Affect Soil Microbial Activity Research Articles

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils-however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with 18O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils-which are often more water limited and pulse driven-have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.

A high-fidelity dual-channel fluorescence probe for benzoyl peroxide detection and toxicity early warning in food, zebrafish, and mice

Benzoyl peroxide (BPO), as a widely used organic peroxide, has attracted widespread attention from all sectors of society for its environmental hazards and potential risks to human health. Herein, we employed a Förster resonance energy transfer (FRET) strategy to construct a novel ratiometric fluorescent probe CY-DCI for BPO detection in food, zebrafish, and mice. Specifically, a hemicyanine fluorophore and a dicyanoisophorone fluorophore were connected with a piperazine group as donor and acceptor, respectively, and an olefinic unsaturated bond as the reaction site. CY-DCI has favorable selectivity and an excellent detection limit as low as 58.1 nM, and the recovery rates for real-sample detection ranged from 95.8 % to 104 %, with relative standard deviations (RSD) less than 2.58 %. To further improve its practicality, silica gel plates and test strips containing CY-DCI (0–50 μM) were developed for naked-eye detection of BPO with satisfactory results. Additionally, this novel probe was then applied for ratiometric imaging of living zebrafish and mice and showed high ratiometric imaging resolution in the green and red channels, thus demonstrating its practical application for BPO detection and toxicity early warning in food and biosystems.

Response of petroleum-contaminated soil to chemical oxidation combined with biostimulation

In this study, a microcosm experiment was conducted to investigate the effects of Na2S2O8 preoxidation combined with biostimulation on petroleum-contaminated soil remediation. The response of microbial community during this process was explored using BIOLOG ECO microplate carbon utilization method and 16 s rDNA high-throughput sequencing. The results showed that use of 10 mg/g Na2S2O8 removed 19.8 % of the petroleum hydrocarbons, reduced soil biotoxicity and did not affect soil microbial activity compared to other concentrations. Therefore, sodium persulfate of ca. 10 mg/g was used to oxidize petroleum in soil before the biostimulation experiment with organic and inorganic fertilizers. Our finding showed that the content of total petroleum hydrocarbons (TPHs) in soil was reduced by 43.3 % in inorganic fertilizer treatment after 60 days. The results of BIOLOG ECO microplate carbon utilization analysis and 16 S rDNA high-throughput sequencing further confirmed that biostimulation quickly restored the microbial activities in oxidant treated soil. The main marker bacteria in chemical oxidation combined with biostimulation remediation were Arthrobacter and Paenarthrobacter, and their relative abundances were both significantly negatively correlated with the content of petroleum hydrocarbons in soil.

Compost and Mineral Fertilizer Application Affects Soil Microbial Activity and Nutrient Mineralization in an Ultisol

ABSTRACT Organic additions help improve soil biophysical qualities, but they are insufficient to supply nutrient demand and could result in unintentional nutrient immobilization in soils, particularly soils with low fertility status. A 16-week laboratory incubation study was conducted to determine how the method of application of compost and inorganic fertilizers influence microbial respiration, nitrogen (N), and phosphorus (P) mineralization. Topsoil (500 g, 0–15 cm) was amended with compost (0, 5, and 10 g kg−1) and either inorganic N (50 kg N ha−1) or P (30 kg P ha−1). Two soil amendment strategies, applying compost and inorganic fertilizer separately to opposite sides of the soil using a divider and mixing them evenly throughout the soil, were compared for their effects on microbial activity and nutrient mineralization. The cumulative amounts of carbon dioxide (CO2) evolved were measured fortnightly using the static CO2 absorption method and inorganic N and P mineralization. N mineralization was unaffected by the method of compost and inorganic fertilizer application (p > .05), while at the end of day 42, available P in separate applications of compost and mineral N fertilizers was 33% greater than combined applications. Compost and inorganic P fertilizer had favorable N priming effects, but compost and inorganic N had negative effects. The different N priming effects of compost and inorganic N and P fertilizers may be attributable to microbial nutrient demand. The data suggest that composting with conventional fertilizers may change microbial nutrient demand and crop nutrient availability.

