Comprehensive reviews in food science and food safetyRafael Bianchini Fulindi, Argemiro Soares da Silva Sobrinho, Anderson S Sant'Ana
The persistence of foodborne pathogens on industrial food contact surfaces continues to challenge global food safety despite advances in sanitation technologies. A central limitation of current antimicrobial strategies lies in their validation under simplified laboratory conditions that overlook the physicochemically driven formation of food matrix conditioning films. Upon contact with food residues, organic macromolecules reorganize at the solid‒liquid interface, forming conditioning layers that mask engineered surface functionalities and facilitate microbial attachment. This review examines how such interfacial transformations constrain conventional bactericidal approaches and contribute to sanitization failures in industrial environments. Plasma surface engineering is evaluated as a matrix-aware strategy capable of tailoring surface energy, hydration behavior, and nanoscale architecture through plasma-enhanced chemical vapor deposition and magnetron sputtering. These approaches may mitigate organic fouling and modulate bacterial surface sensing under controlled conditions. Particular attention is given to mechanotransduction pathways implicated in early biofilm formation, highlighting how nanoscale surface cues influence c-di-GMP signaling and biofilm commitment in both Gram-negative and Gram-positive foodborne pathogens, including Salmonella spp. and Listeria monocytogenes. Significant translational gaps remain, including long-term durability under repeated cleaning-in-place cycles, antimicrobial transport through complex conditioning films, and adaptive tolerance under chronic exposure. This review situates plasma surface engineering within a preventive interfacial design framework, offering an evidence-based rationale for the development of food contact materials capable of meeting the durability, safety, and regulatory demands of modern processing environments.
Veterinary ophthalmologySarah Hoke, Anne Gemensky-Metzler, Christine Boles, Bailey George, Joany Van Balen Rubio, Dubraska Diaz-Campos, Georgina Newbold, Dixie Mollenkopf, Thomas Witt…
OBJECTIVE: To establish surveillance of organisms found on high-touch clinical surfaces within a veterinary teaching hospital ophthalmology service and record trends that may foster additional studies investigating links between environmental microbiota and pathogenic bacteria affecting the ocular surface. PROCEDURES: Samples from 17 high touch surfaces in the ophthalmology department of a veterinary teaching hospital were collected over four consecutive Monday mornings, with additional samples taken 9 months later on a Monday morning and Thursday afternoon of the same week. Samples were processed using standard culture methods, with additional specific testing for Salmonella species, carbapenemase-producing Enterobacteriaceae (CRE), and methicillin-resistant Staphylococcus (MRSsp). RESULTS: Out of 102 samples collected for aerobic bacterial culture, 11 (11%) showed no growth and 91 (89%) yielded positive results. Of the 211 total isolates found, all exhibited a low colony count. Of the isolates identified, 66/211 (31%) were Staphylococcus spp., followed by 45/211 (21%) Bacillus spp. Exam tables (25/211, 11.8%) and countertops (24/211, 11.4%) had the highest number of isolates. There was no clinically significant difference in the number of isolates found between Monday morning and Thursday afternoon of the same week. CONCLUSIONS: All isolates were considered incidental environmental findings and cultured in low numbers. When routine cleaning and disinfection procedures are maintained, common surfaces and equipment of ophthalmology departments are unlikely to be pathogenic reservoirs, posing minimal risk to patients. Further studies are recommended to explore correlations between environmental microbiota and pathogenic bacteria affecting the ocular surface in patients.
Veterinary medicine and scienceMohammad Reza Heidari, Amir Shakerian, Reza Sharafati Chaleshtori, Ebrahim Rahimi
INTRODUCTION AND AIM: Listeria monocytogenes (L. monocytogenes) is a major food pathogen that causes severe infections, especially in the susceptible population. Dairy products and milk are some of the possible vehicles through which it can be transmitted both as a threat to the health of people and as an economic issue. The study conducted was to explore the prevalence, virulence characteristics, and antimicrobial resistance patterns of L. monocytogenes along the supply chain of milk in Yazd Province, Iran. MATERIAL AND METHOD: Collection of 370 samples (raw milk, pasteurised milk, dairy equipment, transport containers and hands and gowns of workers) was done between 2022 and 2023. Identification and isolation of L. monocytogenes was done using standard biochemical, bacteriological and molecular tests. The assessment of antimicrobial susceptibility was done using the Kirby-Bauer disk diffusion, and the multi-antibiotic resistance (MAR) index was determined. The presence of important virulence genes and resistance determinants was identified by PCR. RESULTS: Overall, 10 isolates (2.7%) were confirmed as L. monocytogenes. Raw milk had the highest contamination rate (5.29%), while pasteurised milk and worker samples were negative. High-level resistance was observed against nalidixic acid, penicillin G, ceftazidime (100%), cefepime and ceftriaxone (90%), whereas first-line clinical drugs such as gentamicin, amikacin, levofloxacin, vancomycin, trimethoprim-sulfamethoxazole and erythromycin showed full susceptibility. Virulence genes prfA, inlA and iap were universally present, with high prevalence of resistance genes including lnuA/B, ermA/B and tetA/M. CONCLUSION: The results suggest that raw milk may be a significant reservoir of multi-drug-resistant L. monocytogenes in this region and the studied supply chain. Therefore, hygiene measures and continuous monitoring are key to preventing contamination and protecting public health.
This study examined short-term responses of barley to polyethylene and polyvinyl chloride microplastics in a controlled 60-day greenhouse rhizobox experiment with three replicates per treatment. Microplastics were applied at 0, 2, and 4% of dry soil mass, corresponding to high experimental loadings of 20,000 and 40,000 mg kg-1, respectively. Bulk and rhizosphere soils were evaluated separately using enzyme zymography, nutrient analysis, amplicon sequencing, microbial network analysis, Mantel tests, and structural equation modeling. Higher polyethylene exposure and both polyvinyl chloride treatments reduced superoxide dismutase activity by 16.27-39.12%, increased peroxidase activity by 33.09-67.07%, and reduced net photosynthetic rate by 18.02-24.79%. Microplastic treatments also altered the availability of ammonium, nitrate, and Olsen phosphorus and reorganized the spatial distribution of extracellular enzyme activity. Selected β-1,4-glucosidase, β-1,4-xylosidase, and 4-N-acetyl-glucosaminidase hotspots increased, whereas phosphatase hotspots declined across all microplastic treatments. Changes were also detected in bacterial and fungal diversity and microbial network organization, with lower bacterial network complexity and greater fungal network complexity in the rhizosphere. Structural equation modeling explained approximately 60% of the variation in net photosynthetic rate, with barley antioxidant enzyme responses and soil hydrolytic activity showing the strongest negative associations. These results provide short-term evidence that high microplastic loadings can modify interconnected plant and rhizosphere processes under controlled greenhouse conditions. Given the limited replication, short experimental duration, and high exposure levels, these responses should not be interpreted as evidence of field-level causality. Field experiments using environmentally realistic concentrations and longer exposure periods are required to determine their agricultural relevance.
Functional plant biology : FPBStephanie J Watts-Williams, Alison R Gill, Thi Diem Nguyen, Shervin Kabiri
Environmental contamination due to per- and poly-fluoroalkyl substances (PFAS) is a growing concern globally, as they do not easily degrade and their toxicity causes chronic health issues in humans. When present in water and soil, PFAS bioaccumulate in crops and pastures, and are subsequently taken up by livestock and humans. This study examined how arbuscular mycorrhizal (AM) fungi interact with PFAS in soil, and the subsequent effects on the growth of three pasture legume crops (Medicago truncatula, Medicago sativa and Trifolium subterraneum). To do this, we used a sterilised soil spiked with PFAS, and soil collected from a PFAS-contaminated site, and inoculated soils with the AM fungus Rhizophagus irregularis. The pasture legume species grown in these experiments were highly sensitive to the presence of PFAS in the soil, with only the M. truncatula variety Parabinga displaying tolerance. Inoculation with AM fungi greatly increased plant biomass, but did not confer tolerance of the host plant to PFAS contamination. PFAS contamination did not suppress AM fungi colonisation of the roots; in some cases, colonisation was stimulated by PFAS. PFAS contamination of agricultural soils will likely reduce the growth and yield of pasture legume crops, and AM fungi will likely be unable to buffer the negative effects.
