the effects of risk elements (REs) on organic carbon use and microbial activities in organic soils in the Arctic during the summer snowmelt period. Soils were artificially spiked with Cd, Pb, Cr, Ni, Cu, As, and a combination of these REs according to the levels measured in Arctic soils from REs-polluted industrial sites. During the incubation period, microbial activities and microbial biomass carbon (MBC) formation were inhibited, and microbial quotient (qCO2) values were relatively high in the spiked soils indicating that more energy was used by microbes for maintenance under REs stress. Meanwhile, microbial metabolism was significantly restrained. Microbial Specific phospholipid fatty acids (PLFAs) were reduced in RE spiked soils relative to the control, especially in the As- and multi-RE-spiked soils. The abundance of both fungi and bacteria was reduced in response to RE amendments by 14-24% and 1-55%, respectively. PLFA biomarkers indicated a shift in soil microbial community structure and activities influenced by REs, consequently having a negative effect on soil organic carbon degradation. This study addresses the knowledge gap regarding the alternation of biochemical reactions in Arctic soils under anthropogenic REs with relevant contamination levels.

Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world

Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa-fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils-which can vary independently of other abiotic and geographic gradients-in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.

Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiome of Sorghum bicolor

Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California's San Joaquin Valley that is under long-term cultivation with 1) standard (ST) or no tilling (NT) and 2) cover-cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal communities, versus bacterial. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. Additionally, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome and inform future efforts to configure trait-associated microbiomes in crops.Importance While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, there is very little work published on how the corresponding crop plant microbiome is impacted. With bacteria and fungi known to critically affect soil health and plant growth, we concurrently compared how the practices of no and standard tillage, in combination with either cover-cropping or fallow fields, shape soil and plant-associated microbiomes between the two classifications. In determining not only the response to treatment in microbial diversity and composition, but for activity as well, this work demonstrates the significance of agronomic practice in modulating plant-microbe interactions, as well as encourages future work on the mechanisms involved in community assemblages supporting similar crop outcomes.

Soil carbon, nitrogen and phosphorus ecological stoichiometry shifts with tree species in subalpine plantations

Understanding ecological stoichiometric characteristics of soil nutrient elements, such as carbon (C), nitrogen (N) and phosphorus (P) is crucial to guide ecological restoration of plantations in ecologically vulnerable areas, such as alpine and subalpine regions. However, there has been only a few related studies, and thus whether and how different tree species would affect soil C:N:P ecological stoichiometry remains unclear. We compared soil C:N:P ecological stoichiometry of Pinus tabulaeformis, Larix kaempferi and Cercidiphyllum japonicum to primary shrubland in a subalpine region. We observed strong tree-specific and depth-dependent effects on soil C:N:P stoichiometry in subalpine plantations. In general, the C:N, C:P and N:P of topsoil (0-10 cm) are higher than subsoil (>10 cm) layer at 0-30 cm depth profiles. The differences in C:N, N:P and C:P at the topsoil across target tree species were significantly linked to standing litter stock, tree biomass/total aboveground biomass and Margalef's index of plant community, respectively, whereas the observed variations of C:N, N:P and C:P ratio among soil profiles are closely related to differences in soil bulk density, soil moisture, the quantity and quality of aboveground litter inputs as well as underground fine root across plantations examined. Our results highlight that soil nutrients in plantation depend on litter quantity and quality of selected tree species as well as soil physical attributes. Therefore, matching site with trees is crucial to enhance ecological functioning in degraded regions resulting from human activity.

Topography and plant community structure contribute to spatial heterogeneity of soil respiration in a subtropical forest

Soil respiration is the largest carbon (C) flux from terrestrial ecosystems into the atmosphere. Accurate estimates of the magnitude and distribution of soil respiration are critically important to models of global C cycling and predictions of future climate change. One of the greatest challenges to accurate large-scale estimation of soil respiration is its great spatial heterogeneity at the site level. Our study explored how soil respiration varies in space and the drivers that lead to this variance in a natural subtropical evergreen broadleaf forest in Southern China. We conducted a two-year soil respiration measurement for 168 randomly selected sampling points in a 4 ha plot. We measured the spatial variance of soil respiration and tested its correlation to a variety of abiotic and biotic factors including topography, aboveground plant community structure, soil environmental factors, soil organic matter, and microbial community structure. We found that soil respiration was highly varied across the study plot, with a spatial variation coefficient (CV) of 32.75%. The structural equation modeling (SEM) analysis showed that elevation influenced tree species diversity, productivity, and soil water content, which in turn affected soil respiration via soil C content, clay content, fungal:bacterial ratio, annual litterfall, and fine root biomass. 31% of the total spatial variation of soil respiration was accounted for in the SEM, mostly by elevation, soil C content, annual litterfall biomass, tree species diversity as estimated by the Simpson's index, and soil water content, with standardized total effects of 0.31, -0.31, 0.29, 0.19, and -0.18, respectively. Our data demonstrated that soil respiration was highly spatially varied at the fine scale, and was primarily regulated by factors of topography and plant community structure. More studies investigating the spatial variation of soil respiration are therefore needed to better understand and assess terrestrial ecosystem C cycling.

