Bulk and spatially resolved extracellular metabolomics of free-living nitrogen fixation

Soil microorganisms drive ecosystem function, but challenges of scale between microbe and ecosystem hinder our ability to accurately quantify and predictively model the soil microbe-ecosystem function relationship. Quantifying this relationship necessitates studies that systematically characterize multi-omics of soil microorganisms and their activity across sampling scales from spatially resolved to bulk measures, and structural complexity, from liquid pure culture to in situ. To address this need, we cultured two diazotrophic bacteria in liquid and solid media, with and without nitrogen (N) to quantify differences in extracellular metabolites associated with nitrogen fixation under increasing environmental structural complexity. We also quantified extracellular metabolites across sampling scales including bulk sampling via GC-MS analysis and spatially resolved analysis via MALDI mass spectrometry imaging. We found extracellular production of inorganic and organic N during free-living nitrogen fixation activity, highlighting a key mechanism of terrestrial N contributions from this process. Additionally, our results emphasize the need to consider the structural complexity of the environment and spatial scale when quantifying microbial activity. We found differences in metabolite profiles between culture conditions, supporting previous work indicating environmental structure influences microbial function, and across scales, underscoring the need to quantify microbial scale conditions to accurately interpret microbial function.

Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine

The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood, being hardly observed. Here, we assessed the invasions of manure-borne bacteria during a coalescence event between manure and soil, in different soils and in the presence or absence of antibiotics. To this end, microcosms of four different soils were amended or not with manure at an agronomical dose and/or exposed or not to the antibiotic sulfamethazine (SMZ). After one month of incubation, the diversity, structure and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible one month after the soil amendment. The results obtained with the soil already amended in situ with manure six months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms. It was significant in only one soil, where it enhanced the invasion potential of some manure-borne invaders.

Mapping Soil Productivity Index on Plantation Land in ATP Jatikerto, Kromengan District, Malang Regency

It is feared that the decline in productivity of plantation crops in Malang Regency, so it is necessary to analyze the soil productivity index at ATP Jatikerto as one of the locations for producing plantation plants. This soil productivity index assessment was presented in the form of a map to make it easier to see the distribution pattern of soil productivity in ATP Jatikerto. The results of the calculation of the productivity index showed that the land potential varied from land with poor to sufficient criteria, namely maize land with an IP (Productivity Index) of 43.27, which is included in the bad IP criteria. In coffee, cocoa, sugarcane, papaya, and citrus fields, they are categorized as moderate with IPs of 50.14, respectively; 45.82; 39.45; 52.26; and 45.82. Actions that can be taken to overcome the problem of decreasing productivity are to carry out regular fertilization, both organic and inorganic, to keep nutrients available for cultivated plants, as well as adding organic matter using litter which not only serves to add nutrients but can also be used as organic mulch to prevent raindrops from falling directly to the ground so that the loss of topsoil can be minimized and increase the population of soil microorganisms. In addition, it can also use bagasse, blotong or manure which can improve the physical condition of the soil by reducing soil density and increasing macropores for better root growth, and ultimately increasing sugarcane yield.

Screening and Characterization of Soil Microbes Producing Antimicrobial Compounds in Makkah Province, Saudi Arabia

This study aimed to investigate a method to manage antimicrobial resistance (AMR) issues by exploring soil microorganisms that are capable of producing bioactive compounds. Eight different types of soil were selected from three locations to screen, isolate, and identify microorganisms that are capable of producing antimicrobial compounds. The multi-drug resistant strains are Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Candida albicans were selected for primary and secondary screening using the crowded plate method and the agar well diffusion method. Inhibition zones were measured, and data were assessed using statistical tests to check for normality and differences between parametric variables and nonparametric data. This was followed by biochemical characterization, DNA isolation, and polymerase chain reaction (PCR). Molecular identification was performed using 16S rRNA amplification and sequencing. Here, 86 isolates containing bacteria and fungi were successfully extracted from soil samples. Further, 49 of 86 microbes showed possible antimicrobial activity, but only 12 isolates resulted in distinct inhibition zones with the selected multi-drug resistant strains. The following different taxa were identified: Firmicutes (nine strains), Proteobacteria (one strain), Actinobacteria (one strain), and Azotobacter (one strain). Species are represented in a phylogenetic tree, which was constructed using the unweighted pair-group method with arithmetic mean (UPGMA) method. The evolutionary distances were computed using the Maximum Composite Likelihood method. The identified microorganisms showed antimicrobial activity, confirming that soil microorganisms have great potential to address AMR issues.

Enhancement of Interplanting of Ficus carica L. with Taxus cuspidata Sieb. et Zucc. on Growth of Two Plants

Medicinal-agroforestry systems are one of the multi-functional medicinal plant production systems, gaining attention as a sustainable alternative to traditional monoculture systems. In this study, three planting patterns were established which included: (1) monoculture F. carica (MF); (2) monoculture T. cuspidata (MT); and (3) interplanting F. carica with T. cuspidata (IFT). The differences of growth biomass, photosynthesis, soil nutrients, soil enzyme activities, soil microorganisms, and main secondary metabolites of F. carica and T. cuspidata under the above three models were investigated. Compared with the MF and MT patterns, IFT pattern for 5 months significantly increased the plant growth biomass, photosynthesis, soil organic carbon, total nitrogen, and secondary metabolites content. The activities of acid phosphatase, sucrase, protease, polyphenol oxidase, urease, dehydrogenase, and catalase in soil of IFT were significantly higher than MF and MT patterns. Results showed that IFT pattern is preferred compared to the MF and MT patterns. Our result will help to provide a feasible theoretical basis for the large-scale establishment of F. carica and T. cuspidata mixed forests and obtain high-quality medicine sources for extracting important active ingredients, psoralen and paclitaxel, which are crucial to the long-term sustainable development and production of medicinal plants.