Soil Microbial Abundance Research Articles

Legacy effects of earthworms on soil microbial abundance, diversity, and community dynamics

The earthworm species Lumbricus terrestris L. feeds on plant litter mixed with surrounding soil. Here, we analyzed with a mesocosm approach and soil incubations how that activity and subsequent ageing of casts (feces) affects the abundance and diversity of the soil microbiome. Earthworms were fed either with straw of sainfoin (SA, Onobrychis viciifolia; C/N ratio 22) or winter wheat (WW, Triticum aestivum, C/N ratio 101). The gut transit increased the abundances of bacteria and fungi, but reduced archaea. As indicated at the DNA and RNA level, main beneficiaries of the facilitated access to nutrients were members of Bacteroidota, especially Flavobacteriales with an estimated generation time of only 2 h. While Alphaproteobacteria were reduced, Gammaproteobacteria also increased in abundance and activity. SA was more nutritious for L. terrestris, and supported a higher bacterial abundance, probably because more N was available for growth and denitrification. During cast ageing, prokaryotic community compositions became increasingly similar to bulk soil communities. However, they remained distinguishable even after 168 d, suggesting that effects can last beyond a vegetation period. Dry-wet conditions preserved these differences better than continuous moisture. During ageing, more complex prokaryotic networks were detected with WW and dry-wet conditions. Thus, N and water limitations appeared to enhance cooperation rather than competition between the prokaryotes. Overall, this study demonstrates that earthworm soil interactions strongly affect the diversity and temporal dynamics of the soil microbiome. Legacy effects of earthworm activities should thus be kept in mind when investigating the environmental variation of soil microbiomes.

Effect of an organophosphorus insecticide, soil texture and earthworm species on the turnover of soil, gut and cast microbiota during the earthworm's gut transit

The growing usage of plant protection products in agroecosystems questions their unintentional deleterious effects on non-target organisms such as earthworms and their related ecological function. The aim of this study was to investigate the turnover of soil microbiota during the gut transit of two endogeic earthworms (Aporrectodea caliginosa and Allolobophora chlorotica) and how it is possibly affected by the organophosphorus insecticide ethyl-parathion (Pt). We measured prokaryotic and micro-eukaryotic community composition and abundances using two different soil types in the continuum of bulk soil, gut and casts samples collected during and after one week exposure to Pt. The presence of earthworm and Pt had limited effects on the soil microbiota, although Pt altered temporarily soil microbial abundances in the presence of earthworms, not in their absence. The earthworms’ gut harbored a remarkably low prokaryotic diversity, dominated by two molecular Operational Taxonomic Units (mOTUs) affiliated to Rhodococcus and Pseudarthrobacter. Contrastingly, gut micro-eukaryotic communities were maintained at diversity levels similar to that of the soil, yet Pt augmented their diversity and changed their composition. Fresh casts collected out of the soil revealed evident variation of abundance, diversity and community composition according to the soil origin and the earthworm species. In particular, following gut transit casts were enriched with Bacteroidia and γ-Proteobacteria while depleted of Acidobacteria. Exposure to Pt increased the diversity and relative abundance of depleted mOTUs, which paves the way for future investigations on the role of Pt in rising microbial consumption due to an over-excitation of gastrointestinal motility.

Seasonal soil moisture thresholds inhibit bacterial activity and decomposition during drought in a tallgrass prairie