Neonicotinoid Effects on Soil Microorganisms: Responses and Mitigation Strategies

Pesticides play a critical role in pest management and agricultural productivity; however, their misuse or overuse can lead to adverse effects on human health and the environment, including impacts on ecosystems and contamination. Currently, neonicotinoids (NNIs) are the most widely used systemic insecticides and are questioned worldwide for their possible impacts on pollinators. After NNI application, a substantial portion is not absorbed by the plant and may accumulate in the soil, affecting the soil microbial community. In this review, we explore the main studies carried out either in the laboratory or in the field about this matter. The studies report that the application of NNIs affects soil microbial activity and can act on microbial communities differently due to their unique chemical properties, degradation in soil, soil type, effects on soil properties, and methods of application. NNIs alter the diversity, structure, and abundance of soil microbes, in some cases increasing or decreasing their representativeness in soil. Bacterial phyla like Pseudomonadota, Bacillota, Actinomycetota, and Nitrospirota increase after NNI exposure, just like the families Nitrosomonadaceae, Nitrososphaeraceae, Nitrospiraceae, Sphingomonadaceae, Streptomycetaceae, and Catenulisporaceae. At the bacterial genus level, Nitrospira was associated with a decrease in nitrification processes in soil. The bacterial genera Sphingomonas, Streptomyces, Catenulispora, Brevundimonas, Pedobacter, and Hydrogenophaga are related to NNI degradation after application. Microorganisms could minimize the impacts of NNIs in agricultural soil. Therefore, the use of bioinoculation as a bioremediation tool is explored as an alternative to contribute to agricultural sustainability.

Mixing of pine and arbuscular mycorrhizal tree species changed soil organic carbon storage by affecting soil microbial characteristics

Pure and mixed pine forests are found all over the world. The mycorrhizal type affects soil microbial activity and carbon sequestration capacity in pure forests. However, the effects of mycorrhizal type on microbial characteristics and carbon sequestration capacity in pine mixed forests remain untested. Further, making it difficult to predict carbon storage of the conversion from pure pine forests to mixed forests at larger scales. Herein, a meta-analysis showed that the contents of soil microbial biomass, mineral-associated organic carbon, and soil organic carbon in pine mixed forests with introduced arbuscular mycorrhizal tree species (PMAM) increased by 26.41 %, 58.55 %, and 27.41 %, respectively, compared to pure pine forests, whereas those of pine mixed forests without arbuscular mycorrhizal tree species (PMEcM) remained unchanged. Furthermore, the effect size of microbial biomass, mineral-associated organic carbon and organic carbon contents in subsoil of PMAM are 56.48 %, 78.49 % and 43.05 %, respectively, which are higher than those in topsoil. The improvement of carbon sinks throughout the PMAM soil profile is positively correlated with increases in microbial biomass and mineral-associated organic carbon in subsoil, according to regression analysis and structural equation modelling. In summary, these results highlight that the positive effects of introducing arbuscular mycorrhizal tree species rather than ectomycorrhizal tree species into pure pine forests on soil microbial biomass and carbon sequestration. The positive link between microbial biomass, mineral-associated organic carbon, and soil organic carbon suggests an underlying mechanism for how soil microorganisms store carbon in pine mixed forests. Nevertheless, our findings also imply that the soil carbon pool of PMAM may be vulnerable under climate change. Based on the above findings, we propose that incorporating mycorrhizal type of tree species and soil thickness into mixed forests management and biodiversity conservation.