Increasing temperature can modify the effect of straw mulching on soil C fractions, soil respiration, and microbial community composition

Straw mulching has been widely adopted in dryland cropping but its effect on soil respiration and microbial communities under warming are not well understood. Soil samples were collected from a corn field with straw mulching (SM) for nine years and without straw mulching (CK), and incubated at 15°C, 25°C, and 35°C for 60 days. Soil respiration, C fractions and bacterial and fungal community structure were measured SM had greater soil organic carbon and potential C mineralization and a similar microbial biomass carbon throughout the incubation when compared with CK. Soil respiration increased with increasing temperature and its temperature sensitivity (Q10) was lower with SM than CK. Similar microbial community composition was found in the soils with SM and CK before incubation. However, SM had a greater bacterial richness and the relative abundances of Proteobacteria, Acidobacteria, Nitrospirae, Planctomycetes, Bacteroidetes, and Basidiomycota, but lower relative abundances of Actinobacteria, Chloroflexi, and Ascomycota than CK after incubation. Bacterial richness and diversity were greater at 15°C and 25°C than 35°C, but there was no difference in fungal richness and diversity among the incubation temperatures. As temperature increased, the relative abundances of Chloroflexi, Acidobacteria, and Bacteroidetes decreased, but Gemmatimonadetes and Ascomycota increased, and were significantly correlated with soil C fractions and respiration. These findings indicated that the effect of straw mulching on soil C cycling and microbial community structure can be highly modified by increasing temperature.

Microbial taxonomic and functional attributes consistently predict soil CO2 emissions across contrasting croplands

Despite distinct roles of soil microbes in regulating carbon (C) respiration in diverse environments, it remains unclear whether microbial taxonomic and functional attributes can consistently predict soil C emissions across contrasting ecosystems. Here, we conducted a large-scale sampling event across two contrasting croplands (rice and wheat-corn crop rotation) to identify specific soil microbial phylotypes and functional genes associated with soil respiration rates. The results of structural equation modeling indicated that bacterial community composition had a strong link with C respiration rates in the two contrasting cropland types; however, this link was weaker for fungal communities. More importantly, we found that the relative abundances of bacterial Solirubrobacterales_480-2, Myxococcales_mle1-27 and fungal Westerdykella had consistently negative correlation with respiration rates across paddy and upland soils. We also identified taxa that are significantly correlated to C respiration in the paddy (e.g. Methylocaldum) and upland soils (e.g. Kribbella), respectively. Further, we found multiple associations between functional genes involved in microbial C metabolism and soil respiration rates. Our findings provide novel insights into understanding microbial predictors of soil CO₂ emissions in diverse croplands, which have important implications for improving C emission predictions in terrestrial ecosystems.

Effects of EDTA and plant growth-promoting rhizobacteria on plant growth and heavy metal uptake of hyperaccumulator Sedum alfredii Hance

Phytoremediation is a cost-effective and environment-friendly strategy for decontaminating heavy-metal-contaminated soil. However, the practical use of phytoremediation is constrained by the low biomass of plants and low bioavailability of heavy metals in soil. A pot experiment was conducted to investigate the effects of the metal chelator ethylenediaminetetraacetic acid (EDTA) and EDTA in combination with plant growth-promoting rhizobacteria (Burkholderia sp. D54 or Burkholderia sp. D416) on the growth and metal uptake of the hyperaccumulator Sedum alfredii Hance. According to the results, EDTA application decreased shoot and root biomass by 50% and 43%, respectively. The soil respiration and Cd, Pb, Zn uptake were depressed, while the photosynthetic rate, glutathione and phytochelatin (PC) contents were increased by EDTA application. Interestingly, Burkholderia sp. D54 and Burkholderia sp. D416 inoculation significantly relieved the inhibitory effects of EDTA on plant growth and soil respiration. Compared with the control, EDTA + D416 treatment increased the Cd concentration in shoots and decreased the Pb concentration in shoots and roots, but did not change the Zn concentration in S. alfredii plants. Furthermore, EDTA, EDTA + D54 and EDTA + D416 application increased the cysteine and PC contents in S. alfredii (p < 0.05); among all tested PCs, the most abundant species was PC2, and compared with the control, the PC2 content was increased by 371.0%, 1158.6% and 815.6%, respectively. These results will provide some insights into the practical use of EDTA and PGPR in the phytoremediation of heavy-metal-contaminated soil by S. alfredii.