Soil moisture reductions during drought often inhibit soil microbial activity and inhibit decomposition rates by reducing microbial biomass or by altering microbial communities. Evidence suggests that soil water must drop below a critical threshold to inhibit microbial activity. Thus, it is likely that the seasonal timing of drought will determine the extent to which belowground processes are adversely impacted by drought. Specifically, the effects of drought might be minimal during cool, wet periods typical of late spring but dramatic during hot summer months with high evapotranspiration rates that lower soil moisture levels below the critical threshold. Here, we present results from a study designed to quantify the effect of drought on soil microbial abundance, community composition, and soil water diffusion across four months, and to then assess how drought impacts the microbial decomposition of leaf matter. We imposed a season‐long drought in a Wisconsin tallgrass prairie and measured soil moisture, bacterial composition and abundance, microbial respiration, and decomposition rates throughout the growing season. Bacterial communities varied considerably among dates, but drought did not affect either bacterial abundance or community composition. Microbial respiration declined significantly during periods of drought when soil pores likely became hydrologically isolated, ultimately reducing cumulative microbial respiration by 10%. The reduction in microbial activity in drought treatments caused a 50% decline in the decomposition of refractory material. Our study highlights that sublethal effects of drought on microbial communities, occurring only when soil moisture declined below a tolerance threshold, can have large impacts on microbial carbon release or decomposition, highlighting the need to incorporate such measures into future studies.

Organic amendments enhance transpiration efficiency of corn plants via changes in soil microbial abundance and leaf hormones

Organic amendments enhance transpiration efficiency of corn plants via changes in soil microbial abundance and leaf hormones

Seasonal trends in lysogeny in an Appalachian oak-hickory forest soil.

Since 1989, investigations into viral ecology have revealed how bacteriophages can influence microbial dynamics within ecosystems at global scales. Most of the information we know about temperate phages, which can integrate themselves into the host genome and remain dormant via a process called lysogeny, has come from research in aquatic ecosystems. Soil environments remain under-studied, and more research is necessary to fully understand the range of impacts phage infections have on the soil bacteria they infect. The aims of this study were to compare the efficacy of different prophage-inducing agents and to elucidate potential temporal trends in lysogeny within a soil bacterial community. In addition to mitomycin C and acyl-homoserine lactones, our results indicated that halosulfuron methyl herbicides may also be potent inducing agents. In optimizing chemical induction assays, we determined that taking steps to reduce background virus particles and starve cells was critical in obtaining consistent results. A clear seasonal trend in inducible lysogeny was observed in an Appalachian oak-hickory forest soil. The average monthly air temperature was negatively correlated with inducible fraction and burst size, supporting the idea that lysogeny provides a mechanism for phage persistence when temperatures are low and host metabolism is slower. Furthermore, the inducible fraction was negatively correlated with both soil bacterial and soil viral abundance, supporting the idea that lysogeny provides a mechanism for temperate phage persistence when host density is lower. The present study is the first of its kind to reveal clear seasonal trends in inducible lysogeny in any soil.IMPORTANCELysogeny is a relationship in which certain viruses that infect bacteria (phages) may exist within their bacterial host cell as a segment of nucleic acid. In this state, the phage genome is protected from environmental damage and retains the potential to generate progeny particles in the future. It is thought that lysogeny provides a mechanism for long-term persistence for phages when host density is low or hosts are starved-two conditions likely to be found in soils. In the present study, we provide the first known evidence for a seasonal trend in lysogeny in a forest soil. Based on clear relationships observed between lysogeny, temperature, and soil microbial abundance, we find support for previous hypotheses regarding the factors governing lysogeny.

Inoculation with a microbial consortium increases soil microbial diversity and improves agronomic traits of tomato under water and nitrogen deficiency.

Microbial-based biostimulants, functioning as biotic and abiotic stress protectants and growth enhancers, are becoming increasingly important in agriculture also in the context of climate change. The search for new products that can help reduce chemical inputs under a variety of field conditions is the new challenge. In this study, we tested whether the combination of two microbial growth enhancers with complementary modes of action, Azotobacter chroococcum 76A and Trichoderma afroharzianum T22, could facilitate tomato adaptation to a 30% reduction of optimal water and nitrogen requirements. The microbial inoculum increased tomato yield (+48.5%) under optimal water and nutrient conditions. In addition, the microbial application improved leaf water potential under stress conditions (+9.5%), decreased the overall leaf temperature (-4.6%), and increased shoot fresh weight (+15%), indicating that this consortium could act as a positive regulator of plant water relations under limited water and nitrogen availability. A significant increase in microbial populations in the rhizosphere with applications of A. chroococcum 76A and T. afroharzianum T22 under stress conditions, suggested that these inoculants could enhance soil microbial abundance, including the abundance of native beneficial microorganisms. Sampling time, limited water and nitrogen regimes and microbial inoculations all affected bacterial and fungal populations in the rhizospheric soil. Overall, these results indicated that the selected microbial consortium could function as plant growth enhancer and stress protectant, possibly by triggering adaptation mechanisms via functional changes in the soil microbial diversity and relative abundance.

