Labile organic carbon fractions drive soil microbial communities after long-term fertilization

Global hierarchical meta-analysis to identify the factors for controlling effects of antibiotics on soil microbiota

It is widely known that antibiotics can affect the structure and function of soil microbial communities, but the specific degree of impact and controlled factors on different indicators remain inconclusive. We conducted a multiple hierarchical mixed effects meta-analysis on 2564 observations that were extracted from 60 publications, to comprehensively assess the impact of antibiotics on soil microbiota. The results showed that antibiotics had significant negative effects on soil microbial biomass, α-diversity and soil enzyme activity. Under neutral initial soil, when soil was derived from agricultural land or had a fine-textured, the negative impacts of antibiotics on soil microbial community were exacerbated. Both single and mixed additions of antibiotics had significant inhibitory effects on soil microbial enzyme activities. The Random Forest model predicted the following key moderators involved in the effects of antibiotics on the soil microbiome, and antibiotics type, soil texture were key moderators on the severity of soil microbial biomass changes. Soil texture, temperature and single or combined application constitute of antibiotics were the main drivers of effects on soil enzyme activities. The reported results can be helpful to assess the ecological risk of antibiotics in a soil environment and provides a scientific basis for the rational of antibiotics use in the soil environment.

Changes in soil organic carbon components and microbial community following spent mushroom substrate application

While spent mushroom substrate (SMS) has shown promise in increasing soil organic carbon (SOC) and improving soil quality, research on the interplay between SOC components and microbial community following the application of diverse SMS types remains scant. A laboratory soil incubation experiment was conducted with application of two types of SMSs from cultivation of Pleurotus eryngii (PE) and Agaricus bisporus (AB), each at three application rates (3, 5.5, and 8%). Advanced techniques, including solid-state 13C nuclear magnetic resonance (NMR) and high-throughput sequencing, were employed to investigate on SOC fractions and chemical structure, microbial community composition and functionality. Compared to SMS-AB, SMS-PE application increased the relative abundances of carbohydrate carbon and O-alkyl C in SOC. In addition, SMS-PE application increased the relative abundance of the bacterial phylum Proteobacteria and those of the fungal phyla Basidiomycota and Ascomycota. The relative abundances of cellulose-degrading bacterial (e.g., Flavisolibacter and Agromyces) and fungal genera (e.g., Myceliophthora, Thermomyces, and Conocybe) were increased as well. The application of SMS-AB increased the aromaticity index of SOC, the relative abundance of aromatic C, and the contents of humic acid and heavy fraction organic carbon. In addition, SMS-AB application significantly increased the relative abundances of the bacterial phyla Firmicutes and Actinobacteria. Notably, the genera Actinomadura, Ilumatobacter, and Bacillus, which were positively correlated with humic acid, experienced an increase in relative abundance. Functional prediction revealed that SMS-PE application elevated carbohydrate metabolism and reduced the prevalence of fungal pathogens, particularly Fusarium. The application of high-rate SMS-AB (8%) enhanced bacterial amino acid metabolism and the relative abundances of plant pathogenic fungi. Our research provides strategies for utilizing SMS to enrich soil organic carbon and fortify soil health, facilitating the achievement of sustainable soil management.

Microbial community structure and carbon transformation characteristics of different aggregates in black soil

Background

Previous research on whole-soil measurements has failed to explain the spatial distribution of soil carbon transformations, which is essential for a precise understanding of the microorganisms responsible for carbon transformations. The microorganisms involved in the transformation of soil carbon were investigated at the microscopic scale by combining 16S rDNA sequencing technology with particle-level soil classification.

Methods

In this experiment,16S rDNA sequencing analysis was used to evaluate the variations in the microbial community structure of different aggregates in no-tillage black soil. The prokaryotic microorganisms involved in carbon transformation were measured before and after the freezing and thawing of various aggregates in no-tillage black soil. Each sample was divided into six categories based on aggregate grain size: >5, 2-5, 1-2, 0.5-1, 0.25-0.5, <0.25 mm, and bulk soil.

