Latin America harbours an exceptional diversity of extreme and polyextreme environments resulting from the interplay of tectonics, volcanism, climatic heterogeneity, and long-term geological evolution. Hypersaline lakes and salt flats, geothermal and volcanic systems, hyperarid deserts, high-altitude ecosystems, polar and subpolar regions, and insular Caribbean extremes together form a mosaic of natural laboratories where life persists under intense and often overlapping physicochemical stressors. In this perspective-driven review, we synthesize representative examples from across the region-including continental and insular settings such as Mexico, the Andes, Patagonia, and the Dominican Republic-to illustrate how microbial life in Latin America challenges traditional, single-stressor definitions of extremophily. Instead, these ecosystems are characterized by the convergence of salinity, temperature, pH, radiation, low water activity, nutrient limitation, and high heavy metal concentrations, selecting for microbial communities with remarkable physiological plasticity and metabolic versatility. We argue that this complexity has fostered unique adaptive strategies and functional traits with broad implications for ecology, evolution, and biotechnology, including the production of extremozymes, bioactive compounds, stress-protective and catalyst pigments, and myriad other microbial resources relevant for bioremediation and sustainable agriculture. Despite their importance, many Latin American extreme environments remain underexplored and increasingly threatened by climate change, resource exploitation, and land-use transformation. We emphasize the need for coordinated regional efforts integrating omics approaches, culture-based studies, biobanking, and interdisciplinary collaboration, while recognizing the value of local knowledge and biocultural perspectives. Preserving and studying these extreme ecosystems is essential not only for understanding the limits of life but also for unlocking their potential to inform sustainable innovation in a rapidly changing world.
Crude oil, primarily consisting of alkanes, and plastic derivatives are integral to modern society, yet their widespread use has led to persistent pollution that devastates ecosystems worldwide. Enzymatic and microbial biodegradation are highly desirable to become alternatives to conventional methods for the control of these pollutants in terrestrial and aquatic environments. Consequently, investigating the enzymatic machinery of specialized microbes that thrive in contaminated areas and possess the catabolic potential to degrade alkanes and plastics is of considerable interest. In this study, we present a genomic and proteomic analysis of Acinetobacter towneri RMS-02 that was isolated from sludge obtained from mixed food waste and sewage. Consistent with its ability to grow and persist in this environment, the genome of A. towneri RMS-02 encodes enzymes to catabolize different types of polyphenols and aromatic compounds, including trans-cinnamic acid, o-cresol, toluene, benzene, and benzoate. In addition, it encodes serine proteases, metallopeptidase, and transporters facilitating the uptake of amino acids and possibly small peptides, as well as enzymes potentially involved in the depolymerization of alkanes and 2-ketones. Proteomics analysis of A. towneri RMS-02 revealed an extensive repertoire of enzymes involved in terminal and subterminal oxidation of medium- and long-chain alkanes and ketones, which were specifically more abundant during growth on a product that consists of a mixture of these compounds and an oxidized low-molecular-weight polyethylene (LMWPE). Substrate characterization following bacterial growth confirmed the selective utilization of alkanes with chain lengths of C10-C25 and 2-ketones of C13-C26, while the polymeric fraction of the substrate remained unaltered.IMPORTANCECrude oil and plastic pollution threaten ecosystems worldwide, creating an urgent need for sustainable remediation strategies. Microbial and enzymatic degradation provides a sustainable alternative to physical, chemical, and thermal treatments by biologically breaking down hydrocarbons into harmless products or recyclable monomers. Here, we describe a detailed genomic characterization of A. towneri RMS-02, identifying core metabolic functions underlying its potential to utilize phenols, aromatic compounds, proteins, and small-chain hydrocarbons. Using proteomics, we show that a diverse enzymatic arsenal is deployed when growing on an oxidized LMWPE product that includes a mixture of alkanes and 2-ketones. Remarkably, the proteomics results were corroborated by advanced analysis of the spent substrate, confirming that A. towneri RMS-02 metabolizes alkanes and 2-ketones but is unable to interact with the polymeric LMWPE component. Our results expand the understanding of the metabolic repertoire supporting Acinetobacter towneri's survival and identify candidate enzymes with potential for the bioremediation of alkanes and 2-ketones.