Biochar application for enhancing water and nitrogen use efficiency of understory acacia species in a suburban native forest subjected to nitrogen deposition in Southeast Queensland

Abstract Purpose The fuel reduction prescribed burning and biochar application can have significant impacts on water and nitrogen (N) use efficiency of understory acacia species as well as soil carbon (C) and N pools in a suburban native forest subject to N deposition in Southeast Queensland, Australia. Methods We evaluated the impact of biochar application rates (0, 5.0 and 10.0 t biochar per hectare) and prescribed burning on soil-plant interactions in carbon (C) and N cycling in a suburban native forest in the first two years of biochar application or three and half years of the recently prescribed burning. Results Anthropogenic N deposition not only enhanced N losses caused by N leaching and denitrification, but also inhibited biological N fixation (BNF) by increasing N availability in forest systems. The Acacia leiocalyx with higher water use efficiency was more inclined to utilize easily available N resources (from N deposition), compared with A. disparismma. In this study, biochar application could indeed reduce N loss in forest soil and improve soil fertility by improving plant water and N use efficiency. Meanwhile, soil moisture content affected by biochar application also influenced soil N transformations by affecting soil microbial activity. Conclusion For urban forest soils, the high N availability caused by N deposition could inhibit the BNF in a suburban native forest ecosystem. The high-porosity physical structure of biochar applied increased the soil water content and soil N retention capacity.

Labile and recalcitrant carbon inputs differ in their effects on microbial phosphorus transformation in a flooded paddy soil with rice (Oryza sativa L.)

Organic carbon (C) can greatly affect soil microbial activity and thus alter the nutrient availability in soil. However, little is known about the microbial-mediated P transformation processes with organic C inputs in flooded soils. This study used high-throughput sequencing technology to investigate the effects of labile (glucose) and recalcitrant (lignin) organic C inputs on P availability and microbial communities in the bulk and rhizosphere soil under rice growth, aiming to clarify the key microorganisms involved in soil P transformation. Glucose addition enhanced microbial P immobilization and decreased P availability in the rhizosphere soil, while lignin amendment increased available P concentration in bulk soil through increased soil pH and altered bacterial community. Organic C inputs stimulated the growth and cooperation of specific P-solubilizing bacteria (e.g., Acetobacter and Phenylobacterium), facilitating the transformation of non-labile P to labile P in bulk soils, but also stimulated the growth of Clostridium_sensu_stricto, immobilizing labile P into their biomass. Irrespective of C supply, soil P availability was correlated positively with the abundances of Phenylobacterium and Desulfosporosinus but negatively with those of Acetobacter, Clostridium_sensu_stricto, Clostridium_IV, Gluconacetobacter and Syntrophomonas. This study emphasized the contrasting effects of labile and recalcitrant C on microbial mechanisms of P transformation in a flooded paddy soil. These findings provide potential strategies for microbially mediated P management in paddy fields.

Animal manures increased maize yield by promoting microbial activities and inorganic phosphorus transformation in reclaimed soil aggregates

Animal manures positively affect soil microbial activity and inorganic phosphorus (Pi) accumulation. However, how different types of manures affect microbial-driven Pi transformation at the aggregate scale is largely unclear. Here, we conducted a field experiment focused on maize cultivation in a reclamation site. Five fertilization treatments included no fertilizer (CK), chemical fertilizer (CF), chicken manure (CHM), pig manure (PM), and cow manure (CM). We examined microbial biomass, soil extracellular enzyme activities associated with carbon and phosphorus cycling, and Pi fractions (Labile-P, Moderately labile-P, and Stable-P) in three aggregate sizes (> 2 mm large macro-aggregates, 0.25–2 mm small macro-aggregates, and < 0.25 mm micro-aggregates), as well as grain yield. The results showed that manures addition significantly increased the proportion of large macro-aggregates and aggregate stability compared to chemical fertilizer. Stable-P constituted the largest proportion among the Pi fractions, accounting for 63 %–72 %. However, manures reduced Stable-P (5.4 %–10.7 %) and increased Labile-P (111 %–190 %) in Pi, especially in micro-aggregates. Both chemical fertilizer and manures increased microbial biomass and enzyme activities in aggregates, with manures causing a greater enhancement of soil microbial biomass carbon (SMBC) and C-cycling enzymes, especially under pig manure, and improving soil microbial biomass phosphorus (SMBP) and P-cycling enzymes, especially under chicken manure. Phytase, phosphatase and SMBP accounted for 81.4 %, 81.2 % and 87 % of the differences in large macro-aggregates, small macro-aggregates, and micro-aggregates, respectively. The structural equation model (SEM) demonstrated that manures facilitated the transformation of Stable-P to Labile-P by regulating aggregates and microbial activity, which consequently increased yield. In summary, manures addition, particularly chicken manure, can enhance inorganic phosphate (Pi) accumulation and transformation, thereby mitigating phosphorus (P) limitation in calcareous reclamation soils.