Comparison of soil microbial abundances and co-occurrence networks in the volcanic soil of the cone and crater

Volcanism changes the earth's surface building environments where new ecosystems can be constructed. However, the effects of volcanic environmental conditions (e.g. soil moisture, soil organic matter, and available K) on soil microbial communities remains unclear. In the present study, soil samples were collected from two natural habitats (the cone and crater) in Nushan Volcano, China, to investigate the abundances (absolute and relative), compositions, and functions of soil bacterial and fungal communities. The results showed higher 16S rRNA copies, and ITS rRNA copies in the crater compared to the cone. The bacterial and fungal diversities in the crater were higher than in the cone. The soil of the cone and crater displayed distinct bacterial and fungal community compositions based on the nonmetric multidimensional scaling (NMDS). Co-occurrence network analysis revealed the interspecific relationship of soil bacterial and fungal communities was closer in the cone with more links. The number of keystone taxa in the cone was higher than that in the crater. Meanwhile, Nordella and Arthrobacter in bacteria and Stilbella, Tausonia, and Marasmius in fungi were found as the keystone taxa. Moreover, structural equation models (SEM) revealed that soil physicochemical properties had the greatest impact on the composition of bacteria and fungi. Overall, the results advance further research on the effects of microbes on the functions and services of associated ecosystems in extreme environments.

Fostering sustainable banana cultivation: Maximizing red soil performance with lignin-based humic acid liquid fertilizer

A novel lignin-based humic acid liquid fertilizer (LHF) was prepared by supplementing traditional humic acid fertilizer with lignin. The impact of LHF treatments in two distinct red soils was assessed through examination of soil nutrient content, enzyme activity, microbial abundance, and banana biomass. Compared to the conventional composite liquid fertilizer (CF) treatment, LHF treatment improved soil nutrients, including ammonium nitrogen, nitrate nitrogen, available nitrogen, available phosphorus, and organic matter. These improvements correlated with shifts in enzymatic activities and increases in microbial populations. The LHF treatments significantly promoted nutrient uptake in banana seedlings, and consequently, accelerated growth. This system allowed for precise determination of correlations between soil physicochemical properties and soil microorganisms, increasing our fundamental understanding of the impact of soil fertilization on microbial communities. The integration of lignin into liquid fertilizers represents a step forward in the research and development of high-efficiency fertilizers. Through the improvement of soil fertility and nutrient uptake, lignin application has the potential to significantly contribute to the advancement of sustainable agriculture.

Soil Chemical Properties and Microbial Behavior under Short-Term Organic and Mineral Fertilization within Different Crops