Results

The relative abundance of Actinobacteria phylum in <0.25 mm aggregates was significantly higher compared to that in other aggregates. The Chao1 index, Shannon index, and phylogenetic diversity (PD) whole tree index of <0.25 mm aggregates were significantly smaller than those of in bulk soil and >5 mm aggregates. Orthogonal partial least-squares discrimination analysis showed that the microbial community composition of black soil aggregates was significantly different between <1 and >1 mm. The redundancy analysis (RDA) showed that the organic carbon conversion rate of 0.25-0.5 mm agglomerates had a significantly greater effect on their bacterial community structure. Moreover, humic acid conversion rates on aggregates <0.5 mm had a greater impact on community structure. The linear discriminant analysis effect size (LEfSe) analysis and RDA analysis were combined. Bradyrhizobium, Actinoplane, Streptomyces, Dactylosporangium, Yonghaparkia, Fleivirga, and Xiangella in <0.25 mm aggregates were positively correlated with soil organic carbon conversion rates. Blastococcus and Pseudarthrobacter were positively correlated with soil organic carbon conversion rates in 0.25-0.5 mm aggregates. In aggregates smaller than 1 mm, the higher the abundance of functional bacteria that contributed to the soil's ability to fix carbon and nitrogen.

Discussion

There were large differences in prokaryotic microbial community composition between <1 and >1 mm aggregates. The <1 mm aggregates play an important role in soil carbon transformation and carbon fixation. The 0.25-0.5 mm aggregates had the fastest organic carbon conversion rate and increased significantly more than the other aggregates. Some genus or species of Actinobacteria and Proteobacteria play a positive role in the carbon transformation of <1 mm aggregates. Such analyses may help to identify microbial partners that play an important role in carbon transformation at the micro scale of no-till black soils.

Unlike chemical fertilizer reduction, organic fertilizer substitution increases soil organic carbon stock and soil fertility in wheat fields

BACKGROUND

Improvements in farmland soil organic carbon (SOC) stock enhance crop yield and soil fertility while mitigating climate change. Rational fertilization in agricultural production is crucial for safeguarding SOC stock. In this study, field experiments were conducted with different ratios of chemical fertilizer reduction and organic fertilizer substitution for three consecutive years (2018-2020) to explore their effects and interlinkages on SOC fractions, soil properties and SOC stock.

RESULTS

The results showed that organic fertilizer substitution increased SOC and its fractions content, SOC stock (by 3.98-12.98% and 7.15-18.13%) and soil fertility index (by 11.76-49.26% and 33.33-91.47%) compared to conventional fertilization in 2019 and 2020, while chemical fertilizer reduction had the opposite effect. Moreover, soil properties (except total nitrogen to total phosphorus ratio, N/P) and SOC fractions significantly affected SOC stock, with SOC fractions contributing more than soil properties. The high sensitivity of microbial biomass carbon (MBC) and dissolved organic carbon (DOC) can indicate changes in soil carbon pool. Structural equation modeling (SEM) revealed that organic fertilizer substitution increased SOC content and stock by increasing SOC fractions [recalcitrant organic carbon (ROC) and labile organic carbon (LOC) fractions] content and soil fertility.

CONCLUSIONS

Our study revealed the corresponding mechanisms of the two fertilization modes affecting SOC stock changes. The use of organic fertilizer substitution is recommended to increase SOC stocks and soil fertility in wheat fields. © 2023 Society of Chemical Industry.

Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors

The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.

Effects of Hanwoo (Korean cattle) manure as organic fertilizer on plant growth, feed quality, and soil bacterial community

INTRODUCTION

The development of organic manure from livestock excreta is a useful source for sustainable crop production in environment-friendly agriculture. Organic manure increases soil microbial activity and organic matter (OM) supply. The excessive use of chemical fertilizers (CFs) leads to air and water pollution caused by toxic chemicals and gases, and soil quality degradation via nutrient imbalance due to supplying specific chemical components. Thus, the use of organic manure will serve as a long-term supply of various nutrients in soil via OM decomposition reaction as well as the maintenance of environment.