Current microbiologySibel Derviş, Muharrem Türkkan, Göksel Özer
The arthroconidial yeast genera Geotrichum and Magnusiomyces exhibit a striking dual nature, simultaneously acting as destructive postharvest pathogens, essential agents in dairy fermentation, and life-threatening opportunistic pathogens in immunocompromised hosts. Despite extensive domain-specific research, the mechanistic basis of this functional divergence remains poorly integrated across taxonomy, plant pathology, food microbiology, and clinical mycology. This review proposes a cross-domain framework that integrates taxonomic uncertainty, conserved molecular mechanisms, ecological plasticity, and exposure dynamics to explain this functional divergence. Here, "cross-domain" is used in a non-taxonomic sense and refers to integration across disciplinary and ecological/application contexts-plant pathology, food and dairy microbiology, and clinical mycology-rather than to the formal biological taxonomic rank Domain. The functional versatility of these yeasts can be partly interpreted through the context-dependent deployment of broadly conserved fungal mechanisms-including cell wall-degrading enzymes, CYP51-mediated sterol metabolism, secreted proteins/effectors, and stress-response pathways-operating under contrasting ecological and selective pressures, rather than by fundamentally distinct biological systems. Critically, this framework distinguishes unidirectional exposure pathways linking agricultural, food, and clinical environments from bidirectional feedback systems that may contribute to the emergence and circulation of adaptive traits. Within this perspective, we identify three cross-domain connections: a putative antifungal resistance cycle driven by converging agricultural and clinical azole selection, a dairy-clinical interface shaped by host-associated transmission and strain recombination, and a diagnostic blind spot linked to cross-reactivity in fungal detection systems. These insights are translated into testable hypotheses on genome-based species delimitation, resistance evolution, and domestication stability, providing a structured research agenda for coordinated risk assessment and resistance management within a One Health framework.
Fluctuating temperatures profoundly affect microorganisms' coexistence, biogeographic distributions and responses to future climate change. However, how microorganisms respond to fluctuating temperatures with different frequencies in natural communities remains unknown. We conducted a 120-day temperature manipulation experiment with soil-bacterial communities subjected to constant low, medium and high temperatures, as well as fluctuating temperatures with three different frequencies. Four groups of temperature-responsive species were identified, including species favoured by constant high or low temperature, and species favoured or disfavoured by rapid temperature fluctuations. Further analyses confirmed that species in the first two groups only responded to the constant temperatures, and their performances at all fluctuating temperatures were roughly equal to their time-averaged performances at high and low temperatures. Species in the last two groups showed specific responses to frequent temperature transitions. Our results revealed that the performances of bacterial species under slow temperature fluctuation closely resembled their time-averaged performances at high and low temperatures, but deviated from those at medium temperature, due to the nonlinearity of temperature-dependent performances. Our study highlights that soil bacteria show unique responses to both rapid and slow temperature fluctuations compared to medium temperature, which is crucial to understand microbial community dynamics in variable thermal environments.
World journal of microbiology & biotechnologyAyodele Timilehin Adesoji, Vittoria Mattioni Marchetti, Claudia Cortimiglia, Francesca Piscopiello, Ilaria Petrizzi, Aurora Piazza, Emmanuel Dayo Alabi, Pier S…
BACKGROUND: Extended-spectrum β-lactamases (ESBL) and AmpC β-lactamase-producing Enterobacter species are pathogens of public health concern. In this study, we investigated the resistome, virulome, and plasmidome of circulating Enterobacter hormaechei isolated from humans, animals, and ready-to-eat (RTE) food in Dutsin-Ma, northwest Nigeria. MATERIALS AND METHODS: Enterobacter species were isolated from human, and RTE food samples using MacConkey and CHROM agar. Species identification and antibiotics susceptibility testing (AST) were performed using Microscan autoSCAN-4 and MALDI-TOF MS, respectively. Whole-genome sequencing (WGS) and bioinformatics analysis were performed to validate the species identities. WGS also determined sequence types (STs), resistome, plasmidome, and virulome using PubMLST, ResFinder, PlasmidFinder, and Virulence Factors Database (VFDB) via ABRicate, respectively. RESULTS: E. hormaechei subs. xiangfangensis was the dominant species isolated from humans (6/8, 75%) and animals (1/8, 12.5%), while E. hormaechei subs. oharae was exclusively found in RTE food (1/8, 12.5%). The most frequent sequence type (ST) was ST813, found solely in humans, along with ST511, ST454, and the emerging high-risk ST171. ST68 was identified in food, and novel ST (ST3186) were identified in animal and human samples, respectively. All isolates exhibited 100% resistance to ampicillin and amoxicillin-clavulanic acid, with 62.5% resistant to each of aztreonam, ceftazidime, ciprofloxacin, gentamicin, tobramycin and cefotaxime, and 25% to colistin. E. hormaechei (62.5%) isolates carried the blaCTX-M-15 gene, encoding ESBL-production, along with AmpC genes such as blaCMH-3, and also harbored resistance genes for aminoglycosides, fluoroquinolones, sulfonamides, tetracyclines, and trimethoprim. The IncHI2 (50%) was identified as the dominant plasmid type followed by Col (pHAD28) (25%), IncFIB (25%), and IncFII (11.1%). The most (62.5%) prevalence virulence gene among the isolates is ompA encoding adhesion while each of entA, entB and fepD encoding iron acquisition were least (12.5%) occurred. CONCLUSION: This study provides the first genomic insight into Enterobacter species in northwest Nigeria, highlighting their role in the spread of antimicrobial resistance. E. hormaechei subsp. xiangfangensis was identified as the main reservoir of ESBL and AmpC β-lactamases in this study. The discovery of novel STs with diverse virulence factors and plasmid replicon indicates potential horizontal gene transfer across different ecological niches. Our findings underscore the need for robust surveillance and control measures to combat the spread of MDR Enterobacter species across human, animal, and food niches.
MycorrhizaSamaneh Tajik, Florence Breuillin-Sessoms, Timothy Frey, Jelmer W Poelstra, Horacio D Lopez-Nicora, Maria Soledad Benitez Ponce
Arbuscular mycorrhizal fungi (AMF) play a crucial role in crop productivity and agroecosystem processes. However, the composition of soil AMF communities and the factors associated with their diversity and distribution in Ohio remain poorly understood. We profiled both soil AMF and physico-chemical characteristics in 18 soybean fields across agricultural regions in Ohio. AMF sequences were recovered through amplicon sequencing of the 18S ribosomal gene coupled with PacBio technology. We detected 14 genera belonging to six families of the Glomeromycota. The family Glomeraceae accounted for 39% of the AMF reads recovered, while the families Gigasporaceae and Archaeosporaceae were rare (detected in < 25% of samples). At the genus level, Entrophospora, Nanoglomus, Paraglomus, and Funneliformis were widespread, contrasting with rare taxa such as Gigaspora, Dominikia, and Archaeospora. For the studied soil parameters, only phosphorus was significantly associated with AMF community composition. These findings provide a baseline of AMF communities in Ohio soybean fields and highlight abiotic components influencing these communities. Future research should expand sampling to other regions of the state and evaluate root colonization and evaluation of AMF impacts on soybean yields in Ohio.