Endocrine-disrupting chemicals (EDCs), including synthetic hormones, pesticides, and personal care products (PPCPs), are frequently detected in wastewater treatment plant (WWTP) effluents. EDCs' persistence in aquatic environments poses risks to human and ecological health, given that EDCs are not firmly regulated under South African legislation. The chemical and microbial compositions of a WWTP utilizing maturation ponds in Bloemfontein, South Africa, focusing on selected EDCs (atrazine [ATZ], 17α-ethinylestradiol [EE2], triclosan [TCS], and bisphenol A [BPA]) were investigated. The physicochemical parameters of wastewater samples collected over 6 months were measured onsite. LC-MS/MS analysis and bacterial 16S rRNA and eukaryotic sequencing were performed to determine the EDC concentrations and microbial compositions. Wastewater samples exhibited alkaline, oxic, mesophilic, and oxidative conditions. The EDC concentrations showed variability, with 17α-ethinylestradiol reaching 125 µg/L. Bisphenol A concentration ranged between 0.003 and 0.587 µg/L, that of atrazine from 0.009 to 0.134 µg/L, and that of triclosan from 0.069 to 0.316 µg/L, which were lower than those reported in other South African studies. Microbial community structures revealed Proteobacteria (35.12%) and Bacteroidetes (18.50%) as the dominant bacterial phyla. Among eukaryotes, Ascomycota and unclassified taxa accounted for 13.14% and 68.85%, respectively. Flavobacterium and Microcystis were the most abundant bacterial genera (9.50% and 6.22%), while unidentified taxa represented 85.88% of eukaryotic genera. Functional analysis revealed potential xenobiotic degradation pathways associated with bisphenol A and atrazine, indicating microbial potential for EDC degradation. These findings established the presence of EDCs and microbial compositions of maturation ponds with an estimated hydraulic retention time of ~9 days, emphasizing the need for improved wastewater treatment strategies and bioremediation approaches.IMPORTANCEEndocrine-disrupting chemicals (EDCs) are increasingly found in treated wastewater, yet their removal is not guaranteed in conventional treatment systems. This study examined maturation ponds of South African wastewater treatment plant and provided new insights into their chemical pollutant retention and microbial dynamics. By tracking selected EDCs together with bacterial and eukaryotic communities, the study showed how environmental conditions and microbial populations interact within the ponds. The detection of microbes with potential to degrade pollutants highlighted a natural capacity that could be strengthened for bioremediation. South Africa relies heavily on treated wastewater as a supplementary water source, and understanding the presence of EDCs and the biological process within these ponds is essential. These findings contribute to improving wastewater treatment practices and developing sustainable, microbially driven solutions for safer water management.