Effects of seasonal precipitation change on soil respiration processes in a seasonally dry tropical forest

Precipitation is projected to change intensity and seasonal regime under current global projections. However, little is known about how seasonal precipitation changes will affect soil respiration, especially in seasonally dry tropical forests. In a seasonally dry tropical forest in South China, we conducted a precipitation manipulation experiment to simulate a delayed wet season (DW) and a wetter wet season (WW) over a three-year period. In DW, we reduced 60% throughfall in April and May to delay the onset of the wet season and irrigated the same amount water into the plots in October and November to extend the end of the wet season. In WW, we irrigated 25% annual precipitation into plots in July and August. A control treatment (CT) receiving ambient precipitation was also established. Compared with CT, DW significantly increased soil moisture by 54% during October to November, and by 30% during December to April. The treatment of WW did not significantly affect monthly measured soil moisture. In 2015, DW significantly increased leaf area index and soil microbial biomass but decreased fine root biomass. In contrast, WW significantly decreased fine root biomass and forest floor litter stocks. Soil respiration was not affected by DW, which could be attributed to the increased microbial biomass offsetting the decrease in fine root biomass. In contrast, WW significantly increased soil respiration from 3.40 to 3.90 μmol m-2 s-1 in the third year, mainly due to the increased litter decomposition and soil pH (from 4.48 to 4.68). The present study suggests that both a delayed wet season and a wetter wet season will have significant impacts on soil respiration-associated ecosystem components. However, the ecosystem components can respond in different directions to the same change in precipitation, which ultimately affected soil respiration.

The sensitivity of soil microbial respiration declined due to crop straw addition but did not depend on the type of crop straw

An incubation experiment was conducted to investigate whether the type of crop straw added to soil influenced the temperature sensitivity of soil microbial respiration. The soil for incubation was collected from a winter wheat-soybean rotation cropland. Five temperature levels (5, 10, 15, 20, and 25 °C), five crop straw types (soybean, peanut, rice, winter wheat, and maize), and a control (CK, no crop straw addition) were established. Soil microbial respiration rates were measured on days 1, 2, 3, 5, 7, 10, 14, 20, and 27 after crop straw addition using an infrared CO₂ analyser. Soil enzyme activities of invertase, urea, and catalase and the dissolved organic carbon (DOC) content were measured after incubation. Estimated Q₁₀ (temperature sensitivity of soil microbial respiration) ranged from 1.472 ± 0.045 to 1.970 ± 0.020 and showed no significant (P > 0.05) difference between straw addition treatments, but there was significantly (P < 0.001) higher temperature sensitivity (1.970 ± 0.020) for CK. A significant (P = 0.002) relationship was found between the Q₁₀ of cumulative soil microbial respiration and basal soil microbial respiration (soil microbial respiration at 0 °C). Moreover, a marginally significant (P < 0.1) relationship was found between the Q₁₀ at different incubation stages and basal soil microbial respiration. A quadratic function was used to explain the relationship between estimated basal microbial respiration and the lignin content. Soil microbial respiration was positively correlated with the activities of invertase, urease, and catalase and the dissolved organic carbon (DOC) content in all treatments. This study indicated that crop straw addition significantly (P < 0.001) reduced the Q₁₀ of soil microbial respiration and that the types of crop straw added to soil did not significantly (P > 0.05) change the Q₁₀ value.

Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps

We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed. Bacteria and fungi display similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae show a more patchy distribution, though still clearly stratified between taxa, which seems to be a response to both structural properties of the habitat and interaction with specific bacterial and fungal taxa. Finally, we report a high number of myxomycete OTUs not represented in a reference database from fructifications, which might represent novel species.

