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The activity of many antibiotics depends on the initial density of cells used in bacterial growth inhibition assays. This phenomenon, termed the inoculum effect, can have important consequences for the therapeutic efficacy of the drugs, because bacterial loads vary by several orders of magnitude in clinically relevant infections. Antimicrobial peptides are a promising class of molecules in the fight against drug-resistant bacteria because they act mainly by perturbing the cell membranes rather than by inhibiting intracellular targets. Here, we report a systematic characterization of the inoculum effect for this class of antibacterial compounds. Minimum inhibitory concentration values were measured for 13 peptides (including all-D enantiomers) and peptidomimetics, covering more than seven orders of magnitude in inoculated cell density. In most cases, the inoculum effect was significant for cell densities above the standard inoculum of 5 × 10⁵ cells/mL, while for lower densities the active concentrations remained essentially constant, with values in the micromolar range. In the case of membrane-active peptides, these data can be rationalized by considering a simple model, taking into account peptide–cell association, and hypothesizing that a threshold number of cell-bound peptide molecules is required in order to cause bacterial killing. The observed effect questions the clinical utility of activity and selectivity determinations performed at a fixed, standardized cell density. A routine evaluation of the dependence of the activity of antimicrobial peptides and peptidomimetics on the inoculum should be considered.

Soil salinity is a limiting factor in crop productivity. Inoculating crops with microorganisms adapted to salt stress is an alternative to increasing plant salinity tolerance. Few studies have simultaneously propagated arbuscular mycorrhizal fungi (AMF) and dark septate fungi (DSF) using different sources of native inoculum from halophyte plants and evaluated their effectiveness. In alfalfa plants as trap culture, this study assessed the infectivity of 38 microbial consortia native from rhizosphere soil (19) or roots (19) from six halophyte plants, as well as their effectiveness in mitigating salinity stress. Inoculation with soil resulted in 26–56% colonization by AMF and 12–32% by DSF. Root inoculation produced 10–56% and 8–24% colonization by AMF and DSF, respectively. There was no difference in the number of spores of AMF produced with both inoculum types. The effective consortia were selected based on low Na but high P and K shoot concentrations that are variable and are relevant for plant nutrition and salt stress mitigation. This microbial consortia selection may be a novel and applicable model, which would allow the production of native microbial inoculants adapted to salinity to diminish the harmful effects of salinity stress in glycophyte plants in the context of sustainable agriculture.

Rational use of antibiotic is the key approach to improve the antibiotic performance and tackling of the antimicrobial resistance. The efficacy of antimicrobials are influenced by many factors: (1) bacterial status (susceptibility and resistance, tolerance, persistence, biofilm) and inoculum size; (2) antimicrobial concentrations [mutant selection window (MSW) and sub-inhibitory concentration]; (3) host factors (serum effect and impact on gut micro-biota). Additional understandings regarding the linkage between antimicrobial usages, bacterial status and host response offers us new insights and encourage the struggle for the designing of antimicrobial treatment regimens that reaching better clinical outcome and minimizing the emergence of resistance at the same time.

Background. Recurrent Clostridium difficile infection (CDI) with poor response to standard antimicrobial therapy is a growing medical concern. We aimed to investigate the outcomes of fecal microbiota transplant (FMT) for relapsing CDI using a frozen suspension from unrelated donors, comparing colonoscopic and nasogastric tube (NGT) administration. Methods. Healthy volunteer donors were screened and a frozen fecal suspension was generated. Patients with relapsing/refractory CDI were randomized to receive an infusion of donor stools by colonoscopy or NGT. The primary endpoint was clinical resolution of diarrhea without relapse after 8 weeks. The secondary endpoint was self-reported health score using standardized questionnaires. Results. A total of 20 patients were enrolled, 10 in each treatment arm. Patients had a median of 4 (range, 2–16) relapses prior to study enrollment, with 5 (range, 3–15) antibiotic treatment failures. Resolution of diarrhea was achieved in 14 patients (70%) after a single FMT (8 of 10 in the colonoscopy group and 6 of 10 in the NGT group). Five patients were retreated, with 4 obtaining cure, resulting in an overall cure rate of 90%. Daily number of bowel movements changed from a median of 7 (interquartile range [IQR], 5–10) the day prior to FMT to 2 (IQR, 1–2) after the infusion. Self-ranked health score improved significantly, from a median of 4 (IQR, 2–6) before transplant to 8 (IQR, 5–9) after transplant. No serious or unexpected adverse events occurred. Conclusions. In our initial feasibility study, FMT using a frozen inoculum from unrelated donors is effective in treating relapsing CDI. NGT administration appears to be as effective as colonoscopic administration. Clinical Trials Registration. NCT01704937.