Agronomic practices can have a negative impact on soil health and quality and ecosystem resilience. The objectives of the study were (1) to evaluate the soil chemical properties and microbial abundance under short-term application of organic and mineral fertilizers and different cultivated crops and (2) to observe the antifungal efficacy of microorganisms isolated from the studied soil. A field trial was conducted in the 2021–2022 period on a preluvosoil-type soil in four randomized blocks with eight fertilizer treatments based on manure compost (MC) and MC + mineral fertilizer (V1—control-soil; V2—NPK only; V3—15 t/ha MC; V4—15 t/ha MC + NPK; V5—30 t/ha MC; V6—30 t/ha MC + NPK; V7—60 t/ha MC; and V8—60 t/ha MC +NPK) and four crops (winter wheat—Triticum aestivum L., maize—Zea mays L., soybean—Glycine max L., and a mixture of perennial grasses and legumes). In almost all treatments, the soil pH decreased during the summer–autumn period. The organic carbon (Corg) and humus contents increased compared to the initial state of the soil after the application of different doses of MC and MC + NPK fertilization in almost all treatments. The microbial load of the soil was influenced by the fertilization regime and crop species, but there were no significant differences between the variants. The highest bacterial load was recorded in soil cultivated with a mixture of perennial grasses and grain legumes, i.e., in the variant with 15 t/ha MC, followed by soil cultivated with maize and fertilized with 30 t/ha and 60 t/ha MC. A higher number of fungi was observed in the mixture of perennial grasses and legumes, and Rhizobium population was higher, especially in the winter wheat plots, despite the fertilization regime. The antifungal efficacy of the microorganisms isolated from the samples was medium to low, except in the winter wheat experiment, where the efficacy against Fusarium culmorum was medium to high and against other pathogens was medium. In the other crops within the experiment, the antagonistic activity of the soil microorganisms was medium to low.

Effects of tillage practices on soil organic carbon, microbial community and necromass in a double rice cropping system

No-tillage (NT) can enhance the accumulation of soil organic carbon (SOC), thereby aiding in climate change mitigation and improving soil fertility. However, the relations of soil microbial abundance, composition, and necromass to SOC increase under NT are still unclear, limiting the knowledge of SOC stabilization. We performed a 5-year paddy field experiment in southern China including NT, reduced tillage (RT) and conventional tillage (CT). Soil microbial necromass C (MC, including fungal and bacterial necromass C, FC, and BC) were analyzed, as well as soil bacterial and fungal community composition. At a depth of 0–10 cm, NT increased FC (by 48.6 %–50.2 %, P < 0.05), BC (28.6 %–41.7 %), and MC (38.5 %–45.1 %, P < 0.05) but did not significantly alter the FC/BC and MC/SOC ratios. The increase rate of MC (NT vs. CT and RT) was 12.8–16.2 % higher than that of total SOC. Compared with 0–10 cm and 10–20 cm, the MC/SOC ratio was 12.5 %–14.1 % lower at 20–30 cm. Linear regression indicated significant positive correlations of SOC with MC, BC, and FC, whereas no significant correlation was found between bacterial (or fungal) α-diversity (expressed by Shannon index) and BC (or FC). The Random Forest Model showed that several important fungal and bacterial Amplicon Sequence Variants (ASVs) explained 14 %–73 % of the FC and BC variations. Therefore, the composition of the microbial community may play a pivotal role in driving the accumulation of MC. Short-term NT in rice paddies resulted in increased levels of both MC and SOC. Notably, the rate of increase in MC exceeded that of SOC, suggesting the potential for SOC stabilization.

Effects of Continuous Manure Application on the Microbial Community and Labile Organic Carbon Fractions

The application of organic materials contributes to the sustainable development of agriculture. Increased manure inputs have a fundamental effect on the composition and dynamics of soil organic carbon (SOC). In this study, we conducted a 10-year field experiment in Changchun, Jilin, Northeast China, to investigate the effects of manure addition on soil organic carbon components and soil microorganisms. Specifically, we established four treatments: (i) chemical fertilizer or no addition of manure (CK), (ii) pig manure with chemical fertilizer (ZF), (iii) cow manure with chemical fertilizer (NF), and (iv) chicken manure with chemical fertilizer (JF). The results showed that the JF treatment significantly increased the soil organic carbon (SOC), dissolved organic carbon (DOC), and readily oxidized organic carbon (ROC) content by 20.36%, 105.9%, and 61.32%, respectively, relative to CK. The microbial biomass carbon (MBC) content in JF, ZF, and NF treatments were significantly higher than that of CK, which increased by 107.24%, 116.45%, and 96.71%, respectively. The particulate organic carbon (POC) content in NF and JF treatments differed significantly, increasing by 25.61% and 19.01%, respectively, relative to CK. Redundancy analysis showed that continuous manure application had a positive effect on soil microbial community diversity and abundance, which was favorable for the accumulation of soil carbon. We also found that soil fungi were more sensitive than bacteria to changes in soil carbon composition following manure application. In conclusion, adding different organic materials can better support biodiversity conservation and realize ecosystem services of surface carbon storage and soil conservation. Our results reveal the importance of microbial fixation in soil carbon dynamics according to the different distribution of active organic carbon pools, which will help enhance our understanding of the carbon cycle.