Environmental geochemistry and healthFernando Igne Rocha, Ana Carolina Borsanelli, Aline Pacobahyba de Oliveira, Cecílio Viega Soares Filho, Marcia Reed Rodrigues Coelho, Stefan Schwab, Carlos Mag…
Forest-to-pasture conversion can alter soil properties, forage composition, and microbial communities, but whether these changes are associated with bovine periodontitis remains unclear. We compared eight pasture systems in the Western Brazilian Amazon classified by high or low herd-level prevalence of periodontal lesions. Soil physicochemical properties, forage composition, microbial communities in soil, forage, and bovine subgingival biofilms, and the relative abundance of the streptomycin biosynthesis gene strB1 were evaluated. Although the systems had similar deforestation histories, low-prevalence pastures had finer-textured soils, greater soil Cu and forage Zn, and greater representation of Bacilli and Gammaproteobacteria. High-prevalence pastures had sandier soils, greater soil C:N ratios, lower micronutrient availability, and greater representation of Actinobacteria and Bacteroidetes. Microbial communities differed between prevalence classes in all three compartments, with higher alpha and gamma diversity and more compartmentalized co-occurrence networks in high-prevalence systems. Tax4Fun predicted greater representation of pathways related to carbohydrate metabolism and glycan biosynthesis in these systems, while qPCR showed higher strB1 abundance normalized to bacterial 16S rRNA gene abundance in soil and forage. These concurrent differences in soil properties, forage composition, and microbial communities were associated with bovine periodontitis prevalence. They do not demonstrate microbial transfer or causality but support the hypothesis that soil and forage conditions may influence environmental exposures related to oral microbiome dysbiosis.
Mycotoxin researchOluwawapelumi A Oyedele, Muiz O Akinyemi, Michael Sulyok, Rudolf Krska, Jos Houbraken, Chibundu N Ezekiel
This study applied a polyphasic characterization approach and LC-MS/MS analysis to elucidate fungal and mycotoxin contamination dynamics during conventional (CPRP) and improved (IPRP) postharvest processing and a 90-day storage of rice in Nigeria. Three hundred and twenty-five fungal isolates belonging to 21 genera (10 moulds, one crust fungus, 10 yeasts) and 54 species were recovered from rice across both processing chains. The CPRP chain had greater diversity of fungal genera compared to the IPRP chain. Aspergillus predominated both processing chains while yeasts occurred only in the CPRP chain. Species belonging to Aspergillus sections Aspergillus, Candidi, Flavi and Nidulantes, and Penicillium section Citrina predominated in stored rice in the two processing chains. A total of 106 extrolites including several uncommon extrolites and potential species markers were identified in agar cultures of 38 strains from 19 mould species. Fifteen mycotoxins were detected in rice along the processing and storage chains. Processing of rice in the IPRP chain and hermetic storage for 90 days reduced total aflatoxins by 9% compared to non-reduction in CPRP chain. Conventionally processed and stored rice in jute bags after 90 days recorded at least twice higher percentage reductions of total fumonisin, nivalenol and tenuazonic acid compared to hermetically stored rice from the IPRP chain. However, citrinin+dihydrocitrinone levels in rice from the two storage types increased progressively during the 90-day storage period. This study highlights the critical control points in the two rice process chains and provides insights into possible mycotoxin control approaches along the chain including in storage.
The in situ relevance of biosynthetic gene clusters (BGCs) remains poorly understood. We apply meta-omics to characterize BGC diversity and activity along a peatland redox gradient. From seven metagenomes, we recover 9,694 BGCs, spanning diverse taxa, most lacking close relatives in reference databases, indicating extensive novelty. Only 9-27% of this potential is expressed in situ, with Acidobacteriota, despite moderate repertoires, accounting for over half of all BGC transcription. Talented producers with up to 24 clusters are largely silent, and expression is inversely related to BGCs per genome. Acidobacteriota, specialized in complex carbon processing potential express a larger proportion of their BGC repertoires than BGC-rich Pseudomonadota, which had shorter doubling times and lower potential for complex carbon processing. At the genome level, the degree of BGC expression is most strongly coupled to carbohydrate-active enzyme expression, particularly glycoside hydrolases, linking secondary metabolism to active carbon processing in peatland microbes. Thus, although BGCs are widespread, BGC expression in situ is integrated into the carbon-cycling activity of individual taxa rather than a shared physiological state.
The southern coastal fringe of the Río de la Plata estuary hosts multiple activities, serving as an economic resource, freshwater supply and recreational center for the largest populations in Argentina. The bacteriological quality of eight beaches was assessed in 78 km of the coast, to measure the presence of two fecal pollution indicators (Escherichia coli and Enterococcus) both in the water and in sand samples. Results indicate that the abundance of microorganisms was generally higher in the sediment than in the water, and in most beaches, they exceeded the recommended guides for the use of recreational waters. Microbial abundances were negatively associated with distance from sewage discharges for both indicators in sand and for Enterococcus in the water, while the abundance of the former in water was also negatively associated with dissolved oxygen. The abundance of E. coli was always higher than Enterococcus, suggesting that it may be a more generalized indicator of fecal contamination in the area.
Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]Mayara S Tavares, Patrícia G Paulino, Daniele S Juliano, Roberto Laureano-Melo, Huarrisson A Santos, Rosa H Luchese
This research aimed to access the incidence of Listeria sp. and L. monocytogenes in frozen ready-to-eat (RTE) fish products immediately after purchasing, and after refrigerated storage. Out of 72 kani-kama samples, 17 (23,6%) and 16 out of 48 samples (33,3%) of smoked salmon samples, tested positive for Listeria sp. by the traditional culture method, whereas 45,8% and 56.2% were positive by PCR, for kani-kama and smoked salmon samples, respectively. Applying qPCR, 21 samples of kani-kama out of 72 (29.2%) and 23 out of 48 samples of smoked and sliced salmon (47.9%) were positive for L. monocytogenes. Quantification was performed by culture to account only for viable cells, and confirmation was carried out via PCR and qPCR for Listeria sp. and L. monocytogenes, respectively. The average counts of L. monocytogenes did not exceed 2 Log CFU/g, both in kani-kama or smoked salmon. However, 15.3% of individual kani-kama samples and 14,6% of smoked salmon samples showed counts of up to 3.2 Log CFU/g, some even immediately after purchasing. Higher number of positive samples was observed during refrigerated storage compared to the number of samples analysed immediately after purchasing, indicating that refrigeration for a long time can pose an additional health threat. Unlike kani-kama, which is a heat-processed product, a higher background microbiota count was detected in smoked salmon. However, this background microbiota apparently did not influence the growth of Listeria spp.