Coastal salt flats, locally known as sabkhas, are hypersaline, alkaline desert ecosystems that impose extreme abiotic stress on microbial and plant life. Despite their ecological significance, plant-associated microbiomes in these habitats remain poorly characterized. In this study, we investigated the bacterial communities of native halophytes across three sabkha sites in southern Morocco using an integrated culture-independent and culture-dependent framework. Soil physicochemical analyses revealed strong gradients in salinity and ionic composition, along with consistent alkaline pH across sites. These conditions strongly structured bacterial assemblage: alpha diversity declined progressively from bulk soil to rhizosphere soil, root, and shoot; and beta diversity showed clear compartmental separation driven by environmental factors. Canonical correspondence analysis identified electrical conductivity (EC), Na₂O, K₂O, and carbonate fractions as the main abiotic drivers. Across plant species, bacterial communities converged toward a stable halophilic core microbiome dominated by Halomonas, Kushneria, and Marinococcus, with 66% of amplicon sequencing variants (ASVs) shared across compartments. Host identity played a secondary role as environmental filtering overshadowed host-specific associations. Culture-dependent isolation recovered 19 halophilic and halotolerant bacterial strains, including representatives of Halomonas, Idiomarina, Marinobacter, Psychrobacter, Planomicrobium, and Bacillus. These isolates exhibited robust growth on saline Marine Agar medium, indicating strong salt tolerance consistent with their occurrence in hypersaline environments. The strong concordance between cultured isolates and metabarcoding profile confirms that dominant halophilic lineages are both ecologically robust and readily culturable. Together, these findings demonstrate that sabkha plant microbiomes are primarily shaped by deterministic abiotic filtering and harbor resilient, stress-adapted bacterial communities. Sabkhas thus represent promising reservoirs of halophilic microbes with potential applications in saline agriculture and improving crop resilience under extreme environmental conditions.IMPORTANCECoastal salt flats (sabkhas) are among the most extreme terrestrial environments, characterized by high salinity, alkalinity, and limited water availability. As soil salinization expands worldwide, understanding how life persists in such habitats is increasingly important for sustainable agriculture. This study shows that sabkha ecosystems impose strong environmental filtering on plant-associated bacterial communities, leading to highly structured microbiomes across soil, root, and shoot compartments. Despite differences among sites and plant species, bacterial communities converged toward a shared halophilic core microbiome, dominated by salt-adapted genera that are resilient to extreme ionic stress. Importantly, many of these dominant bacteria were readily culturable, highlighting sabkhas as accessible reservoirs of stress-tolerant microbes. Our findings demonstrate that abiotic conditions outweigh plant identity in shaping microbiome assembly under extreme stress and reveal sabkha halophytes as valuable natural models for discovering microbes with potential applications in saline agriculture, soil restoration, and crop resilience in salt-affected environments.
Despite the successful cultivation of many microbes from rich bacterial communities inhabiting alkaline soda lakes, members of the bacterial phylum Verrucomicrobiota have so far been detected only through metagenomics. Here, we used alginate as a selective substrate to enrich and isolate two strains of haloalkaliphilic Verrucomicrobiota. The isolates share identical 16S rRNA gene sequences representing a new genus lineage, and, together with other metagenome assembled genomes, a new family within Opitutales. Cells of strains AB-alg1T (from soda lakes) and AB-alg4 (from soda solonchak soils) are small and motile cocci forming submerged colonies in soft alginate agar. They are saccharolytic heterotrophs growing aerobically on polysaccharides (alginate, starch, and inulin) and sugars (glucose, fructose, mannose, sucrose, melezitose, maltose, and cellobiose). They also grow anaerobically by fermentation of alginate and D-mannose and by coupling incomplete denitrification to oxidation of alginate. Both isolates are obligately alkaliphilic and moderately salt-tolerant. The dominant membrane phospholipids include phosphatidylcholines and diphosphatidylglycerols (cardiolipins). The genome of AB-alg1T features polysaccharide lyases of the PL6, 7, 15, 17, 38, and 39 families for depolymerization of alginate. Based on distinct phenotype and phylogeny, we propose classification of strains AB-alg1T (JCM 35393T=UQM 41574T) and AB-alg4 as Verruconatronum alginivorum gen. nov., sp. nov. within a new family Verruconatronumaceae.IMPORTANCEAlkaline soda lakes and soils are extreme habitats dominated by obligate haloalkaliphic prokaryotes, some of which can produce alkali- and salt-stable polysaccharide-degrading exoenzymes useful for industrial and domestic applications. However, so far, little was known about the microbial potential for mineralization of acidic polysaccharides, such as alginate, in these habitats. The described isolates are the first representatives of a new family within the phylum Verrucomicrobiota specializing in the degradation of alginate and related polysaccharides. We present the key enzymatic machinery for alginate breakdown. These enzymes are high-pH tolerant and have potential for industry applications, for example, in washing powders and biomass waste recycling. Furthermore, the new family is one of the most abundant taxa in alkaline environments, and these environments are not known to harbor signature alginate producing biota, such as brown algae. This way, our study opens a new window on polysaccharide turnover in alkaline environments.