Long-Term Experiences with Fertilizers on Wheat and Maize Crops in the Pedoclimatic Conditions of the Bârlad Plateau

A large number of long-term field experiments demonstrate that optimal application of nitrogen fertilizers to crops did not result in loss of organic matter, nor did it adversely affect soil microbial activity. Optimal use of fertilizers on agricultural crops reduces soil erosion, but repeated application of high doses of nitrogen fertilizer can lead to soil acidification, a negative trait of soil health. The main objective of this paper is to study the particular effect, interaction and complementarity of NP, NPK and organo-mineral fertilizers on the production of agricultural crops. This paper presents production data as well as references that can be used to define the scientific bases of the multi-year application of fertilizers. The experimental technique is specific to the polyfactorial character and the analytical methods used are specific and current in the field. In this scientific paper, we present the results obtained for the cultivation of wheat and corn, during the period 2018-2023, at the “Mircea Moțoc” Perieni Research-Development Station for Combating Soil Erosion, by fertilizing with several types of organo-mineral fertilizers. The results obtained come from the long-term experiences with fertilizers with 25 variants in the NP experience, respectively 16 variants in the NPK experience and the organo-mineral experience, all being placed according to the block method with parcels subdivided into 6 repetitions. The obtained results were interpreted by analysis of variance. From the results of this long-term experience, it is concluded that the effect of long-term fertilization with NP, NPK and organo-minerals responds to the maximization of profit and the optimization of the soil-plant system and environmental protection.

Microbial diversity in pesticidal and non-pesticidal paddy soil microbiomes

Abstract. Susanti R, Kenarni NR, Jaya AF, Nisa’ FF, Mukaromah RL, Widiatningrum T, Martuti NKT, Rahayuningsih M. 2023. Microbial diversity in pesticidal and non-pesticidal paddy soil microbiomes. Biodiversitas 24: 4723-4730. The use of pesticides can affect the physical and chemical properties of paddy soil. Soil physical and chemical properties can indicate soil quality because they affect soil microbial activity. This study used an exploratory observational method to analyze the diversity and abundance of microbes in the soil microbiome of pesticide paddy fields (PPF) and non-pesticide paddy fields (PF). The PPF samples were taken from Purwosari Village, Mijen Subdistrict, Semarang City, while the PF samples were taken from Tambangan Village, Mijen Subdistrict, Semarang City. Soil samples were taken for chemical and metagenomic analysis based on 16S rRNA gene marker region V3-V4. The results showed that microbial PPF diversity was higher than PF's based on the Shannon and Simpson index. The PPF microbiome is dominated by 3 bacterial phyla, namely Proteobacteria (26.61%), Actinobacteriota (15.13%) and Acidobacteriota (11.44%). Meanwhile, the PF microbiome was dominated by Proteobacteria (28.73%), Acidobacteriota (12.80%), and Chloroflexi (11.41%). The Archaea phylum that dominates PPF are Halobacterota (62.78%), Euryarchaeota (20.82%), and Crenarchaeota (10.89%), while in PF it is dominated by Halobacterota (80.43%), Crenarchaeota (11.03%) and Euryarchaeota (5.04%). The phylum that plays an important role in the biodegradation of organochlorine pesticides is Actinobacteria, which dominates in PPF; low abundance of Nitrospirota in PPF as a bioindicator of organochlorine pesticide contamination.