BMC microbiologyTianqing Feng, Jun Shang, Yonggui Ma, Juan Li, Yanrong Qin, Jitao Zhang, Shiyan Cheng, Gaosen Zhang, Huichun Xie
Notopterygium incisum is not only a traditional Chinese medicine but also an endemic herb. Artificial domestication and large-scale cultivation are crucial for resolving the crisis of wild resources and the supply-demand imbalance of N. incisum, yet current techniques have failed to stably provide the herb medicine in good quality. Metagenomic analyses revealed significant differences in the rhizomicrobiota between wild and cultivated N. incisum, particularly in microbial composition, gene functions, and community assembly. The rhizomicrobiota of the wild N. incisum from 3 different sites with an altitude drop over 1400 m had a similar composition when being compared with the cultivated samples. The wild N. incisum had higher abundances of beneficial microbes, particularly Hyphomicrobiales (Rhizobiales) (21.27% on average). In contrast, the rhizosphere microbial communities of the cultivated N. incisum showed a high prevalence of functional genes involved in the pathways of DNA repair and recombination proteins, replication and repair, peptidases and inhibitors, DNA replication proteins, and transfer RNA biogenesis. The co-occurrence networks analysis indicated that the stability of the wild samples' network remained significantly more robust when nodes were proportionally removed, as the wild samples' network had approximately the same positive and negative links while the cultivated samples' network had nearly all positive links and many fewer connectors. This is related to the conclusion that wild N. incisum exhibits superior efficacy, as reported in previous studies. Additionally, it can be observed from the sampling images that the root surface of wild N. incisum has more pronounced tiny protrusions, which may be associated with rhizobial attachment, thereby enhancing the nitrogen fixation process. Importantly, the observed shifts in rhizosphere microbial communities, particularly the enrichment of beneficial rhizobia in wild plants, are closely linked to enhanced accumulation of bioactive secondary metabolites such as coumarins and volatile oils. These microbiome-driven differences are likely associated with the superior medicinal quality of wild N. incisum compared to cultivated counterparts, highlighting the pivotal role of rhizosphere microbes in shaping therapeutic efficacy.
Acid mine drainage (AMD) can lead to severe pollution of surrounding aquatic systems like rivers. Although microbial ecosystems have been documented in the AMD-impacted riverine systems, the ecological patterns and potential assembly mechanisms of abundant and rare taxa are still largely unexplored. Herein, we examined the diversity, composition, co-occurrence networks and assembly of the whole prokaryotic communities, abundant taxa, and rare taxa along an AMD-impacted river. The results revealed a strong correlation between prokaryotic communities and environmental variables in the AMD-impacted river. Significant spatial variations in diversity and composition were observed for the whole community and abundant taxa in sediment habitats, but not in water habitats. Specifically, in sediment habitats, the relative abundances of Gamma- and Beta-proteobacteria decreased along the river, while Alphaproteobacteria and Acidobacteriota increased. Conversely, water habitats were characterized by Acidovorax and Acidocella. Furthermore, the alpha diversity of rare taxa showed no significant correlation with spatial distance in either sediment or water habitats. However, rare taxa occupied important topological positions in the co-occurrence network. Stochastic processes (dispersal limitation and undominated processes) generally dominated community assembly especially for rare taxa, but the roles of deterministic processes (heterogeneous and homogeneous selection) in shaping whole communities and abundant taxa of sediment habitats should not be neglected. These findings offer novel insights into microbial patterns and assembly mechanisms in AMD-impacted riverine ecosystem.
World journal of microbiology & biotechnologyMary Therese J Balabat, Edgardo J Loquero, Najiha B Amer, Jade C Coñado, Harold Jade B Cabolbol, Rodolfo A Romarate, Jhonamie Mabuhay-Omar, Kozo Watanabe, Mei-…
Urban road dust is a reservoir and transport medium for diverse microorganisms, yet its bacterial communities in tropical environments remain poorly understood. This study examined the spatial variation of road dust bacterial communities across three Philippine metropolitan areas: Metro Manila, Metro Cebu, and Metro Cagayan de Oro, spanning the country's three principal island groups. Dust from nine sites was analyzed using 16 S rRNA gene metabarcoding (V3-V4), with community composition, diversity, predicted functional potential (PICRUSt2), and metal associations evaluated; contamination was assessed using pollution indices (PLI, degree of contamination, and ecological risk). Proteobacteria and Actinobacteria dominated all sites, and a small core of genera: Paracoccus, Acinetobacter, Kocuria, and Deinococcus, was consistently detected. Alpha diversity did not differ among cities (Kruskal-Wallis, p > 0.05), whereas community composition did (PERMANOVA: R² = 0.466, p = 0.004), with distinct metropolitan clustering. This decoupling indicates that local conditions shape which taxa dominate rather than overall diversity, consistent with environmental filtering of a shared regional pool. Alkanindiges reached its highest relative abundance at Metro Cebu's commercial core. In Metro Cagayan de Oro, Paracoccus increased toward the most trace-metal-laden site (D3) and correlated positively with cobalt and nickel; with elevated predicted denitrification in this area, this points to a possible pollution-responsive signal. Metro Cagayan de Oro also showed a pronounced higher relative abundance of Chloroflexi, marking it as a distinctive, transitional urban environment. Pollution indices indicated baseline-to-moderate contamination across the sampled roadsides. Predicted function paralleled taxonomy (R² = 0.467). These findings establish a baseline for tropical road-dust microbiota and support integrating microbial assessment into urban environmental monitoring.
PeerJSiwei Liang, Guogeng Jia, Hui Chen, Can Zhou, Wenjie Peng, Shuxing Liu, Chao Ai, Yan Zhang, Guangda Ding
The excessive application of chemical fertilizers is a prevalent issue in modern agriculture, as it increases production costs, undermines economic returns, and degrades soil health. In this study, the effects of two compositionally distinct yeast derivatives, namely Yeast Glycoside Type I (YD1) and Water-Soluble Yeast Glycoside (YD2), on the growth, nutrient use efficiency, low-temperature (LT) stress tolerance, and rhizosphere microbial communities of pepper (Capsicum annuum L.) were investigated. The yeast derivatives (YD) were characterized using scanning electron microscopy (SEM) and biochemical analysis, which revealed distinct profiles: YD2 contained higher nitrogen (11.89%), isindole-3-acetic acid (IAA), and 1-Aminocyclopropane-1-carboxylic acid (ACC), whereas YD1 was enriched in cytokinins (isopentenyl adenine, iP; trans-zeatin, tZ). Under normal temperature (NT) conditions, application of YD2 at concentrations of 1% significantly enhanced pepper yield, shoot biomass, and nitrogen/potassium use efficiency, whereas YD1 exerted minimal effects. However, under low-temperature (LT) stress, applications of YD1 and YD2 did not significantly increase yield. Despite this, YD2 maintained root activity, mitigated chlorophyll degradation, and increased the activities of antioxidant enzymes under LT stress. Both YD altered rhizosphere bacterial community structure under NT conditions (PC1: 42.09%, p = 0.007); however, this effect was attenuated under LT stress (PC1: 24.85%, p = 0.003). Specifically, YD1 was associated with an increased relative abundance of Microscillaceae (NT) and Thiobacillus (LT), while YD2 was linked to an increase in Kaiserbacteria (NT) and Armatimonadales (LT). These findings suggest that the two YDs, particularly YD2, can influence pepper productivity and stress resilience through associations with improved nutrient uptake, physiological adjustments, and shifts in the rhizosphere microbiome. This pot-based study provides insights into the potential of tailored yeast derivatives as biostimulants, offering a basis for developing more sustainable agricultural practices.
Veterinary research communicationsDeepak B Rawool, Radhakrishna Sahu, Niveditha Pollumahanti, Laxman R Chatlod, Yogesh P Gadekar, Vishnuraj M R, Jess Vergis, Nagendra Nath Barman, Sukhadeo B Ba…
In this study, a total of 2818 food samples of animal origin collected from 18 states of India using a stratified random sampling method were processed for isolation of Salmonella spp. PCR serotyping was performed to identify non-typhoidal serovars. All confirmed Salmonella isolates were screened for antibacterial susceptibility and for their virulence potential using the Galleria mellonella larvae. Microbiological screening identified 58 Salmonella spp. isolates (2.06%). Variation in isolation rate was not evident in various types of samples that were screened, and the place of isolation. On PCR serotyping, 39.65% were identified as S. Typhimurium, 32.76% as S. Enteritidis, and the remaining 27.59% were other Salmonella serovars. Notably, 44.83% of the Salmonella isolates exhibited MDR pattern with a MAR index of > 0.2. All the isolates were virulent to G. mellonella larvae. Findings of the study warrants further investigations and appropriate preventive cum control measures to ensure food safety.
