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Few studies have been conducted on adaptations of microbial communities to low and fluctuating temperatures using environmentally relevant conditions. In this study, six Himalayan and two temperate soils were selected as candidates for low-temperature/freeze–thaw (FT)-adapted and susceptible soils, respectively. Redundancy analysis with forward selection was used to create a model of environmental parameters explaining variability in the initial microbial abundance and 4 °C activities. The best predictor was soil carbon, explaining more than 74% of data variability (P=0.002), despite significant differences in the soil characteristics and environmental history. We tested the hypothesis that the reproduced Himalayan FT fluctuations select physiologically similar communities in distinct soils. Microcosms were experimentally subjected to two separate 50 and 60 FT cycle (FTC) experiments. A significant decrease in abundance, 4 °C basal respiration and drastic rearrangements in community-level physiological profiles (CLPP) were observed in microcosms with temperate soils until 40 FTC. CLPP remained distinct from those of the Himalayan soils. Minor changes were observed in the Himalayan soils, confirming that microbial populations with physiological traits consistent with the noncontinuous permafrost conditions reside in the Himalayan soils, whereas the surviving temperate soil microorganisms actively adjusted to novel environmental conditions.

Global prevalence of antibiotic residues (ABX) in rivers requires ecotoxicological impact assessment. River microbial communities serve as effective bioindicators for this purpose. We quantified the effects of eight commonly used ABXs on a freshwater river microbial community using Biolog EcoPlates™, enabling the assessment of growth and physiological profile changes. Microbial community characterization involved 16S rRNA gene sequencing. The river community structure was representative of aquatic ecosystems, with the prevalence of Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes. Our findings reveal that all ABXs at 100 µg/mL reduced microbial community growth and metabolic capacity, particularly for polymers, carbohydrates, carboxylic, and ketonic acids. Chloramphenicol, erythromycin, and gentamicin exhibited the highest toxicity, with chloramphenicol notably impairing the metabolism of all studied metabolite groups. At lower concentrations (1 µg/mL), some ABXs slightly enhanced growth and the capacity to metabolize substrates, such as carbohydrates, carboxylic, and ketonic acids, and amines, except for amoxicillin, which decreased the metabolic capacity across all metabolites. We explored potential correlations between physicochemical parameters and drug mechanisms to understand drug bioavailability. Acute toxicity effects at the river-detected low concentrations (ng/L) are unlikely. However, they may disrupt microbial communities in aquatic ecosystems. The utilization of a wide array of genetically characterized microbial communities, as opposed to a single species, enables a better understanding of the impact of ABXs on complex river ecosystems.

Abstract Previous studies have shown that it is possible to accurately predict wheat grain quality and yields using microbial indicators. However, it is uncertain what the best timing for sampling is. For optimal usefulness of this modeling approach, microbial indicators from samples taken early in the season should have the best predictive power. Here, we sampled a field every two weeks across a single growing season and measured a wide array of microbial parameters (amplicon sequencing, abundance of N-cycle related functional genes, and microbial carbon usage) to find the moment when the microbial predictive power for wheat grain baking quality is highest. We found that the highest predictive power for wheat grain quality was for microbial data derived from samples taken early in the season (May–June), which coincides roughly with the seedling and tillering growth stages, that are important for wheat N nutrition. Our models based on LASSO regression also highlighted a set of microbial parameters highly coherent with our previous surveys, including alpha- and beta-diversity indices and N-cycle genes. Taken together, our results suggest that measuring microbial parameters early in the wheat growing season could help farmers better predict wheat grain quality. Early season soil microbiome can accurately predict wheat grain quality at harvest.