Vegetation restoration of abandoned cropland improves soil phosphorus availability and microbial activities in the Danxia degraded region

Phosphorus is a limiting nutrient in subtropical region soils. The Danxia degraded region (DDR) is a typical ecologically degraded area in the south subtropical region of China, and mitigation measures for reconverting farmland to forest have been implemented to prevent further land degradation. However, whether vegetation restoration can alter soil P fractions (SPF) and P availability in the DDR remains unclear, and the mechanisms influencing P availability require further study. In this study, we collected soil samples from the main vegetation cover types, namely arbor forest, shrubland, and abandoned cropland, in the DDR to explore the characteristics of SPF, acid phosphatase (ACP), microbial community and their influencing factors. Results showed that vegetation restoration significantly affected soil P availability by modifying the SPF. Labile, moderately labile, and aggregate-occluded P content in the soil increased, whereas the proportion of stable P decreased. Vegetation restoration promoted the secretion of soil ACP and significantly increased the abundance of soil bacteria, fungi, actinomycetes, arbuscular mycorrhizal fungi, and the overall microbial abundance. Arbor forest soils presented higher SPF content and microbial activity than the soils from abandoned croplands and shrublands. This increases in soil microbial abundance was significantly correlated with soil microbial biomass and dissolved organic carbon. The results of redundancy and variance partitioning analyses indicated that soil nutrients and soil properties jointly drove SPF transformation in the DDR. Soil nutrient supply significantly affected soil microbial activity and SPF transformation. Vegetation restoration increased microbial activity by increasing the soil nutrient supply, and the resulting synergistic effect altered the SPF distribution and availability. This study provides a theoretical basis for the sustainable use of soil P resources in the DDR.

Soil temperature, microbial biomass and enzyme activity are the critical factors affecting soil respiration in different soil layers in Ziwuling Mountains, China.

Soil microorganisms are critical biological indicators for evaluating soil health and play a vital role in carbon (C)-climate feedback. In recent years, the accuracy of models in terms of predicting soil C pools has been improved by considering the involvement of microbes in the decomposition process in ecosystem models, but the parameter values of these models have been assumed by researchers without combining observed data with the models and without calibrating the microbial decomposition models. Here, we conducted an observational experiment from April 2021 to July 2022 in the Ziwuling Mountains, Loess Plateau, China, to explore the main influencing factors of soil respiration (RS) and determine which parameters can be incorporated into microbial decomposition models. The results showed that the RS rate is significantly correlated with soil temperature (TS) and moisture (MS), indicating that TS increases soil C loss. We attributed the non-significant correlation between RS and soil microbial biomass carbon (MBC) to variations in microbial use efficiency, which mitigated ecosystem C loss by reducing the ability of microorganisms to decompose organic resources at high temperatures. The structural equation modeling (SEM) results demonstrated that TS, microbial biomass, and enzyme activity are crucial factors affecting soil microbial activity. Our study revealed the relations between TS, microbial biomass, enzyme activity, and RS, which had important scientific implications for constructing microbial decomposition models that predict soil microbial activity under climate change in the future. To better understand the relationship between soil dynamics and C emissions, it will be necessary to incorporate climate data as well as RS and microbial parameters into microbial decomposition models, which will be important for soil conservation and reducing soil C loss in the Loess Plateau.

Towards the effects of moss-dominated biocrusts on surface soil aeration in drylands: Air permeability analysis and modeling

