Divergent responses of bacterial activity, structure, and co-occurrence patterns to long-term unbalanced fertilization without nitrogen, phosphorus, or potassium in a cultivated vertisol

Long-term conservation tillage enhances microbial carbon use efficiency by altering multitrophic interactions in soil

Microbial carbon (C) use efficiency (CUE) plays a key role in soil C storage. The predation of protists on bacteria and fungi has potential impacts on the global C cycle. However, under conservation tillage conditions, the effects of multitrophic interactions on soil microbial CUE are still unclear. Here, we investigate the multitrophic network (especially the keystone ecological cluster) and its regulation of soil microbial CUE and soil organic C (SOC) under different long-term (15-year) tillage practices. We found that conservation tillage (CT) significantly enhanced microbial CUE, turnover, and SOC (P < 0.05) compared to traditional tillage (control, CK). At the same time, tillage practice and soil depth had significant effects on the structure of fungal and protistan communities. Furthermore, the soil biodiversity of the keystone cluster was positively correlated with the microbial physiological traits (CUE, microbial growth rate (MGR), microbial respiration rate (Rs), microbial turnover) and SOC (P < 0.05). Protistan richness played the strongest role in directly shaping the keystone cluster. Compared with CK, CT generally enhanced the correlation between microbial communities and microbial physiological characteristics and SOC. Overall, our results illustrate that the top-down control (the organisms at higher trophic levels affect the organisms at lower trophic levels) of protists in the soil micro-food web plays an important role in improving microbial CUE under conservation tillage. Our findings provide a theoretical basis for promoting the application of protists in targeted microbial engineering and contribute to the promotion of conservation agriculture and the improvement of soil C sequestration potential.

Oxygen availability regulates the quality of soil dissolved organic matter by mediating microbial metabolism and iron oxidation

Dissolved organic matter (DOM) plays a vital role in biogeochemical processes and in determining the responses of soil organic matter (SOM) to global change. Although the quantity of soil DOM has been inventoried across diverse spatio-temporal scales, the underlying mechanisms accounting for variability in DOM dynamics remain unclear especially in upland ecosystems. Here, a gradient of SOM storage across 12 croplands in northeast China was used to understand links between DOM dynamics, microbial metabolism, and abiotic conditions. We assessed the composition, biodegradability, and key biodegradable components of DOM. In addition, SOM and mineral-associated organic matter (MAOM) composition, soil enzyme activities, oxygen availability, soil texture, and iron (Fe), Fe-bound organic matter, and nutrient concentrations were quantified to clarify the drivers of DOM quality (composition and biodegradability). The proportion of biodegradable DOM increased exponentially with decreasing initial DOM concentration due to larger fractions of depolymerized DOM that was rich in small-molecular phenols and proteinaceous components. Unexpectedly, the composition of DOM was decoupled from that of SOM or MAOM, but significantly related to enzymatic properties. These results indicate that microbial metabolism exhibited a dominant role in DOM generation. As DOM concentration declined, increased soil oxygen availability regulated DOM composition and enhanced its biodegradability mainly through mediating microbial metabolism and Fe oxidation. The oxygen-induced oxidation of Fe(II) to Fe(III) removed complex DOM compounds with large molecular weight. Moreover, increased oxygen availability stimulated oxidase-catalyzed depolymerization of aromatic substances, and promoted production of protein-like DOM components due to lower enzymatic C/N acquisition ratio. As global changes in temperature and moisture will have large impacts on soil oxygen availability, the role of oxygen in regulating DOM dynamics highlights the importance of integrating soil oxygen supply with microbial metabolism and Fe redox status to improve model predictions of soil carbon under climate change.

