Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials

Microbial diversity and interactions: Synergistic effects and potential applications of Pseudomonas and Bacillus consortia

Microbial diversity and interactions in the rhizosphere play a crucial role in plant health and ecosystem functioning. Among the myriads of rhizosphere microbes, Pseudomonas and Bacillus are prominent players known for their multifaceted functionalities and beneficial effects on plant growth. The molecular mechanism of interspecies interactions between natural isolates of Bacillus and Pseudomonas in medium conditions is well understood, but the interaction between the two in vivo remains unclear. This paper focuses on the possible synergies between Pseudomonas and Bacillus associated in practical applications (such as recruiting beneficial microbes, cross-feeding and niche complementarity), and looks forward to the application prospects of the consortium in agriculture, human health and bioremediation. Through in-depth understanding of the interactions between Pseudomonas and Bacillus as well as their application prospects in various fields, this study is expected to provide a new theoretical basis and practical guidance for promoting the research and application of rhizosphere microbes.

Mulches assist degraded soil recovery via stimulating biogeochemical cycling: metagenomic analysis

Soil degradation of urban greening has caused soil fertility loss and soil organic carbon depletion. Organic mulches are made from natural origin materials, and represent a cost-effective and environment-friendly remediation method for urban greening. To reveal the effects of organic mulch on soil physicochemical characteristics and fertility, we selected a site that was covered with organic mulch for 6 years and a nearby lawn-covered site. The results showed that soil organic matter, total nitrogen, and available phosphorus levels were improved, especially at a depth of 0-20 cm. The activities of cellulase, invertase, and dehydrogenase in soil covered with organic mulch were 17.46%, 78.98%, and 283.19% higher than those under lawn, respectively. The marker genes of fermentation, aerobic respiration, methanogenesis, and methane oxidation were also enriched in the soil under organic mulch. Nitrogen cycling was generally repressed by the organic mulch, but the assimilatory nitrate and nitrite reduction processes were enhanced. The activity of alkaline phosphatase was 12.63% higher in the mulch-covered soil, and functional genes involved in phosphorus cycling were also enriched. This study presents a comprehensive investigation of the influence of organic mulch on soil microbes and provides a deeper insight into the recovery strategy for soil degradation following urban greening. KEY POINTS: • Long-term cover with organic mulches assists soil recovery from degradation • Soil physical and chemical properties were changed by organic mulches • Organic mulches enhanced genes involved in microbially mediated C and P cycling • Soil organic matter was derived from decomposition of organic mulch and carbon fixation • N cycling was repressed by mulches, except for assimilatory NO2- and NO3- reductions.

Soil Microclimate and Persistence of Foodborne Pathogens Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica Newport in Soil Affected by Mulch Type

Mulching is a common agricultural practice that benefits crop production through soil moisture retention, weed suppression, and soil temperature regulation. However, little is known about the effect of mulch on foodborne pathogens present in soil. In this study, the influence of polyethylene plastic, biodegradable corn-based plastic, paper, and straw mulches on Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica Newport populations in soil was investigated. Silt loam soil in troughs was inoculated with a cocktail of the pathogens and covered with mulch or left bare, then incubated for 21 days, during which bacteria were enumerated and environmental parameters monitored. Bacterial counts declined in all treatments over time (p < 0.001) but persisted at 21 days at 0.8-0.95 log CFU/g. Pathogens also declined as a factor of mulch cover (p < 0.01). An exponential decay with asymptote model fit to the data revealed slower rates of decline in soil under mulches for all pathogens (p < 0.05) relative to bare soil. Compared to the average for all treatments, rates of decay in bare soil were 0.60 (p < 0.001), 0.45 (p < 0.05), and 0.63 (p < 0.001) log CFU/g/d for E. coli O157:H7, L. monocytogenes, and Salmonella, respectively. Linear multiple regression revealed that soil hydrological parameters were positively correlated (p < 0.05) with bacterial counts, while day soil temperatures were negatively correlated (p < 0.001), suggesting that higher day temperatures and lower moisture content of bare soil contributed to the faster decline of pathogens compared to mulched soil. A microcosm experiment using field soil from lettuce cultivation suggested no influence of prior mulch treatment on pathogens. In summary, pathogen decline in soil was modified by the soil microclimate created under mulch covers, but the effect appeared was restricted to the time of soil cover. Slower decline rates of pathogens in mulched soil may pose a risk for contamination of fresh market produce crops.

Effect of biochar and bioorganic fertilizer on the microbial diversity in the rhizosphere soil of Sesbania cannabina in saline-alkaline soil

Introduction

Biochar and bioorganic fertilizer (BOF) application in agriculture has garnered increasing interest recently. However, the effects of biochar and BOF on rhizosphere soil microecology, especially in a region with saline-alkaline soil, remain largely unexplored.

Methods

In this study, we performed Illumina-based 16S rRNA sequencing to investigate the effects of biochar with or without BOF addition, as well as at different addition rates and particles sizes, on the microecology of saline-alkaline rhizosphere soil.