Correlation between rhizosphere environment and content of medicinal components of Arnebia euchroma

This study aimed to explore the correlation between rhizosphere soil microorganisms of wild Arnebia euchroma and the content of medicinal components to provide guidance for the selection of the ecological planting base. The total DNA of rhizosphere soil microorganisms of wild A. euchroma was extracted, and the microbial community structure of rhizosphere soil microorganisms was analyzed by IlluminaMiseq high-throughput sequencing technology. The content of total hydroxynaphthoquinone pigment and β,β'-dimethylacrylalkannin in medicinal materials was determined by high-performance liquid chromatography(HPLC). The physicochemical pro-perties of rhizosphere soil of wild A. euchroma in main producing areas were determined, and the correlation of soil microbial abundance with index component content and soil physicochemical properties was analyzed by SPSS software. The results showed that the species composition of rhizosphere fungi and bacteria in A. euchroma from different habitats was similar at the phylum and genus levels, but their relative abundance, richness index(Chao1), and community diversity(Simpson) index were different. Correlation analysis showed that the content of available phosphorus in soil was positively correlated with the content of total hydroxynaphthoquinone pigment and β,β'-dimethylacrylalkannin, and the abundance of five fungal genera such as Solicoccozyma and six bacterial genera such as Pseudo-nocardia and Bradyrhizobium was positively correlated with the content of medicinal components in medicinal materials. The abundance of Bradyrhizobium was significantly positively correlated with the content of β,β'-dimethylacrylalkanin. The abundance of fungi such as Archaeorhizomyces was significantly positively correlated with the content of available phosphorus in rhizosphere soil, and Bradyrhizobium was significantly negatively correlated with soil pH. Therefore, the abundance of fungi and bacteria in the rhizosphere of A. euchroma has a certain correlation with the medicinal components and the physicochemical properties of the rhizosphere soil, which can provide a scientific basis for the selection of ecological planting bases in the later stage.

Evaluation of agricultural soil health after applying atrazine in maize-planted fields based on the response of soil microbes

Soil health is closely linked to the sustainable development of agriculture, and soil microorganisms are the fundamental and pivotal components in maintaining soil health. Atrazine (ATZ) is a triazine herbicide widely used worldwide, and its ecotoxicity to soil microorganisms has been widely studied. However, previous studies have focused on investigating the ecotoxicity of ATZ active ingredients under laboratory conditions. The damage caused by ATZ formulations to soil health in the actual field environment cannot be ignored. Herein, the toxicity of ATZ formulations (1140 and 1710 g hm−2) in maize fields after 1, 28, and 72 d of exposure was investigated in terms of soil microbial abundance, community structure, soil enzyme activities, functional gene abundance, and ATZ residues. The results showed that ATZ disturbed the microbial functions that maintain soil health by disturbing soil nutrient and carbon cycling as well as enhancing pollution degradation. The promotion of both urease activity and AOB-amoA gene abundance indicated that ATZ accelerated the loss of nitrogen from soil, which was detrimental to soil nitrogen cycling. The abundances of the Pontibacter genus and the cbbLG gene were inhibited, indicating that the ability of soil carbon dioxide fixation was hindered. The abundance of Lysobacter, which helps to degrade pollutants, increased. The integrated biomarker response indicated that the comprehensive toxicity of ATZ to soil microorganisms increased with dose. Additionally, the DT50 of ATZ in agricultural soil was 5.4–5.7 d, and the residual level of ATZ in crop grains was in line with the maximum residue limit recommended by the European Union and China. The findings of the present study reflect the effects of ATZ formulation on soil microbes in the actual agricultural environment and provide insights into the mechanisms of soil health regulation mediated by microorganisms.