Soil aeration is an important factor influencing soil biological and biochemical processes because it directly affects soil microbial activity and respiration. As an important living skin of the soil, biocrusts strongly impact various soil properties and play a vital role in maintaining surface soil structure and multifunctionality. Although there are several studies concerning the effects of biocrusts on soil respiration processes, it is still not well understood how biocrusts affect air permeability (Ka) and soil aeration in drylands. In a semiarid climate region of the northern Chinese Loess Plateau, the Ka and air-filled porosity (εa) of moss-dominated biocrusts established on aeolian sand and loess soil were measured as a function of soil water content under laboratory and in situ conditions and compared to measurements of bare soils. The relative air permeability (Kra) of biocrusts and bare soils was further analyzed and estimated with commonly applied Kra models that are based on the soil water retention curve (SWRC), and the performance of these models was specifically assessed for biocrusts. The in situ measurements yielded a 51.8% and 76.7% higher Ka for the biocrust-colonized aeolian sand and loess soil, respectively, when compared to the bare soils. Correspondingly, in comparison to the bare soils, the εa of the biocrusts also increased by 38.0% for the aeolian sand and by 52.4% for the loess soil. The laboratory measurements showed an 8.5%–9.3% increase of Ka for the biocrust-colonized soils from wet to dry conditions when compared to their bare counterparts, which was mainly attributed to their higher fine particle and organic matter contents as well as to the moss rhizoids. Moreover, a positive linear relationship (R2 > 0.43) was found between the log Ka and log εa for both biocrusts and bare soils. Additionally, the biocrusts exhibited higher water content at almost all matric potentials in comparison to the bare soils. The Kra of biocrusts was 22.0% higher for aeolian sand and 42.1% higher for loess soil when compared to the bare soils. The van Genuchten-Burdine and Brooks and Corey-Burdine models performed best with regard to the estimation of Kra (RMSE ≤ 0.100, bias ≤ 0.018). In general, biocrusts may greatly increase surface soil aeration due to their higher Ka and εa, and the soil aeration status of biocrusts can be indirectly assessed through their effective degree of soil water saturation. Our findings suggest that biocrusts should be carefully considered in further studies of soil aeration related to biological processes and gas and vapor transport in dryland ecosystems.

Responses of soil microbial community structure to litter inputs.

Litter decomposition is one of the most important ecosystem processes, which plays a critical role in regu-lating nutrient cycling and energy flow in terrestrial ecosystems. The influence of litter inputs on soil microbial community is helpful for understanding the relationship between soil microbial diversity and terrestrial ecosystem function. We conducted a meta-analysis to examine how litter inputs affect soil microbial activity (fungi, bacteria, actinomycetes) and microbial biomass carbon, nitrogen in China. The results showed that compared with non-litter input, soil microbial biomass carbon and nitrogen were significantly increased by 3.9% and 4.4% respectively after litter inputs. Soil fungal PLFA, bacterial PLFA, and total microbial PLFA were increased by 4.0%, 3.1% and 2.4%, respectively. The effects of litter inputs differed significantly with climatic region, annual precipitation, vege-tation type, and soil pH. Under different climate conditions, the responses of soil microbe showed the trend of subtropical monsoon climatic region > temperate monsoon climatic region > temperate continental climatic region, which increased first and then decreased with increasing annual precipitation. Under different vegetation types, the responses of soil microbes showed the trend of broad-leaved forest > grassland ≈ mixed forest > coniferous forest.

Effects of fertilizers and soil amendments on the degradation rate of allyl isothiocyanate in two typical soils of China

Allyl isothiocyanate (AITC) is a soil fumigant that protects plants against soil-borne pathogens, weeds and insects when present in the root-zone. However, the degradation of AITC under different fertilizers and soil amendments affects its emission and pest control efficacy. Degradation rates of AITC in soil amended with organic and inorganic fertilizers, zeolite and biochar were determined in the laboratory to improve its field applications. The degradation half-lives of AITC were 24.4 and 35.4h in Fangshan and Yongzhou soils, respectively, without any added fertilizer or soil amendment. Nitrogen fertilizer and organic fertilizer accelerated the degradation rate of AITC, while phosphorus fertilizer had the opposite effect. The degradation rate of AITC on adding unsterilized chicken manure was over 3.5 and 1.1 times higher than that of sterilization in Fangshan and Yongzhou soil. Inorganic and organic fertilizers affected the degradation of AITC by affecting soil microbial activity on the basis of CO2 cumulative release. The degradation rate of AITC increased more than 0.4 times in response to zeolite, but this was independent of particle size. The AITC degradation rate increased 1.0-2.6 and 0.3-9.7 times in response to biochar made from corn stalk and pine wood, respectively. Cow manure biochar manufactured at different pyrolyzation temperatures had different effects on the degradation rate of AITC. Soil type, fertilizers and soil amendments differentially affect the degradation rate of AITC by changing soil physicochemical characteristics, microorganisms, etc., which shows great potential in reducing AITC emissions and increasing pest control efficacy when AITC is applied commercially. © 2022 Society of Chemical Industry.