Phenotypic and Genotypic Diversity Among Symbiotic and Non-symbiotic Bacteria Present in Chickpea Nodules in Morocco

Environmental pollution problems and increased demand for green technologies in production are forcing farmers to introduce agricultural practices with a lower impact on the environment. Chickpea (Cicer arietinum) in arid and semi-arid environments is frequently affected by harsh environmental stresses such as heat, drought and salinity, which limit its growth and productivity and affect biological nitrogen fixation ability of rhizobia. Climate change had further aggravated these stresses. Inoculation with appropriate stress tolerant rhizobia is necessary for an environmentally friendly and sustainable agricultural production. In this study, endophytic bacteria isolated from chickpea nodules from different soil types and regions in Morocco, were evaluated for their phenotypic and genotypic diversity in order to select the most tolerant ones for further inoculation of this crop. Phenotypic characterization of 135 endophytic bacteria from chickpea nodules showed a wide variability for tolerance to heavy metals and antibiotics, variable response to extreme temperatures, salinity, pH and water stress. 56% of isolates were able to nodulate chickpea. Numerical analysis of rep-PCR results showed that nodulating strains fell into 22 genotypes. Sequencing of 16S rRNA gene of endophytic bacteria from chickpea nodules revealed that 55% of isolated bacteria belong to Mesorhizobium genus. Based on MLSA of core genes (recA, atpD, glnII and dnaK), tasted strains were distributed into six clades and were closely related to Mesorhizobium ciceri, Mesorhizobium opportunistum, Mesorhizobium qingshengii, and Mesorhizobium plurifarium. Most of nodulating strains were belonging to a group genetically distinct from reference Mesorhizobium species. Three isolates belong to genus Burkholderia of the class β- proteobacteria, and 55 other strains belong to the class γ- proteobacteria. Some of the stress tolerant isolates have great potential for further inoculation of chickpea in the arid and semiarid environments to enhance biological nitrogen fixation and productivity in the context of climate change adaptation and mitigation.

Warming but Not Nitrogen Addition Alters the Linear Relationship Between Microbial Respiration and Biomass

Soil contains a large amount of organic matter, which constitutes the largest terrestrial carbon pool. Heterotrophic or microbial respiration (R_h) that results from microbial decomposition of soil organic carbon (SOC) constitutes a substantial proportion of soil C efflux. Whether soil microbial biomass is of primary importance in controlling R_h remains under debate, and the question of whether the microbial biomass-decomposition relationship changes with warming and nitrogen (N) deposition has rarely been assessed. We conducted an incubation experiment to test the relationship between R_h and the size of soil microbial communities in two layers of soil collected from a natural subtropical forest and to examine whether the relationship was affected by changes in temperature and by added N in different forms. The results showed that regardless of the added N species, the N load did not significantly affect R_h or the size of the soil microbial communities. These results could be due to a long-term N-rich soil condition that acclimates soil microbial communities to resist N inputs into the studied forest; however, warming may significantly stimulate SOC decomposition, reducing soil microbial biomass under high temperatures. A significant linear soil microbial biomass-decomposition relationship was observed in our study, with the coefficients of determination ranging from 54 to 70%. Temperature rather than N additions significantly modified the linear relationship between soil microbial biomass and respiration. These results suggest that warming could impose a more substantial impact than N addition on the relationship between soil microbial biomass and SOC decomposition.

Climate-driven reduction of genetic variation in plant phenology alters soil communities and nutrient pools

We examined the hypothesis that climate-driven evolution of plant traits will influence associated soil microbiomes and ecosystem function across the landscape. Using a foundation tree species, Populus angustifolia, observational and common garden approaches, and a base population genetic collection that spans 17 river systems in the western United States, from AZ to MT, we show that (a) as mean annual temperature (MAT) increases, genetic and phenotypic variation for bud break phenology decline; (b) soil microbiomes, soil nitrogen (N), and soil carbon (C) vary in response to MAT and conditioning by trees; and (c) with losses of genetic variation due to warming, population-level regulation of community and ecosystem functions strengthen. These results demonstrate a relationship between the potential evolutionary response of populations and subsequent shifts in ecosystem function along a large temperature gradient.

Adaptation of soil microbial growth to temperature: Using a tropical elevation gradient to predict future changes