Comparison of Soil Microbial Community between Managed and Natural Vegetation Restoration along a Climatic Gradient in Karst Regions

Managed and natural vegetation restorations are two vital measures of land restoration; however, their effects on soil microbial communities at a large scale are not clearly understood. Hence, changes in the microbial community composition after 15 years of vegetation restoration along a climatic gradient in the subtropical karst region of Southwest China were assessed based on phospholipid fatty acids (PLFAs) profiles. Managed (plantation forest) and natural (naturally recovered to shrubbery) vegetation restoration types were compared, with cropland and mature forest serving as controls. Soil microbial community abundance was significantly higher under the two vegetation restoration types than in the cropland; however, it was lower than in the mature forest. The abundance, composition, and structure of soil microbial communities did not differ significantly between plantation forest and shrubbery. Soil organic carbon or total nitrogen was the primary factor positively affecting soil microbial abundance, whereas the mean annual temperature (MAT) was recognized as the primary factor contributing to the variation in the soil microbial community structure. Moreover, temperature had opposite effects on different indicators of microbial community structure. That is, it positively and negatively affected the ratios of gram-positive to gram-negative bacterial PLFAs (GP:GN) and fungal to bacterial PLFAs (F:B), respectively. Our results show that both vegetation restoration types have the ability to improve soil productivity in karst areas. Furthermore, shifts in soil microbial community structure (GP:GN and F:B ratios) induced by warming are likely to lead to a higher proportion of labile carbon, which is sensitive to soil tillage. Hence, more attention should be paid to ecological restoration in warmer karst areas to alleviate the severe loss of soil carbon in croplands.

Dissolved organic matter movements from forests influence downstream soil CO2 flux during thawing

Soil CO2 flux is critical for atmospheric carbon emissions and is highly influenced by soil respiration. Dissolved organic matter (DOM) from upland forests can transport to downstream wetlands and then influence soil respiration during thawing. Current studies have mainly focused on a uniform forest or wetland, whereas the soil CO2 flux changing characteristics affected by watershed DOM movements within the forest wetland catchment during thawing are rarely understood. In this study, the in situ measurement, field sampling, and multiple analysis methods were adopted. First, the soil CO2 flux and soil respiration rates were acquired by eddy covariance tower and portable greenhouse analyzer, respectively. The higher soil CO2 flux occurred during thawing might be partly attributed to the bursts of stored CO2. Then, the relationship between dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) concentrations in water samples, and soil CO2 flux was analyzed by linear regression analysis. DOM from forests can be transported to downstream wetlands via surface runoff, and then promotes soil CO2 flux during thawing. Finally, the soil microbial abundances near the in situ measured sites of forests and wetlands were also compared with the corresponding soil respiration rates. LMWs contains in DOM inputs may influence soil respiration rates by altering soil microbial abundance. Overall, watershed DOM movement from forests can influence downstream soil CO2 flux during thawing in which microbes might exert effects via altering soil respiration rates.