Environmental microbiology reportsArefeen Haider, Tasnuva Jahan Esha, Sezanur Rahman, Jannat Akther, Naimul Islam Faysal, Tahsin Khan, Shakhinur Islam Mondal, Anowara Begum, Sudhangshu Kumar Bi…
Bacillus species are environmentally resilient bacteria associated with soil, food, industrial settings and opportunistic infections, yet their bacteriophages remain incompletely characterised, particularly from underexplored environmental sources. We isolated and characterised phage APU1, a dsDNA phage from agricultural soil in Bangladesh. Partial 16S rRNA gene sequencing identified the enrichment host conservatively as Bacillus sp. APU1 has a 153,847 bp genome that encodes 236 predicted proteins, including 84 shorter than 100 amino acids. CheckV classified the genome as high-quality, with an estimated completeness of 99.91% and no detectable host-gene contamination. Functional annotation identified genes associated with DNA replication, structural assembly, packaging and host lysis. PhaBOX classified APU1 as virulent, with PhaTYP and CHERRY prediction scores of 1.0. CARD/VFDB screening did not detect CARD-listed antimicrobial resistance genes or VFDB-listed virulence factor genes. Comparative genomic analyses using VICTOR, VIRIDIC and VIPTree placed APU1 within a group of related Bacillus phages. APU1 shared 89.7%-89.8% intergenomic similarity with its closest relatives, supporting its classification as a genomically distinct phage within this group. This study expands the genomic catalogue of Bacillus-associated phages from Bangladeshi soil and provides a foundation for future studies on phage diversity, host range, morphology and biological properties.
Pakistan journal of biological sciences : PJBSBayu Hari Mukti, Dede Mahdiyah, Dwi Sogi Sri Redjeki, Irfan Alias Kandek, Resha Surya Putri
<b>Background and Objective:</b> Antimicrobial resistance (AMR) drives an urgent need for new antibiotics. A <i>Lysinibacillus</i> sp. isolate from Indonesian peat soil has shown promising broad-spectrum antibacterial activity <i>in vitro</i>. This study aims to evaluate the acute toxicity profile of its cell-free supernatant (CFS) as an initial <i>in vivo</i> safety assessment. <b>Materials and Methods:</b> A single oral dose acute toxicity test was conducted on female mice (n = 3 per group). Treatment groups received CFS at volumes of 0.2 mL, 0.5 mL and 1.0 mL. Control groups received 0.5% Na carboxy methyl cellulose (CMC) and nutrient broth (NB). All animals were observed for 14 days for mortality, behavior and body weight changes, followed by necropsy on day 15. Statistical analysis was conducted using SPSS version 26, applying GLM repeated measures with Shapiro-Wilk normality, Mauchly's sphericity and Bonferroni <i>post-hoc</i> tests at a significance level of p<0.05, with results expressed as Mean±SD. <b>Results:</b> There was no mortality or significant behavioral changes. However, macroscopic necropsy revealed dose-dependent toxicity. At a dose of 0.2 mL, heart swelling and tracheal hemorrhage were found. A dose of 0.5 mL caused lung hemorrhage and a pale trachea. At the highest dose of 1.0 mL, all animals showed kidney swelling, lung hemorrhage and pale digestive tract. The Na CMC control group was normal, while the NB control showed mild abnormalities. <b>Conclusion:</b> The CFS of <i>Lysinibacillus</i> sp. did not show LD<sub>50</sub> toxicity or behavioral changes in mice. Some high doses showed organ-specific toxicity.
International journal of systematic and evolutionary microbiologyWei Han, Yu Du, Shi-Jie Bai, Yin-Xin Zeng
Two Gram-stain-positive, non-motile actinomycetes, designated Or2-10aT and 21So2-11T, were isolated from ornithogenic and pristine soils collected on Ardley Island, Fildes Peninsula, King George Island, maritime Antarctica. 16S rRNA gene sequence analysis revealed that strains Or2-10aT and 21So2-11T showed the highest similarities to Aeromicrobium panaciterrae Gsoil 161T (98.02%) and Streptomyces drozdowiczii NRRL B-24297T (97.85%), respectively. Phylogenetic analyses based on 16S rRNA gene sequences confirmed the close relationships of these strains. Genomic analyses further supported the novel taxonomic status of these two species based on average nucleotide identity and digital DNA-DNA hybridization. Strains Or2-10aT and 21So2-11T contained MK-9 and MK-9 (H8) as the predominant menaquinone, respectively. High abundances of C18 : 1 ω9c and C16 : 0 were detected in Or2-10aT, whereas iso-C16 : 0, anteiso-C15 : 0 and iso-C16 : 1 h were dominant in 21So2-11T. The cell-wall peptidoglycan of both Or2-10aT and 21So2-11T contained ʟʟ-diaminopimelic acid. The whole-cell sugars of the two strains contained ribose and strain Or2-10aT contained additional glucose. Strain Or2-10aT contained diphosphatidylglycerol (DPG), phosphatidylglycerol, phosphatidylinositol (PI), an unidentified phospholipid and an unidentified phosphoglycolipid as major polar lipids, whereas strain 21So2-11T contained DPG, phosphatidylethanolamine, PI and phosphatidylinositol mannoside as major polar lipids. On the basis of polyphasic taxonomy analysis, strains Or2-10aT and 21So2-11T are concluded to represent two novel species of the genera Aeromicrobium and Streptomyces, respectively. The names Aeromicrobium changchenzhani sp. nov. (type strain Or2-10aT=CCTCC AA 2025019T = DSM 120837T=KCTC 59632T) and Streptomyces changchenzhani sp. nov. (type strain 21So2-11T = CCTCC AA 2024063T = DSM 121692T=JCM 38519T) are proposed.
EcologyKazuo Isobe, Ryunosuke Tateno, Karibu Fukuzawa, Nanae Hosokawa, Tomoki Oda, Mark Green, Pamela H Templer, Peter M Groffman
Winter climate change is altering snowpack dynamics in northern forests. Snowpack decline disrupts winter soil thermal and hydrological regimes, alters soil microbial activity beneath the snowpack, and triggers cascading effects on vegetation growth and biogeochemical fluxes into the growing season. Despite growing evidence of these changes, the mechanisms underlying these cascade effects and their regional variation remain poorly understood. This review integrates multi-ecosystem-component monitoring results from snow manipulation studies at two contrasting, well-studied northern forest sites-in the northeastern United States and northern Japan-within a unified cascade framework. We also synthesize findings from a broader range of experiments to explore how regional conditions mediate the impacts of reduced snowpack on northern forests. Finally, we discuss key experimental challenges and propose future research directions to improve predictive understanding of winter climate change impacts on northern forest ecosystems.
MicrobiologyOpenMd Rokibul Hasan Shanto, A S M Ashab Uddin, Md Shakil Mahmud Supto, Nabil Jahan Mahim, Md Matiar Rahman Howlader, Syed Sayeem Uddin Ahmed, Md Bashir Uddin
The emergence of multidrug-resistant (MDR) Escherichia coli in poultry represents a critical One Health concern, particularly in developing countries. This study employed a comparative genomic approach to investigate the genomic characteristics, antimicrobial resistance (AMR) profiles, virulence determinants, of poultry-derived MDR E. coli isolates from Bangladesh. Whole-genome sequencing of three representative MDR isolates, identified with 83 globally diverse poultry, human, and environmental E. coli genomes. Pangenome analysis identified the characteristic open pangenome of E. coli, with core genes comprising only 4.6% of the combined dataset. Resistome analysis shown diverse AMR determinants, including blaCTX-M, blaTEM, sul, tet, and qnrS1, associated with antibiotic inactivation and efflux mechanisms. Virulence profiling revealed diverse genes involved in adhesion (fim, csg), iron acquisition (ent, fep, chu), motility, and secretion systems, with core virulence genes exhibiting > 90% sequence identity, whereas accessory virulence genes were more variable. Plasmid analysis demonstrated heterogeneous replicon types, predominantly IncF and Col plasmids, indicating their role in horizontal gene transfer. Jaccard similarity indices revealed moderate to high genetic overlap with global strains (~0.63 for virulence genes and ~0.55 for AMR profiles), suggesting shared evolutionary backgrounds. Phylogenomic and MLST identified all Bangladeshi isolates as ST457, clustering within a globally distributed clonal complex linked to ST10 and ST131 lineages. These findings suggest that the three Bangladeshi poultry-derived E. coli isolates are genetically related to globally circulating strains while harboring extensive resistance and virulence determinants, emphasizing poultry as an important reservoir of MDR pathogens and reinforcing the need for strengthened antimicrobial stewardship and genomic surveillance.