Microbial toxicity tests play an important role in various scientific and technical fields including the risk assessment of chemical compounds in the environment. There is a large battery of normalized tests available that have been standardized by ISO (International Organization for Standardization) and OECD (Organization for Economic Co-operation and Development) and which are worldwide accepted and applied. The focus of this review is to provide information on microbial toxicity tests, which are used to elucidate effects in other laboratory tests such as biodegradation tests, and for the prediction of effects in natural and technical aqueous compartments in the environment. The various standardized tests as well as not normalized methods are described and their advantages and disadvantages are discussed. In addition, the sensitivity and usefulness of such tests including a short comparison with other ecotoxicological tests is presented. Moreover, the far-reaching influence of microbial toxicity tests on biodegradation tests is also demonstrated. A new concept of the physiological potential of an inoculum (PPI) consisting of microbial toxicity tests whose results are expressed as a chemical resistance potential (CRP) and the biodegradation adaptation potential (BAP) of an inoculum is described that may be helpful to characterize inocula used for biodegradation tests. Key points • Microbial toxicity tests standardized by ISO and OECD have large differences in sensitivity and applicability. • Standardized microbial toxicity tests in combination with biodegradability tests open a new way to characterize inocula for biodegradation tests. • Standardized microbial toxicity tests together with ecotoxicity tests can form a very effective toolbox for the characterization of toxic effects of chemicals.

Continuous‐flow anaerobic digestion (AD) of wheat straw (WS) is often limited by volatile fatty acid (VFA) accumulation at low inoculum‐to‐substrate ratios (ISRs). Here, biochar (8.0 g/L) recovered methane production in overloaded systems (ISR 0.5, HRT 12 days), increasing yields by 658.45 mL/g‐VS. Microbial analysis revealed a shift from Methanomicrobiaceae to Methanosarcinaceae dominance upon biochar addition, correlating with mcrA gene upregulation. This strategy enhances the AD of refractory feedstocks without diluting the organic load. The results offer insights into optimizing biogas systems treating low‐biodegradability feedstocks at low ISRs, highlighting biochar's potential to stabilize performance and enrich functional microbial communities under stress conditions. The study investigated how biochar supplementation can improve biogas production from WS, food waste (FW), and glucose with different biodegradability. Using continuous‐flow anaerobic digesters, ISRs and hydraulic retention times (HRTs) were tested on the substrates. Biochar restored methane generation.

Key messageUrban trees are passively subject to and actively mitigate urban environmental pressures. Suitable selection of tree species and appropriate management can make cities useful habitats for trees.The urban environment is stressful not only because of pollution but also due to heat and drought, creating arid conditions. Trees are passively subject to the microclimate but are also actively modifying it, and they perform important urban ecosystem services. Trees function as bio-indicators of urban conditions by morphological features and by dendrochronology and dendrobiochemistry. Anchorage and mechanical stability need to be surveyed. Among the stresses in addition to deposition of metals, there is gaseous pollution of the atmosphere (SO2, NO2, and O3). Reacting to that are leaf anatomy as well as even the fine-tuning of biochemical pathways, e.g., terpene synthesis. The significant urban stresses are heat and drought. They increase top dieback and lead to a decrease of life crown-top heights from the ground (LCTH), where water relations remain similar in the crowns at various heights. Statistics of dendrochronology allow identification of pointer years with exceptionally wide and narrow tree rings. The prevalence of pointer years helps the selection of species suited for plantation in cities. Measurements of water potential at the turgor-loss point, πtlp, indicative of the permanent wilting point also helped identifying whole-plant drought tolerance. Infection by wood-decay fungi is a hazardous urban problem, as wood-decay builds up over many years increasing the danger of tree fall. Ectomycorrhiza is hampered in urban soils having a low inoculum potential due to chemical and physical soil qualities regarding cation-exchange capacity, permanent wilting point, and availability of water. Management should be based on scientific investigations. Allometry modeling allows for quantifying ecosystem services. Surveying stability is possible for instance by noninvasive acoustic tomography. Practices are irrigation and mulching. With appropriate management, cities can be useful habitats for trees contributing to biological richness and the comfort of life in cities.

