Rhizosphere Microbial Communities Are Significantly Affected by Optimized Phosphorus Management in a Slope Farming System

Endophytic microbial diversity associated with commercial cultivar and crop wild relative banana variety could provide clues for microbial community management

Endophytes, microorganisms inhabiting internal plant tissues, play a pivotal role in plant growth and disease resistance. Moreover, previous studies have established that Musa plants derive disease protective functions from their microbiome. Notably, one of the crop wild relatives of banana, the Calcutta 4 variety, exhibits resistance to various phytopathogens such as Pseudocercospora fijiensis (P. fijiensis), while the Williams commercial cultivar (cv.) is highly susceptible. Therefore, this study aims primarily to characterize and compare the endophytic microbiota composition of Calcutta 4 and Williams banana plants when grown sympatrically. Alongside, differences in endophytic microbiome between plant sections (shoot or roots), growth phases (in vitro or greenhouse) and fitness factors such as the addition of plant growth-promoting bacteria Bacillus subtilis EA-CB0575 (T2 treatment) or infection by P. fijiensis (T3 treatment) were examined. Both culture-dependent and -independent techniques were used to evaluate these differences and assess the culturability of banana endophytes under varying conditions. Microbial cultures resulted in 331 isolates distributed across 54 genera when all treatments were evaluated, whereas 16 S sequencing produced 9510 ASVs assigned in 1456 genera. Alpha and beta diversity exhibited significant differences based on plant section, with an increase in phylogenetic diversity observed in plants with pathogen infection (T3) compared to control plants (T1). Additionally, four differentially abundant genera associated with nitrogen metabolism were identified in T3 plants and seven genera showed differential abundance when comparing varieties. When culture-dependent and -independent methods were compared, it was found that isolates represented 3.7 % of the genera detected by culture-independent methods, accounting for 12-41 % of the total data depending on the treatment. These results are crucial for proposing management strategies derived from crop wild relatives to enhance the resilience of susceptible commercial varieties against fitness factors affecting crop development. Additionally, they help to decipher the pathogenic effects of P. fijiensis in banana plants and advance the understanding of how plant domestication influences the endosphere.

Influence of Geothermal Fumaroles in Driving the Microbial Community Dynamics and Functions of Adjacent Ecosystems

Growing evidence suggests that the hydrochemical properties of geothermal fumaroles may play a crucial role in shaping the diversity and functions of microbial communities in various environments. In the present study, the impact of geothermal furaneols on the microbial communities and their metabolic functions across the rock-soil-plant continuum was explored considering varying distances from the fumarole source. The results revealed that bacterial phylum Proteobacteria was predominant in all sample types, except in the 10 m rock sample, irrespective of the sampling distance. Archaeal phyla, such as Euryarchaeota and Crenarchaeota, were more prevalent in rock and soil samples, whereas bacterial phyla were more prevalent in plant samples. Thermoacidophilic archaeons, including Picrophilus, Ferroplasma, and Thermogymnomonas were dominant in rocks and soil samples of 1 and 5 m distances; acidophilic mesophiles, including Ferrimicrobium and Granulicella were abundant in the rhizoplane samples, whereas rhizosphere-associated microbes including Pseudomonas, Pedobacter, Rhizobium, and Novosphingobium were found dominant in the rhizosphere samples. The functional analysis highlighted the higher expression of sulfur oxidative pathways in the rock and soil samples; dark iron oxidation and nitrate/nitrogen respiratory functions in the rhizosphere samples. The findings underscore microbial adaptations across the rock-soil-plant continuum, emphasizing the intricate relationship between geothermal fumaroles and microbial communities in adjacent ecosystems. These insights offer a crucial understanding of the evolution of microbial life and highlight their pivotal roles in shaping ecosystem dynamics and functions.

Phosphorus addition increases stability and complexity of co-occurrence network of soil microbes in an artificial Leymus chinensis grassland

Introduction

Understanding the response of cross-domain co-occurrence networks of soil microorganisms to phosphorus stability and the resulting impacts is critical in ecosystems, but the underlying mechanism is unclear in artificial grassland ecosystems.

Methods

In this study, the effects of four phosphorus concentrations, P0 (0 kg P ha-1), P1 (15.3 kg P ha-1), P2 (30.6 kg P ha-1), and P3 (45.9 kg P ha-1), on the cross-domain co-occurrence network of bacteria and fungi were investigated in an artificial Leymus chinensis grassland in an arid region.