Soil biodiversity in apple orchards plays a vital role for productivity. We studied the biodiversity of prokaryotes, protists and fungi of 26 apple orchards belonging to the same regional growers' association in Northern-Italy by environmental DNA metabarcoding (16S, 18S, ITS). We assessed alpha- and beta-diversity, distance decay relationships, immigration rates and community assembly processes, variance partitioning between space and environment and putative prokaryotic and fungal functions from the upper 20 cm of soil during summer 2023. Despite uniform management practices, orchards showed a huge variability in alpha diversity, with single orchards having only a small part of total diversity. Protists showed the lowest mean beta-diversity, followed by prokaryotes and fungi. Although immigration rates were low across all organismal groups-reflecting the low number of taxa co-occurring across all orchards-prokaryotes and protists still displayed relatively higher rates than fungi, in support of the size-plasticity hypothesis. Community assembly was governed primarily by stochastic processes, even though deterministic processes were also important. Turnover dominated community composition for all organismal groups. Putative functions of prokaryotes pertained mainly to carbon and nitrogen cycling. Our study provided mechanistic insights into the diversity of soil organisms across different trophic levels found in apple orchards.
MicrobiologyOpenMd Moklesur Rahman, Awis Qurni Sazili, Siti Aqlima Ahmad, Khalilah Abdul Khalil, Mohammad Rashedi Ismail-Fitry, Md Sazedul Karim Sarker
The rise of multidrug-resistant (MDR) pathogens presents a major challenge to food safety, particularly in preservation approaches. Lactic acid bacteria (LAB) gain probiotic recognition by effectively controlling MDR pathogens using antimicrobial substances (AMSs) and bacteriocin-like inhibitory substances (BLISs). The study evaluated the probiotic properties and AMS production potential of five LAB strains: Lactiplantibacillus plantarum NBRC 3070 (LP), Lactobacillus acidophilus ATCC 4356 (LA), Lacticaseibacillus casei ATCC 393 (LC), Lacticaseibacillus rhamnosus GG ATCC 53103 (LGG), and Bifidobacterium animalis subsp. lactis ATCC 27673 (BAL). AMS was extracted from neutralized and concentrated cell-free supernatant and tested for antimicrobial activities against common foodborne pathogens using minimum inhibitory concentrations (MICs). All LAB strains showed antagonistic activity, with LP demonstrating the most substantial antagonism. Four strains are resistant to multiple antibiotics but remain susceptible to azithromycin and tetracycline, while LP is resistant to all tested antibiotics. LP and LC demonstrated the highest probiotic potential based on cell surface hydrophobicity and aggregation abilities. Optimal AMS activity (85.36%-91.29%) occurred between 24 and 36 h at 37°C or 28-48 h at 30°C. LGG exhibited the highest AMS activity with the lowest MIC against Salmonella enterica serovar Typhimurium. Enzyme sensitivity confirmed the peptide nature of BLIS produced by BLIS from LP, LA, LC, and LGG. In conclusion, LAB strains demonstrated significant probiotic traits and the ability to produce AMS, especially BLIS, from four strains, with LP and LC showing the most potential. These findings support their application as natural biopreservation against MDR pathogens; however, further validation in the food system is required.
MicrobiologyOpenShilpy Singh, Varun Kumar Sharma, Dharmsheel Shrivastav, Jayant M Kushwaha, Manoj Kumar Mishra, Mirza Masroor Ali Beg
The increasing limitations of chemical pesticides such as environmental pollution, pathogen resistance, and threats to human and ecosystem health have increased the demand for sustainable, biologically based crop protection methods. Eco-smart biocontrol has emerged as a game-changing paradigm that uses beneficial microorganisms associated with plants to suppress phytopathogens, boost plant immunity, and make agroecosystems more resilient over time. Moving beyond traditional single-strain biocontrol, eco-smart biocontrol integrates multi-omics discovery, artificial intelligence-assisted predictive microbiome design, and dynamic rhizosphere ecology. This review brings together ecological, molecular, and technological dimensions of eco-smart biocontrol, focusing on the rhizosphere as a dynamic hotspot for plant-microbe interactions. We investigate rhizosphere microbiome assembly and demonstrate the preferential recruitment of beneficial bacteria, fungi, actinomycetes, and mycorrhizal symbionts by plant root exudates. Moreover, the review highlights the impact of innovations in multi-omics techniques (metagenomics, transcriptomics, proteomics, and metabolomics), systems biology, and artificial intelligence on microbial biocontrol agent discovery, functional validation, and predictive design. Examples from cereal crops, legumes, and horticulture crops indicate that the application of beneficial microbial inoculants can significantly lower the burden of pests and diseases, enhance crop productivity, and fit perfectly within an integrated pest management system. Lastly, we critically analyze the main challenges preventing large-scale adoption, such as inconsistent field performance, limited microbial survival and competitiveness, and comparative regulatory frameworks across global markets. Ultimately, eco-smart microbial biocontrol combines mechanistic insights with omics-driven discovery, artificial intelligence (AI)- assisted prediction, advanced formulation strategies, and field-level validation, creating a strong, scalable, and environmentally friendly framework for resilient, low-input agricultural systems.
Antonie van LeeuwenhoekMandeep Kumar, Namita Singh
The present study aimed to develop a fermented cucumber juice beverage using Lactobacillus rhamnosus NCDC-347. The fermentation procedure was optimized using Response Surface Methodology (RSM). The independent variables used for optimization were inoculum size (2-5%), pH (5-9), and incubation temperature (30-45 °C), while the responses were Total Phenolic Content (TPC), antioxidant activity, total sugar content and microbial growth. The optimized fermentation conditions were 37.5 °C, pH 7.0, and an inoculum size of 3.5%. Under these conditions, L. rhamnosus NCDC-347 reached approximately 8.0 ± 0.1 Log CFU/mL after 48 h of fermentation. Under the optimized conditions, fermentation significantly reduced the pH from 7.00 ± 00 to 3.29 ± 0.13, and total soluble solids 3.3 ± 0.15 to 1.2 ± 0.05, along with a reduction in total sugar content from 17.94 ± 1.10 g/L to 4.40 ± 0.45 g/L, confirming effective microbial metabolism. A significant increase in TPC from 1.02 ± 0.06 g GAE/L, to 1.5 ± 0.06 g GAE/L was observed which was associated with enhanced antioxidant activity as determined by DPPH (80.79 ± 1.81%), and ABTS (93.43 ± 0.90%) radical scavenging assays. The fermented cucumber juice showed significant inhibitory activity against α-glucosidase (41.66 ± 1.52%), and α-amylase (57.33 ± 2.51%), indicating potential α-amylase and α-glucosidase inhibitory activity in vitro. Gas chromatography-mass spectrometry (GC-MS) was employed for the volatile profiling of fermented and unfermented cucumber juice, which revealed the production of several fermentation-derived compounds. Cell free supernatant of cucumber juice exhibited antimicrobial activity with highest and lowest inhibition against Bacillus subtilis MTCC 441 (16 mm), and pseudomonas aeruginosa ATCC 15692 (09 mm) respectively. The fermented cucumber juice showed cytotoxic activity against MCF-7 cells under the tested conditions. Sensory assessment using a 7-point hedonic scale showed higher mean scores for most evaluated attributes in the fermented juice than in the unfermented juice.