Effects of Litter and Root Manipulations on Soil Bacterial and Fungal Community Structure and Function in a Schrenk's Spruce (Picea schrenkiana) Forest.

Soil microorganisms are the key driver of the geochemical cycle in forest ecosystem. Changes in litter and roots can affect soil microbial activities and nutrient cycling; however, the impact of this change on soil microbial community composition and function remain unclear. Here, we explored the effects of litter and root manipulations [control (CK), doubled litter input (DL), litter removal (NL), root exclusion (NR), and a combination of litter removal and root exclusion (NI)] on soil bacterial and fungal communities and functional groups during a 2-year field experiment, using illumina HiSeq sequencing coupled with the function prediction platform of PICRUSt and FUNGuild. Our results showed that litter and root removal decreased the diversity of soil bacteria and fungi (AEC, Shannon, and Chao1). The bacterial communities under different treatments were dominated by the phyla Proteobacteria, Acidobacteria, and Actinomycetes, and NL and NR reduced the relative abundance of the first two phyla. For the fungal communities, Basidiomycetes, Ascomycota, and Mortierellomycota were the dominant phyla. DL increased the relative abundance of Basidiomycetes, while NL and NR decreased the relative abundance of Ascomycota. We also found that litter and root manipulations altered the functional groups related to the metabolism of cofactors and vitamins, lipid metabolism, biosynthesis of other secondary metabolites, environmental adaptation, cell growth, and death. The functional groups including ectomycorrhizal, ectomycorrhizal-orchid mycorrhizal root-associated biotrophs and soil saprotrophs in the fungal community were also different among the different treatments. Soil organic carbon (SOC), pH, and soil water content are important factors driving changes in bacterial and fungal communities, respectively. Our results demonstrate that the changes in plant detritus altered the soil microbial community structure and function by affecting soil physicochemical factors, which provides important data for understanding the material cycle of forest ecosystems under global change.

Oil degradation and variation of microbial communities in contaminated soils induced by different bacterivorous nematodes species

Oil pollution poses a great threat to environments and makes the remediation of oil-contaminated soils an urgent task. Microorganisms are the main biological factor for oil removal in the environment but microbial remediation is greatly affected by environmental factors. For our research, we inoculated three species of bacterivorous nematodes into oil-contaminated soil to explore how bacterivorous nematodes affect soil microbial activities and community structure in contaminated soil, as well as how efficiently different nematodes remove oil pollution from the soil. Six treatments were set in this experiment: sterilized oil-contaminated soil (SOC); nematode-free soil (S); oil-contaminated soil (OC); oil-contaminated soil + Caenorhabditis elegans (OCN1); oil-contaminated soil + Cephalobus persegnis (OCN2); oil-contaminated soil + Rhabditis marina (OCN3) for a 168-day incubation experiment. After the experiment was done, the oil contents in SOC, OC, OCN1, OCN2, and OCN3 were reduced by 6.5%, 32.3%, 38.2%, 42.8%, and 40.2%, respectively, compared with the beginning of the experiment. The amount of phospholipid fatty acids (PLFAs) of Gram-negative bacteria in OC, OCN1, OCN2, and OCN3 was increased by 50.9%, 43.4%, 37.7%, and 47.9%, respectively, compared with that of S. During the 168-day incubation period, the maximum growth of the number of nematodes in OCN1, OCN2, and OCN3 compared with the initial number of the nematodes were 2.25-, 1.52-, and 1.65-fold, respectively. The amount of oil residue in the contaminated soil negatively correlated with the populations of nematodes, total microorganisms, Gram-negative bacteria, actinomycetes, and eukaryotes. Thus, oil pollution increased the number of Gram-negative bacteria, decreased the ratio of Gram-positive bacteria/Gram-negative bacteria and Fungi/Bacteria significantly, and altered the community structure of soil microorganisms. Each species of bacterivorous nematodes has got its unique effect on the microbial activity and community structure in oil contaminated soils, but those tested can promote oil degradation and thus improve the environment of oil contaminated soils.