Methane gas emissions (CH4) in paddy fields in Minasatene District, Pangkep Regency: Microbial abundance against increased methane gas

Global warming caused by various human activities results in increased concentrations of Greenhouse Gas (GHG) emissions. This causes the problem of climate change. One of the sources of Indonesia’s greenhouse gas (GHG) emissions comes from the agricultural sector. Methane (CH4) is the second most important greenhouse gas and has a global warming potential 25 times greater than CO2. Paddy fields contribute to GHG emissions due to the condition of the rice fields which are always flooded which produce gases such as CO2, N2O and Methane (CH4). This study aims to determine the effect of microbial abundance on increasing emissions of methane gas (CH4) in paddy fields. This research was conducted by collecting samples in the field with variations at 30th, 60th, and 90th day after planting (DAP). The results of laboratory analysis showed that the results of C-Organic analysis were 1.45-2.56%, the results of soil microbial abundance analysis for the total bacterial population ranged from 1.2 x 104 - 6.3 x 105 (CFU/g) and the results of analysis flux of CH4 at 30thDAP sampling from the three sample points ranged from 2.13 - 11.29 (mg/m2/hour). For the 60thDAP sample from the three sample points it ranges from 10.01 - 22.77 (mg/m2/hour). For the 90thDAP sample from the three sample points it ranges from 21.98 - 25.54 (mg/m2/hour). The results of the analysis of methane (CH4) emissions in one growing season show different values of methane emissions at different locations and sampling times.

Diluted pyroligneous vinegar promoted Rhododendron growth by changing functional genes involved in N cycling in the rhizosphere

Excessive chemical fertilization in protected horticulture has caused nutrient accumulation, reduction of soil biodiversity, and subsequently soil degradation. Pyroligneous vinegar is a byproduct of pyrolysis for biochar production. While there has been an increase in interest in using pyroligneous vinegar as an amendment to improve soil quality, a paucity of data exists of its effect on the growth of acidophilous plants such as azalea (Rhododendron). To address this, we investigated the changes in the growth of azalea and soil microbial abundance, specifically those involved in nitrogen cycling in the rhizosphere with amendment of conventional inorganic NPK fertilizer (NPK) and four dilutions of pyroligneous vinegar each with matched NPK content. The results showed that the treatments of pyroligneous vinegar increased plant biomass (51%-99%), root length (29%-81%) and surface area (63%-151%), and nitrogen use efficiency (83%-299%) compared to NPK alone. The pyroligneous vinegar treatments decreased soil pH and increased the contents of rhizosphere soil dissolved organic carbon and nitrate, and changed potential denitrification activity. Compared with NPK, pyroligneous vinegar increased archaeal and bacterial amoA genes (AOA and AOB) abundances (45% − 79% and 39% − 75%, respectively) in nitrification, but inhibited the denitrification gene abundances (i.e. nirS and nirK abundance up to 21% lower). Pyroligneous vinegar increased the ratio of nosZ/(nirS + nirK), suggesting an increased potential to lower nitrous oxide emissions.Correlation analysis indicated that nitrogen use efficiency correlated positively with AOA and AOB, but negatively with nirS and nirK abundance. Therefore, our study suggests that pyroligneous vinegar could improve the growth of acidophilous plants and increase their nitrogen use efficiency by changing nitrogen cycling related functional genes, and could be a potential soil amendment in protected horticulture.

Roots exert greater influence on soil respiration than aboveground litter in a subalpine Cambisol