World journal of microbiology & biotechnologyChang Zhou, Wenfang Wen, Lei Ji, Fanyong Song, Yingna Xing, Qi Li, Tianyuan Li, Xiaowen Fu
Petroleum hydrocarbon pollutants pose a significant threat to the ecological security of oilfields. In these contaminated habitats, Suaeda salsa is a dominant halophyte of the coastal wetlands and oilfields, which has shown potential in remediation of petroleum polluted saline soils. However, the role of plant-associated microbial communities in pollutant attenuation remains poorly understood, particularly regarding niche-specific responses within the root zone. In this study, bacterial community structures associated with the halophyte Suaeda salsa in China's Yellow River Delta were investigated across three ecological niches comprising the endophytic tissues, rhizosphere soils, and bulk soils. A total of 54 samples from 6 sites were collected and analyzed using high-throughput absolute quantification sequencing and physicochemical analyses. Results demonstrated that petroleum hydrocarbons were the primary environmental drivers shaping bacterial community structure across all niches. Comparisons among ecological niches indicated that the rhizosphere effect further promoted the selection and enrichment of specific bacterial taxa, especially the genus Sphingomonas. Contrasting ecological strategies between niches were clearly resolved by co-occurrence network analysis, which showed highly connected networks in rhizosphere communities and modular structures in endophytic ones. Functional predictions further indicated niche-specific metabolic specialization, with endophytic communities enhancing xenobiotic degradation pathways and rhizosphere communities upregulating motility-related functions. These findings reveal the niche-dependent assembly and functional specialization of root-zone microbiomes under petroleum stress, thereby advancing our understanding of plant-microbe adaptive strategies in contaminated ecosystems.
To understand the prevalence of opportunistic bacterial pathogens in the bioaerosols, outdoor air-sampling was performed during the peak season of air pollution prior to the onslaught of the COVID-19 pandemic in the national capital of India, Delhi, during the month of November 2019. Employing a sophisticated plate exposure technique using the Merck Mas Eco-100 instrument, culturable bacterial samples were collected from six locations in Delhi. Among the identified bacterial samples, multiple species of the opportunistic pathogen Staphylococcus, namely, S. gallinarum, S. haemolyticus, and S. arlettae were present. To further characterize these isolates, whole genome sequencing coupled with phenotypic microarray, antibiotic resistance profiling, and biofilm formation in the presence of a known air pollutant, black carbon, was performed. The comparative genomics analysis highlighted the presence of the urease gene cluster (ureABCDEFG) in S. arlettae Naraina and S. haemolyticus Yojna Vihar 1 that may provide a fitness advantage to these strains, as urease activity in S. haemolyticus and S. arlettae is usually reported as negative.
Wetland soils are among the ecosystems most vulnerable to anthropogenic disturbances, and they play critical roles in biogeochemical cycling and energy exchange. In this study, we investigated the characteristics of heavy metal distribution and microbial community structures in soil samples from Shengjin Lake and Caizi Lake in China. Analysis of soil physicochemical properties revealed a significant difference in soil pH between the two lakes, whereas no significant differences were detected in organic matter content or cation exchange capacity. Soils from Caizi Lake exhibited significantly higher concentrations of Pb, As, and Hg than those from Shengjin Lake, whereas Cd and Cr concentrations did not differ significantly between the two lakes. Soil microbial analysis demonstrated that Proteobacteria, Actinobacteriota, and Chloroflexi were the dominant phyla across all samples. Alpha diversity and principal coordinate analysis revealed significant differences in soil microbial communities between Shengjin and Caizi Lakes. LEfSe analysis indicated that Pedobacter, Nocardioides, and Flavobacterium were significantly enriched in the soils from Shengjin Lake, whereas Arthrobacter was significantly more abundant in the soils from Caizi Lake. To further explore the relationships between heavy metals and microbial communities, we analyzed the correlation heatmaps of the associations among heavy metals, microbial taxa, and KEGG functional pathways in samples from both lakes. Collectively, this study enhances the current understanding of heavy metal distribution and microbial community characteristics in wetland soils and provides a scientific basis for early environmental pollution warnings in the wetland ecosystems of Shengjin and Caizi Lakes.
Environmental microbiology reportsTingting Li, Rong Mao, Yang Zhang, Ximei Zhang
In response to anthropogenic environmental changes, biological communities often undergo compositional changes, which are traditionally thought to represent adaptation. However, this hypothesis and its mechanism remain surprisingly underexplored. In this study, we conducted a 10-year nitrogen deposition experiment in the Eurasian steppe, manipulating nine intensities under two management strategies (fencing or mowing). As the intensity increased from 0-20 to 50 g N m-2 yr-1, the succession rates of both plant and soil microbial communities first increased but then decreased, implying that high intensities of N deposition exceed the capacity of community adaptation. In addition, both the succession rate of the deterministic component of community compositional variation and the succession rate of soil physicochemical characteristics increased and then decreased with increasing N intensity. They were positively correlated, demonstrating that adaptation is primarily driven by deterministic ecological processes. Meanwhile, mowing promoted the plant community's adaptation, while fencing promoted adaptation of the microbial community, both by restraining stochastic processes. Overall, to enable biological communities to adapt compositionally to environmental changes, we should aim to limit the intensity of changes below certain thresholds, and implement reasonable strategies, whether deterministic (e.g., restoring soil physicochemical conditions) or stochastic (e.g., adding seeds of adaptive species).
Environmental microbiologySimon Maréchal, Benjamin Heiniger, Shaohua Gu, Swagatika Dash, Christian H Ahrens, Rolf Kümmerli
Auxotrophy, the inability of bacteria to synthesize one or multiple essential metabolites, is thought to be common among bacteria. However, studies often rely on either bioinformatic genome-based prediction of auxotrophies or on experiments with low strain numbers. Here, we combine experimental and bioinformatic approaches to assess amino acid auxotrophies among 315 co-isolated natural Pseudomonas strains from pond and soil habitats. Experiments revealed that Pseudomonas isolates are predominantly prototrophs. We identified one histidine auxotroph, one auxotroph with complex intertwined dependencies and four 'fragile' phenotypes showing delayed growth without supplemented amino acids. Applying three bioinformatic pipelines largely confirmed experimental data but yielded specific biases in auxotrophy over- or underestimation. Moreover, none of the pipelines could resolve the genetic basis of the slow-growing phenotypes or of more complex dependencies. Our analysis further revealed the existence of multiple alternative biosynthesis pathways for methionine, proline and phenylalanine, with significant pathway enrichments being linked to phylogeny and habitat. We conclude that combining experiments with bioinformatics is a powerful approach to assess the metabolic potential of environmental bacteria. Moreover, taxa like Pseudomonas can be predominantly prototrophic possibly owing to their generalist lifestyle, thus calling for nuanced ecological concepts predicting auxotrophy levels based on lifestyle and habitat.
This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.