Results and discussion

The results of the present study showed that phosphorus addition significantly altered the stem number, biomass and plant height of the Leymus chinensis but had no significant effect on the soil bacterial or fungal alpha (ACE) diversity or beta diversity. The phosphorus treatments all increased the cross-domain co-occurrence network edge, node, proportion of positively correlated edges, edge density, average degree, proximity to centrality, and robustness and increased the complexity and stability of the bacterial-fungal cross-domain co-occurrence network after 3 years of continuous phosphorus addition. Among them, fungi (Ascomycota, Basidiomycota, Mortierellomycota and Glomeromycota) play important roles as keystone species in the co-occurrence network, and they are significantly associated with soil AN, AK and EC. Finally, the growth of Leymus chinensis was mainly due to the influence of the soil phosphorus content and AN. This study revealed the factors affecting the growth of Leymus chinense in artificial grasslands in arid areas and provided a theoretical basis for the construction of artificial grasslands.

Short-Term Impact of Recycling-Derived Fertilizers on Their P Supply for Perennial Ryegrass (Lolium perenne)

Various nutrient recycling technologies are currently under development in order to alleviate the dependency of non-renewable raw material for the production of mineral phosphorus fertilizers commonly used in agriculture. The resulting products, such as struvites and ashes, need to be assessed for their application as so-called recycling-derived fertilizers (RDFs) in the agricultural sector prior to commercialization. Here, we conducted a short-term (54 days) trial to investigate the impact of different phosphorus fertilizers on plant growth and the soil P cycling microbiota. Lolium perenne was grown with application of superphosphate (SP) as inorganic fertilizer, two ashes (poultry litter ash (PLA) and sewage sludge ash (SSA)), and two struvites (municipal wastewater struvite (MWS) and commercial CrystalGreen® (CGS)) applied at 20 and 60 kg P ha-1 in four replicates. A P-free control (SP0) was also included in the trial. Struvite application increased plant dry weights, and available P acid phosphatase activity was significantly improved for struvites at the high P application rate. The ash RDFs showed a liming effect at 60 kg P ha-1, and PLA60 negatively affected acid phosphatase activity, while PLA20 had significantly lower phoD copy numbers. P mobilization from phosphonates and phytates was not affected. TCP solubilization was negatively affected by mineral SP fertilizer application at both P concentrations. The bacterial (16S and phoD) communities were only marginally affected by the tested P fertilizers. Overall, struvites appeared to be a suitable substitute for superphosphate fertilization for Irish L. perenne pastures.

Effects of time-space conversion on microflora structure, secondary metabolites composition and antioxidant capacity of Codonopsis pilosula root

In order to study the relationship between medicinal plant Codonopsis pilosula phenotype, secondary metabolites, antioxidant capacity and its rhizosphere soil nutrients, root-related microorganisms under seasonal and geographical changes, high-throughput sequencing technology was used to explore the bacterial community structure and variation in rhizosphere soil and root endosphere from six regions of Dingxi City, Gansu Province during four seasons. Secondary metabolites composition and antioxidant capacities of C. pilosula root collected successively from four seasons were determined. The chemical properties, nutrient content and enzyme activities of rhizosphere of C. pilosula were significantly different under different temporal and spatial conditions. All soil samples were alkaline (pH 7.64-8.42), with water content ranging from 9.53% to 19.95%, and electrical conductivity varied widely, showing obvious time-scale effects. Different time scales were the main reasons for the diversity and structure of rhizosphere bacterial community of C. pilosula. The diversity and richness of rhizosphere bacterial community in autumn and winter were higher than those in spring and summer, and bacterial community structure in spring and summer was more similar to that in autumn and winter. The root length and diameter of C. pilosula showed significant time gradient difference under different spatiotemporal conditions. Nutrition and niche competition lead to significant synergistic or antagonistic interactions between rhizosphere bacteria and endophytic bacteria, which invisibly affect soil properties, abundance of functional bacteria and even yield and quality of C. pilosula. Soil properties, rhizosphere bacteria and endophytic bacteria directly promoted root phenotype, stress resistance and polysaccharide accumulation of C. pilosula.

Global profiling of antibiotic resistomes in maize rhizospheres

The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.