METHODS

In this study, we aimed to analyze the diverse effects of Hanwoo manure (HM) on plant growth, feed quality, and soil bacterial communities in comparison with CFs, commercial poultry manure (CM), and the combined use of chemical fertilizer and Hanwoo manure (HM+CF). We analyzed the contents of crude matter (protein, fat, fiber, and ash), P, acid detergent fiber (ADF), and neutral detergent fiber (NDF) through feed quality analysis, and the contents or activities of total phenol, total flavonoid, ABTS, nitrite scavenging, and reducing power via the antioxidant assay. Furthermore, the soil microbial communities were determined using 16S rRNA sequencing. We compared the soil bacteria among different soil samples by using amplicon sequence variant (ASV) analysis.

RESULTS AND DISCUSSION

We observed increased OM in the soil of the HM group compared to that of the CF and non-treated groups over a period of two years. Moreover, HM+CF treatment enormously improved plant growth. Organic manure, especially HM, caused an increase in the content of crude ash and phosphorus in plants. There were no significant differences in total polyphenol, total flavonoid, ABTS, nitrite scavenging, and reducing power in plants between HM and CF groups. Finally, we detected 13 soil bacteria (Acidibacter, Algisphaera, Cystobacter, Microvirga, Ohtaekwangia, Panacagrimonas, Pseudarthrobacter, Reryanella, Rhodoligotrophos, Solirubrobacter, Stenotrophobacter, Tellurimicrobium, and Thermomarinilinea) that were considerably correlated with OM and available phosphorus, and three considerably correlated bacteria were specifically distributed in CF or organic manure. The results suggest that HM is a valuable source of organic manure that can replace CF for sustainable crop production.

Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy

Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.

Influence of tillage and residue management practices on productivity, sustainability, and soil biological properties of rice-barley cropping systems in indo-gangetic plain of India

Introduction

Conservation agriculture is a sustainable system of farming that safeguard and conserves natural resources besides enhancing crop production. The biological properties of soil are the most sensitive indicator to assess the short term impact of management practices such as tillage and residue incorporation.

Methods

Nine treatments of tillage and residue management practices [Reduced till direct seeded rice-zero till barley (RTDSR–ZTB); RTDSR–ZTB–green gram residue (Gg); Zero till direct seeded rice–zero till barley–zero till green gram (ZTDSR–ZTB–ZTGg); RTDSR–ZTB + rice residue at 4 t ha 1 (RTDSR–ZTBRR4); RTDSR–ZTBRR6; un-puddled transplanted rice (UPTR)–ZTB–Gg; UPTR–ZTBRR4; UPTR–ZTBRR6, and puddled transplanted rice (PTR)–RTB] executed under fixed plot for five years on crop productivity and soil biological properties under rice-barley production system.

Results

The shifting in either RTDSR or ZTDSR resulted in yield penalty in rice compared to PTR. The PTR recorded highest pooled grain yield of 3.61 ha−1. The rice grain yield reduced about 10.6% under DSR as compared to PTR. The ZTB along with residue treatments exhibited significantly higher grain yield over ZTB, and the RTDSR-ZTBRR6 registered highest pooled grain yield of barley. The system productivity (12.45 t ha−1) and sustainable yield index (0.87) were highest under UPTR-ZTBRR6. Biological parameters including microbial biomass carbon, soil respiration, microbial enzymes (Alkaline phosphatase, nitrate reductase and peroxidase), fluorescein diacetate hydrolysis, ergosterol, glomalin related soil proteins, microbial population (bacteria, fungi and actinobacteria) were found to be significantly (p &lt; 0.05) effected by different nutrient management practices. Based on the PCA analysis, Fluorescein diacetate hydrolysis, microbial biomass carbon, soil respiration, nitrate reductase and fungi population were the important soil biological parameters indicating soil quality and productivity in present experiment. The results concluded that UPTR-ZTBRR6 was a more suitable practice for maintaining system productivity and soil biological health.

Discussion

The understanding of the impact of different tillage and residue management practices on productivity, soil biological properties and soil quality index under rice-barley cropping system will help in determining the combination of best conservation agriculture practices for improved soil quality and sustainable production.