Soil protists comprise vast eukaryotic diversity and play key roles in microbial food webs, yet their community assembly remains poorly understood from a trait-based perspective. Here, we address this gap by integrating 10 traits related to morphology, behaviour, life history and trophic strategy across broad environmental gradients. RLQ analysis combined with fourth-corner tests revealed two major dimensions of soil protist trait variation. Reduced precipitation drove trait composition towards slower, persistence-oriented strategies, including reduced mobility, narrower niche breadth and increased reliance on asexual reproduction. Nutrient and resource limitation shifted trophic structure away from heterotrophic consumer-related strategies towards autotrophic or mixotrophic energy acquisition. These dimensions were consistently detected in a large-scale field survey and broadly supported by an independent global-change manipulation experiment, indicating that they capture generalizable components of soil protist functional organization. Further functional diversity analyses indicated that environmental gradients primarily constrained the range of occupied trait space rather than consistently reshaping the internal dispersion or evenness of trait distributions. Our study provides a trait-based framework for predicting belowground community assembly and ecosystem functional responses to environmental change.
Environmental microbiology reportsAna Paula Santos Oliveira, Cássia Cristina Rezende Mirza, Cleiton Mateus Sousa, Enderson Petrônio de Brito Ferreira
The common bean holds significant economic and social importance, with Brazil being one of the largest producers and consumers worldwide. Its cultivation requires high soil fertility, leading to the intensive use of mineral fertilizers, with high costs and environmental impacts. An alternative is the application of plant growth-promoting rhizobacteria, which have the potential to ensure grain yield. The aim of this study was to evaluate the agronomic performance of common beans in response to consortia of multifunctional rhizobacteria. The experiments were conducted using a randomized block design with 22 treatments and four replications. Each treatment consisted of a combination of three PGPR strains, along with zero fertilizer and fertilizer-only control treatment. Evaluations were carried out at the beginning of flowering and at harvest to assess root system characteristics, shoot development, and yield components. The consortia Rhizobium sp. (PaJuG2R5) + Bacillus pumilus (BRM063573) + Stenotrophomonas maltophilia (BRM063574), Rhizobium sp. (PaJuG2R5) + Bacillus subtilis (BRM067207) + Bacillus pumilus (BRM067206), and Rhizobium sp. (TilvG1R2) + Bacillus pumilus (BRM063573) + Bacillus pumilus (BRM067206) promoted plant growth and development, resulting in increased grain yield. These results offer a sustainable and accessible strategy for family farming, reducing dependence on mineral fertilizers, production costs, and environmental impacts.
While multi-cropping systems, such as strip-cropping, assemble complex microbial communities that contribute to ecosystem resilience, we have limited understanding of their assembly and functions at field scale. Here, we examined the dynamics and site-specific assembly of soil and phyllosphere microbiomes in a rotational faba bean (Vicia faba) and spring barley (Hordeum vulgare) strip-system during two seasons. Using bacterial 16S and fungal ITS amplicon sequencing, we analysed microbial communities across gradients from the centre towards strip edges. We found that phyllosphere microbiomes are more affected by strip-cropping than soil microbiomes. Neighbouring crops harbour different microbial communities, but with increasing proximity, their phyllosphere microbiomes share more specific microbial taxa. Likewise, we observed gradient-specific microbial distribution, including fungal pathogen taxa. For instance, Puccinia was more abundant in the centre of the spring barley strips and gradually declined towards the edge. Correlation and co-occurrence network analyses revealed distinct microbial interaction patterns across soil and phyllosphere gradients. These networks were more resilient at the edge of the strips compared to central networks of spring barley. Altogether, our findings revealed neighbour-effects modulating host-associated microbiomes across strips that could be harnessed for designing optimal cropping systems, for example, to reduce leaf pathogens.
Microbiology (Reading, England)Finlay Bembridge, Jack K Whitmore, Adrian M Ciesielski, John D Rodgers, Samuel A M Connelly, Aidan J Taylor
Campylobacter, the leading cause of bacterial gastroenteritis worldwide, routinely contaminates UK poultry products, often destined for the kitchens of the general public who risk infection through improper handling. Alongside rising antimicrobial resistance (AMR), the sheer abundance of Campylobacter in the food chain is undermining current intervention strategies. A novel approach to reduce surface contamination on poultry products is violet-blue photodynamic inactivation (VB-PDI), which uses 405 nm visible light to activate endogenous photosensitizers and generate bactericidal intracellular levels of reactive oxygen species. We previously demonstrated VB-PDI is effective against reference strains of Campylobacter jejuni and determined the molecular underpinnings in detail. However, the cross-species efficacy, resistance potential and performance against AMR isolates remained uncharacterized. Here, we evaluate VB-PDI efficacy against 64 Campylobacter field isolates from UK poultry surveillance programmes, comprising three Campylobacter species of various antibiotic resistance profiles. All isolates were susceptible to VB-PDI to a similar level, demonstrating broad efficacy irrespective of species or phenotype. In vitro evolution assays did not result in any detectable increase in VB-PDI tolerance after fifteen repeat exposures which, together with the lack of any notably resistant isolates in our broad screen, indicates the risk of intrinsic or evolved resistance is minimal. Consequently, VB-PDI offers a promising and robust intervention strategy for reducing Campylobacter in the food chain, and here we discuss possible modes of implementation.
Microbial carbon use efficiency (CUE) has been proposed as a critical determinant of soil organic carbon (SOC) dynamics, yet its relative importance compared with plant carbon inputs, edaphic conditions, microbial attributes, and physicochemical protection remains poorly understood. Here, we conducted large-scale soil samplings across a 3000-km aridity gradient on the Tibetan Plateau to evaluate the contribution of microbial CUE to SOC variation. Microbial CUE increased with increasing aridity, whereas SOC declined, resulting in a weak negative relationship between CUE and SOC along the aridity gradient. This increase in CUE was primarily driven by reduced microbial respiration, while microbial growth remained largely unchanged. By contrast, correlation analyses revealed strong positive relationships between SOC and physicochemical protection, plant diversity and carbon inputs, edaphic properties, and microbial attributes. Random forest and structural equation models further showed that SOC variation was more strongly associated with indicators of physicochemical protection, including mineral-associated organic carbon, clay content, calcium-bound carbon, and microbial residue carbon than with microbial CUE. Together, our findings challenge the view that microbial CUE alone governs SOC accumulation and highlight the importance of stabilization processes in regulating SOC variations across the aridity gradient.
World journal of microbiology & biotechnologyDaiki Imanishi, Le Vi Pham, Shouji Takahashi
D-Aspartate (D-Asp) is a bioactive compound involved in neuroendocrine regulation and reproductive function in animals, including humans, with tissue-protective effects reported in experimental models, and has potential applications as a raw material for pharmaceuticals and functional food ingredients. It is also used as a side-chain precursor for semisynthetic antibiotics. An established industrial process for D-Asp uses enzymatic conversion by immobilized microbial cells with chemically synthesized D,L-Asp as the starting material and is constrained by dependence on chemical feedstock synthesis. Sustainable alternatives have therefore attracted attention: whole-cell bioconversion of exogenously supplied L-Asp has been demonstrated, whereas de novo production from a renewable carbon source has not yet been reported. This mini-review briefly notes the physiological and industrial contexts that motivate microbial production, and then focuses on the functions, biosynthesis, metabolism, and transport of D-Asp in microorganisms. We further discuss the screening of high-D-Asp-producing microorganisms using a high-throughput colorimetric assay based on D-aspartate oxidase, together with the molecular and cultivation characteristics of the strains identified. These studies indicate that racemization mediated by aspartate racemase, precursor supply via L-asparaginase, competing metabolism associated with bifunctional aspartate aminotransferase, and pH control during cultivation influence extracellular D-Asp accumulation; the contribution of membrane transport remains unresolved. Finally, we highlight the identification of D-Asp exporters, metabolic engineering of production strains, and optimization of cultivation processes as key future priorities for establishing a sustainable and reproducible fermentation platform for D-Asp production.