Results

In the field experiment, biochar and BOF application altered the rhizosphere soil microecology. Actinobacteriota, Proteobacteria, and Chloroflexi accounted for >60% of the total bacterial population in each treatment. In the different treatments, Actinobacteria and Alphaproteobacteria were the predominant classes; Micromonosporales and Vicinamibacterales were the dominant orders; norank_f__Geminicoccaceae and Micromonosporaceae were the most abundant families; and Micromonospora and norank_f_Geminicoccaceae were the predominant genera. Application of biochar with or without BOF decreased soil electrical conductivity (EC) by 7% -11.58% only at the depth of 10 cm below the surface, again, soil EC can be significantly reduced by an average of 4% at 10 cm depth soil after planting Sesbania cannabina. Soil organic carbon, organic matter, available potassium, and available phosphorus contents had significant effects on the soil bacterial community structure.

Conclusion

Co-application of biochar and BOF resulted in the greatest improvement of rhizosphere soil microecology, either by promoting plant growth or improving the nutrition and physicochemical properties of soil, followed by BOF alone and biochar alone. Additionally, higher application rate of biochar was better than lower application rate, and fine biochar had a stronger effect than coarse biochar. These results provide guidance for the development of new saline-alkaline soil remediation strategies.

Microbiological mechanism for "production while remediating" in Cd-contaminated paddy fields: A field experiment

Security utilization measures (SUMs) for "production while remediating" in moderate and mild Cd-polluted paddy fields had been widely used. To investigate how SUMs drove rhizosphere soil microbial communities and reduced soil Cd bioavailability, a field experiment was conducted using soil biochemical analysis and 16S rRNA high-throughput sequencing. Results showed that SUMs improved rice yield by increasing the number of effective panicles and filled grains, while also inhibiting soil acidification and enhancing disease resistance by improving soil enzyme activities. SUMs also reduced the accumulation of harmful Cd in rice grains and transformed it into FeMn oxidized Cd, organic-bound Cd, and residual Cd in rhizosphere soil. This was partly due to the higher degree of soil DOM aromatization, which helped complex the Cd with DOM. Additionally, the study also found that microbial activity was the primary source of soil DOM, and that SUMs increased the diversity of soil microbes and recruited many beneficial microbes (Arthrobacter, Candidatus_Solibacter, Bryobacter, Bradyrhizobium, and Flavisolibacter) associated with organic matter decomposition, plant growth promotion, and pathogen inhibition. Besides, special taxa (Bradyyrhizobium and Thermodesulfovibrio) involved in sulfate/sulfur ion generation and nitrate/nitrite reduction pathway were observably enriched, which effectively reduced the soil Cd bioavailability through adsorption and co-precipitation. Therefore, SUMs not only changed the soil physicochemical properties (e.g., pH), but also drove rhizosphere microbes to participate in the chemical species transformation of soil Cd, thus reducing Cd accumulation in rice grains.

A comparison of microbial composition under three tree ecosystems using the stochastic process and network complexity approaches

Soil microbes act as "players" in regulating biogeochemical cycles, whereas environmental heterogeneity drives microbial community assembly patterns and is influenced by stochastic and deterministic ecological processes. Currently, the limited understanding of soil microbial community assembly patterns and interactions under temperate forest stand differences pose a challenge in studying the soil microbial involvement during the succession from coniferous to broad-leaved forests. This study investigated the changes in soil bacterial and fungal community diversity and community structure at the regional scale and identified the pathways influencing soil microbial assembly patterns and their interactions. The results showed that broad-leaved forest cover in temperate forests significantly increased soil pH, and effectively increased soil water content, total carbon (TC), total nitrogen (TN), and total phosphorus (TP) contents. Both soil bacterial and fungal alpha diversity indices were correlated with soil physicochemical properties, especially in broad-leaved forest. The bacterial and fungal community composition of coniferous forest was dominated by deterministic process (bacteria: 69.4%; fungi: 88.9%), while the bacterial community composition of broad-leaved forest was dominated by stochastic process (77.8%) and the fungal community composition was dominated by deterministic process (52.8%). Proteobacteria, Acidobacteriota, Actinobacteriota, and Verrucomicrobiota were the dominant phyla of soil bacterial communities in temperate forests. Whereas Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota were the dominant phyla of soil fungal communities in temperate forests. Most members of dominant phylum were regulated by soil physical and chemical properties. In addition, the succession from temperate coniferous forest to broad-leaved forest was conducive to maintaining the complex network of soil bacteria and fungi, and the top 20 degree of the major taxa in the network reflected the positive response of microbial interactions to the changes of soil nutrients during forest succession. This study not only shows the mechanism by which species differences in temperate forests of northern China affect soil microbial community assembly processes, but also further emphasizes the importance of the soil microbiome as a key ecosystem factor through co-occurrence network analysis.