Soil organic carbon stocks and stability of organic matter in permafrost-affected soils of Yamal region, Russian Arctic

Chemical composition of soil organic matter determines its decomposability and may affect soil microbial activity. This is very important for understanding variability in soil organic carbon pools in context of changes in plant cover or climate. This paper is aimed to characterize existing carbon pools and molecular organization of the humic acids, isolated from various permafrost-affected soils of Yamal region and to assess the potential vulnerability of soils organic matter in context of possible mineralization processes. Soils for most of studied sites were characterized predominantly by acidic to strong acidic pH. Profile distribution of carbon, nitrogen and C:N ratio showed non-gradual changing with the depth due to manifestation of cryopedogenesis in soil profiles which lead to cryogenic mass transfer. Mean soil organic carbon stocks for the study area were 7.9 ± 2.2 kg m−2 (for 0–10 cm layer), 15.0 ± 5.5 kg m−2 (for 0–30 cm), 24.0 ± 8.0 kg m−2 (for 0–100 cm). Analysis of soil organic carbon stocks among predominant soil types (Russian soil classification system) revealed relatively high variability of values in 0–10 cm (from 4.5 kg m−2 in Peaty Gleyzem underlain by permafrost to 9.6 kg m−2 in Peaty Podzol underlain by permafrost) and 0–30 cm layers (from 9.9 kg m-2 in Cryic Podbur underlain by permafrost to 24.1 kg m−2 in eutrophic peat soil underlain by permafrost). Results of solid-state 13C NMR spectrometry showed low amounts of aromatic fragments in studied soils. All studied soils are characterized by predominance of aliphatic structures, and also carbohydrates, polysaccharides, ethers and amino acids. High content of aliphatic fragments in studied humic acids shows their similarity fulvic acids. Low level of aromaticity reflects the accumulation in soil of poorly decomposed organic matter due to cold temperatures. Our results provide further evidence of high vulnerability and sensitivity of permafrost-affected soils organic matter to Arctic warming. Consequently, these soils may play a crucial role in global carbon balance under effects of climate warming.

Effect of long‐term fertilization on soil microbial activities and metabolism in Paulownia plantations

AbstractPaulownia is a well‐known, fast‐growing tree genus that is widely planted for commercial cultivation in the warm temperate zone of the North China Plain. Fertilization as a standard practice can efficiently increase wood production and tree yield in those Paulownia plantations, but how different fertilization measures might affect soil microbial activity, microbial biomass and metabolic functioning unclear, especially in the subtropics. To fill this knowledge gap, we initiated long‐term different fertilization experiments from afforestation, using a completely randomized block design consisting of a control, inorganic fertilizer, microelement‐inorganic fertilizer and organic–inorganic compound fertilizer (OIF) treatments in South China's subtropical zone. The results revealed fertilization significantly increased soil enzyme activity and microbial biomass, especially that of urease, invertase, acid phosphatase, as well as the microbial biomass in terms of carbon and nitrogen, all of which increased most significantly in soil under the OIF treatment. The carbon source utilization levels of five carbon substrates under the OIF treatment, namely D‐xylose, glucose‐1‐phosphate, D‐cellobiose, α‐ketobutyric acid and glycogen, were significantly higher than those of the others. From these data, we may reasonably infer that the application of organic fertilizer could offer an effective management practice for use in Paulownia plantations. The five carbon matrices may be the most efficient carbon sources for increasing the abundance of efficient soil microorganisms, improving soil fertility and achieving the sustainable development of Paulownia plantations.