Aboveground plant litter and roots are primary sources of soil organic carbon (SOC), profoundly affecting soil respiration and SOC dynamics. With global change, the quantities of aboveground plant litter and root inputs into soil are changing in the subalpine region; however, the impacts of these changes on soil respiration and the quantity and quality of SOC remain unclear. Here, a three-year detritus input and removal treatment (DIRT) experiment that included six treatments (namely, control, CK; double litter, DL; litter removal, NL; root exclusion, NR; root exclusion plus double litter, NRDL; and root exclusion plus litter removal, NRNL) was conducted in a subalpine Cambisol on the eastern edge of the Tibetan Plateau to assess the different effects of aboveground litter and roots on soil respiration and the quantity and quality of SOC dynamics. Among the treatments, the mean soil respiration in NL, NR and NRNL treatments significantly decreased by 21.7%, 31.9% and 40.5%, respectively, compared to the CK treatment. When with intact roots, double litter (DL) had a positive impact on soil respiration, resulting in a 13.2% increase in soil respiration compared to the CK treatment. In contrast, when with root exclusion (in the absence of roots), combined root exclusion and litter addition (NRDL) hardly influence soil respiration compared with the NR treatment, resulting in a 30.5% decrease in soil respiration. The soil respiration, labile SOC content and the abundance of soil microbes exhibited similar patterns among treatments. Roots excluded (NR, NRDL, NRNL) exerted a stronger effects on soil respiration, temperature sensitivity of soil respiration (Q10), labile SOC content and the recalcitrance index of carbon (RIC) than aboveground plant litter manipulation (CK, DL, NL). Correlation analysis and redundancy analysis revealed that soil respiration and its Q10 were regulated by the quantity and quality of SOC substrates and the abundance of soil microbes. Our results highlighted that roots exerted greater influence on the quantity and quality of SOC, the abundance of soil microbes, soil respiration and its Q10 than aboveground litter manipulation in subalpine Cambisol in response to future climate scenarios, especially the mediating effect of the presence of roots on the function of aboveground plant litter.

Linking niche size and phylogenetic signals to predict future soil microbial relative abundances.

Bacteria provide ecosystem services (e.g., biogeochemical cycling) that regulate climate, purify water, and produce food and other commodities, yet their distribution and likely responses to change or intervention are difficult to predict. Using bacterial 16S rRNA gene surveys of 1,381 soil samples from the Biomes of Australian Soil Environment (BASE) dataset, we were able to model relative abundances of soil bacterial taxonomic groups and describe bacterial niche space and optima. Hold out sample validated hypothetical causal networks (structural equation models; SEM) were able to predict the relative abundances of bacterial taxa from environmental data and elucidate soil bacterial niche space. By using explanatory SEM properties as indicators of microbial traits, we successfully predicted soil bacterial response, and in turn potential ecosystem service response, to near-term expected changes in the Australian climate. The methods developed enable prediction of continental-scale changes in bacterial relative abundances, and demonstrate their utility in predicting changes in bacterial function and thereby ecosystem services. These capabilities will be strengthened in the future with growing genome-level data.

Plant invasion strengthens the linkages between dissolved organic matter composition and the microbial community in coastal wetland soils

Exotic plant invasion dramatically alters soil carbon transformation and shapes the structure and diversity of the microbial community in coastal wetlands. However, it remains unclear how the dissolved organic matter (DOM) optical components and chemical composition and their linkages with soil microorganisms change with increasing time since invasion. Here, we explored the impacts of Spartina alterniflora (S. alterniflora) invasion on DOM compositions and relationships with microbial communities along a short-term chronosequence (i.e., 3-, 5-,10-, and 15-year) in the Yellow River Delta. The results showed an increase in the soil water content, soil organic carbon, dissolved organic carbon, and C/N ratio along the invasion chronosequence, whereas bulk density showed the opposite trend. Moreover, invaded wetland soils had a higher abundance of total phospholipid fatty acids, gram-positive bacteria (G + ), gram-negative bacteria (G-), and fungi than tidal flat soils. The DOM in invaded wetland soils was mainly composed of endogenous protein-like components, and the proportion of autochthonous DOM increased over invasion time. The DOM was characterized by low molecular weight, low aromatic content, and low hydrophobic compounds in S. alterniflora wetland soils, whereas in tidal flat soils, the humification degree and DOM molecular weight were higher. The soil microbial communities exhibited stronger linkages with various environmental variables and DOM fluorescence components in invaded wetlands based on redundancy analysis (RDA) and correlation analysis using Mantel tests. Structural Equation Model (SEM) revealed that the soil microbial abundance and community structure induced by increasing S. alterniflora invasion time were the most important drivers of DOM content and chemical composition. The findings of this work provide a better understanding of labile carbon pool turnover in coastal wetlands invaded by S. alterniflora.