Terrestrial biogeochemical feedbacks to the climate are strongly modulated by the temperature response of soil microorganisms. Tropical forests, in particular, exert a major influence on global climate because they are the most productive terrestrial ecosystem. We used an elevation gradient across tropical forest in the Andes (a gradient of 20°C mean annual temperature, MAT), to test whether soil bacterial and fungal community growth responses are adapted to long-term temperature differences. We evaluated the temperature dependency of soil bacterial and fungal growth using the leucine- and acetate-incorporation methods, respectively, and determined indices for the temperature response of growth: Q₁₀ (temperature sensitivity over a given 10oC range) and T_min (the minimum temperature for growth). For both bacterial and fungal communities, increased MAT (decreased elevation) resulted in increases in Q₁₀ and T_min of growth. Across a MAT range from 6°C to 26°C, the Q₁₀ and T_min varied for bacterial growth (Q_10-20  = 2.4 to 3.5; T_min  = -8°C to -1.5°C) and fungal growth (Q_10-20  = 2.6 to 3.6; T_min  = -6°C to -1°C). Thus, bacteria and fungi did not differ significantly in their growth temperature responses with changes in MAT. Our findings indicate that across natural temperature gradients, each increase in MAT by 1°C results in increases in T_min of microbial growth by approximately 0.3°C and Q_10-20 by 0.05, consistent with long-term temperature adaptation of soil microbial communities. A 2°C warming would increase microbial activity across a MAT gradient of 6°C to 26°C by 28% to 15%, respectively, and temperature adaptation of microbial communities would further increase activity by 1.2% to 0.3%. The impact of warming on microbial activity, and the related impact on soil carbon cycling, is thus greater in regions with lower MAT. These results can be used to predict future changes in the temperature response of microbial activity over different levels of warming and over large temperature ranges, extending to tropical regions.

Cross-biome patterns in soil microbial respiration predictable from evolutionary theory on thermal adaptation

Climate warming may stimulate microbial metabolism of soil carbon, causing a carbon-cycle-climate feedback whereby carbon is redistributed from the soil to atmospheric CO₂. The magnitude of this feedback is uncertain, in part because warming-induced shifts in microbial physiology and/or community composition could retard or accelerate soil carbon losses. Here, we measure microbial respiration rates for soils collected from 22 sites in each of 3 years, at locations spanning boreal to tropical climates. Respiration was measured in the laboratory with standard temperatures, moisture and excess carbon substrate, to allow physiological and community effects to be detected independent of the influence of these abiotic controls. Patterns in respiration for soils collected across the climate gradient are consistent with evolutionary theory on physiological responses that compensate for positive effects of temperature on metabolism. Respiration rates per unit microbial biomass were as much as 2.6 times higher for soils sampled from sites with a mean annual temperature of -2.0 versus 21.7 °C. Subsequent 100-d incubations suggested differences in the plasticity of the thermal response among microbial communities, with communities sampled from sites with higher mean annual temperature having a more plastic response. Our findings are consistent with adaptive metabolic responses to contrasting thermal regimes that are also observed in plants and animals. These results may help build confidence in soil-carbon-climate feedback projections by improving understanding of microbial processes represented in biogeochemical models.

Effect of climate change on humic substances and associated impacts on the quality of surface water and groundwater: A review

Humic substances (HS), a highly transformed part of non-living natural organic matter (NOM), comprise up to 70% of the soil organic matter (SOM), 50-80% of dissolved organic matter (DOM) in surface water, and 25% of DOM in groundwater. They considerably contribute to climate change (CC) by generating greenhouse gases (GHG). On the other hand, CC affects HS, their structure and reactivity. HS important role in global warming has been recognized and extensively studied. However, much less attention has been paid so far to effects on the freshwater quality, which may result from the climate induced impact on HS, and HS interactions with contaminants in soil, surface water and groundwater. It is expected that an increased temperature and enhanced biodegradation of SOM will lead to an increase in the production of DOM, while the flooding and runoff will export it from soil to rivers, lakes, and groundwater. Microbial growth will be stimulated and biodegradation of pollutants in water can be enhanced. However, there may be also negative effects, including an inhibition of solar disinfection in brown lakes. The CC induced desorption from soil and sediments, as well as re-mobilization of metals and organic pollutants are anticipated. In-situ treatment of surface water and groundwater may be affected. Quality of the source freshwater is expected to deteriorate and drinking water production may become more expensive. Many of the possible effects of CC described in this article have yet to be explored and understood. Enormous potential for interesting, multidisciplinary studies in the important research areas has been presented.

Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes

More than 200 years ago, Alexander von Humboldt reported that tropical plant species richness decreased with increasing elevation and decreasing temperature. Surprisingly, coordinated patterns in plant, bacterial, and fungal diversity on tropical mountains have not yet been observed, despite the central role of soil microorganisms in terrestrial biogeochemistry and ecology. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria, and fungi follow similar biogeographical patterns with shared environmental drivers. We found coordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional dissimilarity among communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of coordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi, and plants. These findings suggest that interrelated and fundamental patterns of plant and microbial communities with shared environmental drivers occur across landscape scales. These patterns are revealed where soil pH is relatively constant, and have implications for tropical forest communities under future climate change.