NASA cleanrooms, which are critical for assembling space mission components, are maintained under stringent decontamination protocols to minimize biological contamination. These environments are characterized by nutrient-poor and oligotrophic conditions, leading to low microbial loads. Despite extensive cleaning, oligotrophs capable of surviving in such conditions continue to persist, often remaining undetected due to their low abundance, resistance to environmental stresses, and difficulties in biomolecule extraction. Even with shotgun metagenome sequencing technologies, these microbes may go undetected or be underrepresented due to their robust cell walls and the absence of reference genomes in publicly available databases. Over a 6-month study of Mars 2020 mission cleanrooms, 182 bacterial strains belonging to 19 families were identified using a whole-genome sequencing (WGS) approach. Among these, 14 novel Gram-positive species were discovered, including eight spore formers. Though the novel species comprised only 0.001% of the sequencing data, their successful cultivation allowed for functional characterization. Through WGS data mining, genomic traits associated with resilience in extreme conditions were revealed. These species were found to be involved in nitrogen cycling, carbohydrate metabolism, and radiation resistance, traits essential for survival in extreme environments. Furthermore, 12 biosynthetic gene clusters were identified, including those linked to ectoine and [Formula: see text]-poly-L-lysine production, suggesting potential biotechnological applications. These findings highlight the hidden microbial diversity within cleanrooms and emphasize the necessity of advanced detection strategies. A better understanding of these microbes will provide insights into extremophiles with applications in biotechnology, medical research, and life support systems for future space exploration missions.IMPORTANCEDespite strict decontamination protocols, NASA cleanrooms harbor low-biomass microbial communities adapted to nutrient-poor environments. These oligotrophic microbes often go undetected in shotgun metagenomics methods due to their low abundance, resistance to lysis, and lack of reference genomes. Standard shotgun metagenome sequencing methods fail to retrieve them, as dominant microbial DNA overshadows rare species. Over 6 months of monitoring Mars 2020 mission cleanrooms, 182 bacterial strains from 19 families were identified, including 14 novel Gram-positive species, 8 of which were spore formers. Though present at 0.001% abundance in sequencing data, we successfully cultured them, enabling functional characterization. These microbes exhibited roles in nitrogen cycling, carbohydrate metabolism, and radiation resistance, with 12 biosynthetic gene clusters linked to ectoine and [Formula: see text]-poly-L-lysine production. These findings highlight the previously underestimated microbial diversity in cleanrooms and emphasize the need for advanced detection strategies to explore extremophiles with applications in biotechnology and space exploration.
Stingless bees (Meliponini) are ecologically vital pollinators with deep cultural and economic importance in the Neotropics; however, the biogeographic structure of their gut microbiota and the extent of microbial exchange with managed honey bees (Apis mellifera) remain insufficiently understood. Using full-length 16S rRNA gene sequencing of individually sampled workers from 167 colonies across Brazil, we compared gut bacterial communities of Melipona quadrifasciata and Melipona mondury with those of co-occurring A. mellifera through an integrated taxonomic, phylogenetic, and community ecological framework. The core microbiota of Melipona species was dominated by Lactobacillus, Bifidobacterium, Apilactobacillus, Bombella, and Floricoccus, whose relative abundances covaried inversely with a set of low-prevalence taxa. Although the core communities of stingless bees overlapped only partially with those of honey bees, both groups displayed comparable alpha- and beta-diversity dispersion, suggesting broadly similar assembly dynamics. Notably, 6% of all amplicon sequence variants (ASVs) were shared across hosts, encompassing nearly all canonical honey bee symbionts, consistent with frequent cross-species spillover. Among these, several Snodgrassella ASVs-typically rare in these stingless bee species-reached high abundance in M. quadrifasciata and formed a deeply divergent clade (~96% 16S rRNA identity to Snodgrassella alvi). These patterns indicate that human-mediated management practices, such as mixed apiaries and artificial feeding, create ecological opportunities for interspecific microbial exchange. Overall, our results show that stingless bee gut microbiomes are compositionally stable yet ecologically permeable, shaped jointly by long-term host specificity and recent anthropogenic contact.IMPORTANCEStingless bees are key pollinators in tropical ecosystems and hold long-standing cultural significance in the Neotropics; however, their microbiomes remain far less studied than those of managed honey bees. Understanding how gut bacterial communities vary across landscapes, and whether microbes move between native and non-native hosts, is essential for predicting the ecological consequences of increasing meliponiculture and urban beekeeping. Our study reveals that stingless bee gut microbiota are generally stable and host-associated but nonetheless acquire bacterial symbionts typical of honey bees, indicating that human management practices facilitate cross-species microbial transmission. These findings broaden current knowledge of bee-microbe evolution by showing that gut symbiont boundaries are not fixed but can become permeable under anthropogenic influence. This has important implications for pollinator health, conservation, and biosecurity as managed and native bees increasingly co-occur in human-modified environments.
Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.
Transposon mutagenesis coupled with deep sequencing (Tn-seq) is currently being deployed in microbial eukaryotes, including the opportunistic yeast pathogen Candida glabrata, for functional genomics research. This method depends on the generation of highly diverse pools of transposon insertion mutants to cover all genes while minimizing the presence of markers and remnants of engineering. Up to now, pools of Hermes transposon insertion mutants in C. glabrata were generated in uracil-requiring ura3∆ auxotrophs, limiting their use in nutrient-restricted environments, such as those of the host. Indeed, we found that ura3∆ mutants were outcompeted by URA3+ prototrophs during colonization of the mouse gastrointestinal tract. To avoid using auxotrophs in Tn-seq experiments, a new scheme was developed for generating prototrophic pools of Hermes insertion mutants. The scheme involved introducing a recessive cycloheximide resistance mutation in the chromosomal RPL28 gene, which did not alter fitness during mouse colonization. When implemented in several different strains of C. glabrata, high insertion densities were obtained, and differences in subtelomeric chromatin compaction were observed that correlated with natural variation in the silencing gene, SIR3. However, all the strains lacked insertions in the PDR1 and CDR1 genes, which are necessary for resistance to cycloheximide and other antifungals. We directly tested the effect of pdr1∆ mutants and found that they exhibited moderate fitness defects in the gastrointestinal tract of mice even in the absence of antifungals. Thus, the new scheme easily generates high-quality pools of insertion mutants in prototrophic C. glabrata with only minor and knowable limitations. Treatment of fungal infections may be improved by a deeper understanding of the genetic mechanisms of colonization within host organisms. Current approaches to deep genetic sequencing in eukaryotic microbes often involve engineered components that have significant biases, minimize microbial complexity, or alter the normal in vivo fitness of opportunistic fungal pathogens. This study designs a new method for developing transposon insertion mutants in Candida glabrata that does not innately introduce altered fitness in mouse models of gastrointestinal tract infection. This scheme is also portable across strains and possibly even fungal species. The findings show that the new method can be used in this pathogenic yeast to yield highly complex pools and reliably identify genetic components of colonization in mouse models of infection.