The aim of the study was to examine the effects of inoculation with arbuscular mycorrhizal fungi (AMF) on growth, productivity and mineral contents of chickpeas in pot experiment. The experiment was set in three levels of AMF (50 g, 100 g, and 150 g). Host growth stages of chickpea cultivars had increased positively with the AMF inoculation. Nitrogen concentrations in the rhizospheric soil of Parbath-98 and Noor-2019 cultivars were high (870 mg/kg and 2570 mg/kg, respectively) at low level of AMF inoculum, which indicated the absorption of nitrogen from soil effected inversely. Elemental analysis of chickpea all three cultivars showed good absorption of phosphorus; i.e., 1.50 mg/kg, 0.34 mg/kg, and 2.21 mg/kg at 150 g AMF inoculum. The results of AMF root colonization, spore densities, proximate and elemental analysis revealed that at 150 g AMF inoculum provision, effective outcomes of these indicators seen compare to 50 g and 100 g. The elevated root colonization along spore densities were observed at maximum level of AMF inoculum in all three cultivars of chickpea. The highest AMF root colonization of 66.10% in Dashat-98 directly affected its proximate concentrations. Interaction of AMF with plant proximate and elemental at p  < 0.05, a significant association was observed in the absorption of nutrients. Morphologically identified genera of AMF ( Glomus , Gigaspora Sclerocystis, and Acaulospora ) were in the size range of 33–265 µm in which Glomus was highly abundant. Thirteen AMF taxa were confirmed molecularly by universal AMF primers. It was concluded that AMF inoculum influenced chickpea productivity and a study need in the agricultural fields to explore the diversity of AMF. Graphical Abstract

• Arbuscular mycorrhizal (AM) fungi gain access to nutrient patches outside the rhizosphere by producing an extensive network of fine hyphae. Here, we focused on establishing the mechanism by which AM fungal hyphae reach discrete organic patches with a cohort of functional bacteria transported in a biofilm on their surface. • We investigated the mechanisms and impact of the translocation of phosphate solubilising bacteria (PSB) along AM fungal hyphae in bespoke microcosms. An in vitro culture experiment was also conducted to determine the direct impact of hyphal exudates of AM fungi upon the growth of PSB. • The extraradical hyphae of AM fungi can transport PSB to organic phosphorus (P) patches and enhance organic P mineralisation both under in vitro culture and soil conditions. Bacteria move in a thick water film formed around fungal hyphae. However, the bacteria cannot be transferred to the organic P patch without an energy source in the form of hyphal exudates. • Our results could be harnessed to better manage plant–microbe interactions and improve the ability of biological inocula involving AM fungi and bacteria to enhance the sustainability of agricultural crops in P limited conditions.

Summary Priority effects among wood decomposers have been demonstrated by manipulating fungal assembly history via inoculations in dead wood and then tracking community development using DNA sequencing. Individual wood‐degrading fungi have been shown, however, to initiate decay after having colonized living trees as endophytes. To track these ‘upstream’ colonizers across the endophyte–saprophyte transition, we coupled high‐throughput sequencing with wood physiochemical analyses in stem sections extracted from healthy birch trees (Betula papyrifera; 4–7 cm dia.). We incubated wood in microcosms, limiting communities as endophytes−only or challenging endophytes with Fomes fomentarius or Piptoporus betulinus at high exogenous inoculum potential. Initial fungal richness in birch stems averaged 143 OTUs and decreased nearly threefold after five months of decomposition. Although F. fomentarius successfully colonized some stem sections incubated at 25 °C, decayed wood was generally dominated by saprophytic fungi that were present originally in lower abundances as endophytes. Among saprophytes, fungi in the brown rot functional guild consistently dominated, matching wood residues bearing the chemical hallmarks of brown rot. Despite this functionally redundant outcome, the taxa that rose to dominate in individual sections varied. Surprisingly, the brown rot taxa dominating wood decomposition were better known for lumber degradation rather than log decay in ground contact. Given the isolation from colonizers in our design, this redundancy of brown rot as the outcome suggests that these taxa and more generally brown rot fungi could have adapted to decompose wood where there is lower competitive pressure. Competitive avoidance would complement the diffuse depolymerization mechanisms of brown rot fungi, which are likely more prone to sugar pilfering by other organisms than the processive depolymerization mechanisms of white rot fungi. Overall, this guild‐level predictability of fungal endophyte development and consequence is encouraging given the challenges of predicting wood decomposition, and it provides a base for testing these dynamics under increasing natural complexity. Lay Summary