Biochar fertilization effects on soil bacterial community and soil phosphorus forms depends on the application rate

Biochar plays a key role in soil phosphorus (P) forms and distribution by affecting soil biochemical characteristics with relevant effects on the microbial community. In this study, we aimed to study the role of biochar in the variation of microbial community and P forms, and the relationships between soil properties, microbial community, and P forms. Here, we conducted a five-year field experiment NPK minerally fertilized with different application rates of biochar; control (B0, 0 kg ha^-1 yr^-1), low rate (B1500, 1500 kg ha^-1 yr^-1), medium rate (B3000, 3000 kg ha^-1 yr^-1), high rate (B6000, 6000 kg ha^-1 yr^-1). Our study showed that the highest increases in bacterial diversity and abundances coincided with increases in P forms typically retained in bacterial cells (β-glucosidase, adenosine monophosphate-AMP, choline phosphate, and glucose-6 phosphate) and occurred at medium application rates. At low application rates, N₂-fixing and P solubilizing and mineralizing bacteria (Sphingomonas, Haliangium, and Bradyrhizobium) increased. P forms retained in bacterial cells decreased at the highest application rates while the most stable forms such as DNA and inositol hexaphosphate (IHP), steadily increased. Stereoisomers of IHP derived from soil microbes (scyllo-IHP and D-chiro-IHP) accounted for the total IHP increases at high application rates. pH and available P and K and total P were highest at high biochar application rates whereas the proportion of organic P was reduced. The most relevant genus in such soils was Gemmatimonas, a polyphosphate accumulating and pyrogenic material degrading bacterium. Therefore, it appears that applying biochar at higher rates reduced the abundance of plant growth promoting bacteria while enhancing the abundance of P accumulating and pyrogenic degrading types.

Exogenous enzyme amendment accelerates maturity and changes microflora succession in horse and wildlife animal manure co-composting

Composting has been a rational method to dispose of horse or wildlife animal manures, especially in the developed cities with horse clubs and wildlife parks. However, few studies have focused on the mechanism and improvement methods for composting the horse or wildlife animal manures. In this study, we investigated the effect of exogenous compound enzymes on thermophilic composting, which could potentially support the management of horse and wildlife animal manures. With the presence of exogenous enzymes, the duration of high temperature (> 60 °C) was significantly prolonged (p < 0.05), and the germination index was significantly improved (p < 0.05). More-efficient improvement of composting maturity was associated with the addition of that exogenous enzyme that might influence microflora succession and the interaction among microorganic communities, especially fungal, during the composting process. Furthermore, redundancy and canonical correspondence analyses indicated that the C/N ratio, temperature, and germination index were significant variations to influence bacterial communities (p < 0.05). The dominant Flavobacterium, Thermopolyspora, Thermomonospora, and Chaetomium and Saccobolus could play an essential role in carbohydrate and phytotoxin degradation, while Thermobispora and norank_f_Limnochordaceae could lead to temperature rising.

Microbial diversity and co-occurrence patterns in deep soils contaminated by polycyclic aromatic hydrocarbons (PAHs)

Numerous studies have enriched our knowledge of the microbial community composition and metabolic versatility of contaminated soil. However, there remains a substantial gap regarding the bioassembly patterns of the indigenous microbial community distribution in contaminated deep soils. Herein, the indigenous microbial community structure diversity, function, and co-occurrence relationships in aged PAH-contaminated deep soil collected from an abandoned chemical facility were investigated using high-throughput sequencing. The results showed that the dominant phyla in all samples were responsible for PAH degradation and included Proteobacteria (20.86%-81.37%), Chloroflexi (2.03%-28.44%), Firmicutes (3.06%-31.16%), Actinobacteria (2.92%-11.91%), Acidobacteria (0.41%-12.68%), and Nitrospirae (0.81%-9.21%). Eighty biomarkers were obtained by linear discriminant analysis of effect size (LEfSe), and most of these biomarkers were PAH degraders. Functional predictions using Tax4Fun indicated that the aged contaminated soil has the potential for PAH degradation. Statistical analysis showed that in contrast with the PAH concentration, edaphic properties (nutrients and pH) were significantly correlated (r > 0.25, P < 0.01) with the bacterial community and functional composition. Co-occurrence network analysis (modularity index of 0.781) revealed non-random assembly patterns of the bacterial communities in the PAH-contaminated soils. The modules in the network were mainly involved in carbon and nitrogen cycles, organic substance degradation, and biological electron transfer processes. Microbes from the same module had strong ecological linkages. Additionally, SAR202 clade, Thermoanaerobaculum, Nitrospira, and Xanthomonadales, which were identified as keystone species, played an irreplaceable role in the network. Overall, our results suggested that environmental factors such as nutrients and pH, together with ecological function, are the main factors driving the assembly of microbial communities in aged PAH-contaminated deep soils.