Soil microbial community shifts explain habitat heterogeneity in two Haloxylon species from a nutrient perspective

Haloxylon ammodendron and Haloxylon persicum (as sister taxa) are dominant shrubs in the Gurbantunggut Desert. The former grows in inter-dune lowlands while the latter in sand dunes. However, little information is available regarding the possible role of soil microorganisms in the habitat heterogeneity in the two Haloxylon species from a nutrient perspective. Rhizosphere is the interface of plant-microbe-soil interactions and fertile islands usually occur around the roots of desert shrubs. Given this, we applied quantitative real-time PCR combined with MiSeq amplicon sequencing to compare their rhizosphere effects on microbial abundance and community structures at three soil depths (0-20, 20-40, and 40-60 cm). The rhizosphere effects on microbial activity (respiration) and soil properties had also been estimated. The rhizospheres of both shrubs exerted significant positive effects on microbial activity and abundance (e.g., eukarya, bacteria, and nitrogen-fixing microbes). The rhizosphere effect of H. ammodendron on microbial activity and abundance of bacteria and nitrogen-fixing microbes was greater than that of H. persicum. However, the fertile island effect of H. ammodendron was weaker than that of H. persicum. Moreover, there existed distinct differences in microbial community structure between the two rhizosphere soils. Soil available nitrogen, especially nitrate nitrogen, was shown to be a driver of microbial community differentiation among rhizosphere and non-rhizosphere soils in the desert. In general, the rhizosphere of H. ammodendron recruited more copiotrophs (e.g., Firmicutes, Bacteroidetes, and Proteobacteria), nitrogen-fixing microbes and ammonia-oxidizing bacteria, and with stronger microbial activities. This helps it maintain a competitive advantage in relatively nutrient-rich lowlands. Haloxylon persicum relied more on fungi, actinomycetes, archaea (including ammonia-oxidizing archaea), and eukarya, with higher nutrient use efficiency, which help it adapt to the harsher dune crests. This study provides insights into the microbial mechanisms of habitat heterogeneity in two Haloxylon species in the poor desert soil.

Soil Organic Carbon Sequestration under Long-Term Chemical and Manure Fertilization in a Cinnamon Soil, Northern China

To mitigate climate change and improve food security, it is essential to understand how fertilizer strategies impact the dynamics of soil organic carbon and its fractions. The soil organic carbon (SOC), light fraction organic carbon (LFOC), and particulate organic carbon (POC) were investigated every five years in a corn (Zea mays L.) cropping system with chemical fertilization and manuring over twenty-four years (1992–2016) in a semiarid area of northern China. There were four treatments with chemical fertilizer (i.e., N1P1, N2P2, N3P3, N4P4), three treatments with chemical fertilizer plus manure (i.e., N2P1M1, N3P2M3, N4P2M2), and one treatment with manure alone (i.e., M6), and an unfertilized treatment (control). The carbon sequestration rate (CSR) and efficiency (CSE) of SOC, POC, and LFOC were identified. The results revealed that the fertilization treatments (N2P2, N3P3, N2P1M1, N3P2M3, N4P2M2, and M6) promoted SOC sequestration, with a sequestration rate of 0.19~1.29 Mg ha−1 y−1. The excess application of chemical fertilizer caused a reduction in POC, whereas the application of NP, NPM or manure resulted in greater POC sequestration in soil, with a carbon sequestration rate of 0.04~0.24 Mg ha−1 y−1. The LFOC stocks were 1.43~2.24 Mg ha−1 under the NP treatments, 2.47~6.68 Mg ha−1 under the NPM treatments and 8.12 Mg ha−1 under the M treatment; these stocks were all higher than that of the control treatment. Different fertilization strategies affected the pools of SOC with different sequestration rates. We found the carbon sequestration rates of SOC and LFOC were logarithmically correlated with the annual carbon input. When the annual C input is approximately 1.39 Mg ha−1 y−1, the SOC level will be maintained; when the annual C input is higher than 0.8 Mg ha−1 y−1, the LFOC level increases. This study describes the relationship between carbon inputs and the SOC(LFOC) sequestration rates under continuous fertilization in arid cropland. The results further evidence that the long-term fertilization of NPM and M increases the potential for SOC sequestration and quantifies the amount of exogenous carbon input required for soil organic matter enhancement.