Background Pepper ( Capsicum annuum L.), an annual herbaceous plant of the Solanaceae family, is extensively cultivated as both a fresh vegetable and a condiment, ranking among the most widely grown vegetable crops globally. Pod pepper ( Capsicum annuum var. conoides ), major variety of pepper, often suffers from salt stress during growth, leading to reduced yield and quality. However, systematic multi-omics studies on the salt stress response in pod pepper remain limited. Results To elucidate physiological responses and salt tolerance mechanisms in pepper plants, this study screened 63 pod pepper accessions and selected salt-tolerant (P47) and salt-sensitive (P18) varieties for comparative analysis. Integrated physiological, transcriptomic and metabolomic analyses revealed that P47 exhibited lower leaf relative electrical conductivity, malondialdehyde content, and Na⁺/K⁺ ratio, along with better maintenance of chlorophyll a content and antioxidant enzyme activities. Transmission electron microscopy showed that P47 maintained intact mesophyll cell ultrastructure under stress, while P18 exhibited severe damage, including chloroplast membrane disintegration and starch grain degradation. Integrated transcriptomic and metabolomic analysis further revealed significant enrichment of differential metabolites in pathways such as phenylpropanoid biosynthesis, tyrosine metabolism, alkaloid biosynthesis, and glycerophospholipid metabolism. Key salt-responsive genes, including SAUR , ARF7 , and TAT , involved in plant hormone signal transduction, tyrosine metabolism, and alkaloid biosynthesis, were identified. Conclusions This study, for the first time, systematically reveals the involvement of the alkaloid pathway in the salt stress response of pod pepper through integrated multi-omics approaches. It elucidates the physiological and molecular mechanisms by which the salt-tolerant variety enhances antioxidant capacity, regulates ion homeostasis, and maintains cellular structural integrity under salt stress. These findings provide a theoretical basis and genetic resources for targeted breeding of salt-tolerant pepper cultivars.

In terrestrial ecosystems, deep soils (below 30 cm) are major organic carbon (C) pools. The labile carbon input could alter soil organic carbon (SOC) mineralization, resulting in priming effect (PE), which could be modified by nitrogen (N) availability, however, the underlying mechanism is unclear for deep soils, which complicates the prediction of deep soil C cycling in response to N deposition. A series of N applications with 13 C labeled glucose was set to investigate the effect of labile C and N on deep SOC mineralization. Microbial biomass, functional community, metabolic efficiency and enzyme activities were examined for their effects on SOC mineralization and PE. During incubation, glucose addition promoted SOC mineralization, resulting in positive PE. The magnitude of PE decreased significantly with increasing N. The N-regulated PE was not dependent on extracellular enzyme activities but was positively correlated with carbon use efficiency and negatively with metabolic quotient. Higher N levels resulted in higher microbial biomass and SOC-derived microbial biomass than lower N levels. These results suggest that the decline in the PE under high N availability was mainly controlled by higher microbial metabolic efficiency which allocated more C for growth. Structural equation modelling also revealed that microbial metabolic efficiency rather than enzyme activities was the main factor regulating the PE. The negative effect of additional N suggests that future N deposition could promote soil C sequestration.

Soil is home to microbiota with diverse metabolic activities. These microorganisms play vital roles in many ecological processes. Thus, the assessment of microbial functional diversity is an important quality indicator of soil ecosystems. In this study, we collected soil samples from three distinct forest habitats, i.e., an agroforest, a primary forest (PF), and a secondary forest, within the Angat Watershed Reservation in Bulacan, Northern Philippines. Community-level physiological profiling (CLPP) was done with the BIOLOG EcoPlate™ to analyze the responses of the soil microbial communities from the three forest habitats in the absence or presence of antibiotics. The BIOLOG EcoPlate represents 31 utilizable carbon sources. Based on the CLPP analysis, soil samples from the PF showed significantly higher utilization of most carbon sources than the other forest types ( p  < 0.05). Thus, less disturbed forest types constitute more functionally diverse microbial communities. The presence of antibiotics significantly decreased the carbon utilization patterns of the soil microbial communities ( p  < 0.05), indicating the possible use of CLPP in monitoring contamination in soil.

The study of bacterial communities associated with extreme ecosystems is one of the most important tasks in modern microbial ecology. Despite a large number of studies being performed, the ecosystems that have not been sufficiently explored from the microbiological point of view still exist. Such research is needed for improving the understanding of the limits and mechanisms of bacterial survival under extreme conditions, and for revealing previously undescribed species and their role in global biospheric processes and their functional specifics. The results of the complex microbiological characteristics of permafrost and ice—collected on the Severniy Island in the northern part of the Novaya Zemlya archipelago—which have not previously been described from microbiological point of view, are presented in this article. The analysis included both culture-independent and culture-dependent methods, in particular, the spectra of metabolic activity range analysis in vitro under different temperature, pH and salinity conditions. High values for the total number of prokaryotes in situ (1.9 × 108–3.5 × 108 cells/g), a significant part of which was able to return to a metabolically active state after thawing, and moderate numbers of culturable bacteria (3.3 × 106–7.8 × 107 CFU/g) were revealed. Representatives of Proteobacteria, Actinobacteria, and Bacteroidetes were dominant in situ; Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes were the most abundant phyla in vitro. Physiological assays revealed the mesophilic and neutrophilic optima of temperature and pH of culturing conditions, respectively, and wide temperature and pH ranges of culturable communities’ reproduction activity. Isolated strains were characterized by moderate halotolerant properties and antibiotic resistance, including multiple antibiotic resistance. It was found that almost all cultured bacterial diversity revealed (not just a few resistant species) had extremotolerant properties regarding a number of stress factors. This indicates the high adaptive potential of the studied microbial communities and their high sustainability and capability to retain functional activity under changing environmental (including climatic) conditions in wide ranges.

Walnut (Juglans regia L.) performance and sustainability are closely linked to soil–plant–microbe interactions; nowadays, the combined influence of edaphic context, plantation development and rootstock genotype on walnut-associated microbiomes remains insufficiently resolved. Here, we integrated soil physicochemical characterization, community-level physiological profiling and 16S rRNA gene amplicon sequencing across walnut plantations in four Spanish regions. The design included 14-year clonal stands (Galicia, Gerona, Toledo), an age gradient in Galicia (4, 9 and 14 years), and four rootstocks (MJ209, Vlach, own-rooted ‘Chandler’ and J. regia seedling) in the Córdoba plantation. At the community-level, rhizospheres exhibited higher overall metabolic activity, displaying substrate-specific functional fingerprints across regions. Regarding stand ages, a functional peak was observed at middle age, with a decline in richness and diversity with age. Moreover, rootstock genotype further modulated rhizosphere metabolic function. Sequencing supported compositional differences among regions, ages and rootstocks, identifying a bacterial core of Juglans spp. rhizosphere and detecting 36 putative Plant Growth-Promoting Rhizobacteria (PGPR) genera, suggesting a potential reservoir and possible uses in plant biotechnology. Overall, walnut-associated microbiomes are jointly structured by soil gradients, plantation development and rootstock genotype, supporting site and genotype-tailored microbiome management.

Background Microbial communities inhabiting the rhizosphere play pivotal roles in determining plant health and yield. Manipulation of the rhizosphere microbial community is a promising means to enhance the productivity of economically viable and important agricultural crops such as sunflower ( Helianthus annuus ). This study was designed to gain insights into the taxonomic and functional structures of sunflower rhizosphere and bulk soil microbiome at two different locations (Sheila and Itsoseng) in South Africa. Results Microbial DNA extracted from the sunflower rhizosphere and bulk soils was subjected to next-generation sequencing using 16S amplicon sequencing technique. Firmicutes , Actnobacteria and Proteobacteria predominated sunflower rhizosphere soils. Firmicutes , Cyanobacteria , Deinococcus - Thermus and Fibrobacteres were positively influenced by Na + and clay content, while Actinobacteria , Thaumarchaeota , Bacteroidetes , Planctomycetes , Aquificae and Chloroflexi were positively influenced by soil resistivity (Res) and Mg 2+ . The community-level physiological profiling (CLPP) analysis showed that the microbial communities in SHR and ITR used the amino acids tryptophan and malic acid efficiently. The metabolisms of these carbon substrates may be due to the dominant nature of some of the organisms, such as Actinobacteria in the soils. Conclusion The CLPP measurements of soil from sunflower rhizosphere were different from those of the bulk soil and the degree of the variations were based on the type of carbon substrates and the soil microbial composition. This study has shown the presence of certain taxa of rhizobacteria in sunflower rhizosphere which were positively influenced by Na + and Mg 2+ , and taxa obtained from SHR and ITR were able to effectively utilized tryptophan and malic acid. Many unclassified microbial groups were also discovered and it is therefore recommended that efforts should further be made to isolate, characterize and identify these unclassified microbial species, as it might be plausible to discover new microbial candidates that can further be harnessed for biotechnological purpose.