Introduction. Poultry and poultry products are commonly implicated in human salmonellosis, making effective Salmonella control in the poultry and allied industries an important public health priority. Several factors have been identified which contribute to Salmonella survival and persistence in the environment, including biofilm formation.Gap Statement. Biofilm-forming capability in Salmonella has previously been under-studied in environmental isolates sourced from some commercial poultry production environments, such as poultry feed mills, hatcheries and duck farms.Aim. This study assessed the biofilm-forming capabilities of 96 Salmonella isolates from the environments of commercial poultry premises in Great Britain: feed mills, hatcheries, chicken farms, turkey farms and duck farms.Methodology. A crystal violet microtitre plate biofilm assay was used at environmentally relevant temperatures of 20 °C and 25 °C under aerobic conditions. Analysis of correlations between the biofilm-forming capability and serovar of isolates, assay conditions and origin was undertaken.Results. Ninety-five of the 96 Salmonella isolates formed biofilms. The influence of incubation temperature varied between isolates but increased significantly after an extended incubation period of 72 h. Isolates originating from different types of commercial poultry environments showed significant differences in biofilm-forming capability. However, as different serovars predominated in the isolate panels from each poultry environment, the influences of serovar versus origin could not be differentiated. The influence on biofilm formation of sample type and/or surface material of origin was not statistically significant. Inter-serovar variation was observed with nine serovars also demonstrating intra-serovar variation, consistent with biofilm-forming capability being strain dependent.Conclusion. This study demonstrates that most Salmonella isolated from poultry environments have strong or moderate biofilm-forming capabilities in microtitre plate assays.
Stunting, or impaired child growth due to poor nutrition and infections, is characterized by a low height-for-age and affects 48%-56% of school-aged children worldwide. It is associated with later weight gain and chronic diseases. The gut microbiome in undernourished children may increase obesity risk if they are exposed to high-calorie environments. To investigate this, we assessed whether the intestinal microbiome of stunted children elevates obesity risk upon exposure to an obesogenic environment. Fecal microbiota transplantation (FMT) was performed using pooled stools from healthy (n = 6) or stunted (n = 6) school-aged children from a low-income cohort in Mexico. Eight-week-old male C57BL/6 mice underwent bowel cleansing with polyethylene glycol (PEG), followed by weekly intragastric FMT for 4 weeks. The mice were subsequently fed either a control diet (CT) or a high-fat, high-fructose corn syrup diet (HFFr, including 15% HFCS-55) for 15 weeks. Metabolic outcomes were assessed through body composition, indirect calorimetry, oral glucose tolerance test, insulin tolerance test, and histological analysis of visceral adipose tissue. The microbiota composition was evaluated by 16S rRNA V3-V4 hypervariable region sequencing, and the predicted functional capacity was analyzed using PICRUSt2. FMT from stunted children increased susceptibility to diet-induced obesity, visceral adipose tissue hypertrophy, and insulin resistance. In contrast, FMT from healthy children promoted energy expenditure and visceral adipose tissue hyperplasia, conferring a protective effect against diet-induced obesity and insulin resistance in the mice. Healthy-FMT led to sustained enrichment of Akkermansia and Parabacteroides, whereas stunting-FMT increased Proteobacteria, Veillonella, Desulfovibrionaceae, and Bifidobacterium. Microbial‒phenotypic correlations showed that Akkermansia and Parabacteroides were negatively correlated with fasting glucose, body weight, and fat mass, and positively correlated with postprandial RER, VO2, and lean mass. In conclusion, stunting-FMT recipient mice showed a higher risk of obesity and metabolic issues in an obesogenic environment. Healthy-FMT confers metabolic resilience, characterized by increased abundance of taxa such as Akkermansia and Parabacteroides, which are linked to enhanced energy expenditure, improved glucose metabolism, and favorable adipose tissue structure.
Microplastics (MPs), plastic particles smaller than 5 mm, are increasingly recognized as pervasive pollutants in terrestrial ecosystems, especially agricultural soils, which serve as long-term sinks. While early research prioritized aquatic environments, recent studies underscore the diverse pathways through which MPs infiltrate soils, via plastic mulching, wastewater irrigation, sewage sludge, compost, and atmospheric deposition. This review provides a comprehensive overview of emerging insights into MPs-plant-microbe interactions within soil systems, emphasizing both their complex ecological effects and key knowledge gaps. The main objective of this review is to consolidate current evidence on how MPs affect plant physiology and soil microbial dynamics, and to highlight methodological limitations impeding progress in this field. MPs exhibit variable but often detrimental effects on plant health, including delayed germination, inhibited growth, impaired photosynthesis, and disrupted nutrient uptake. These outcomes are largely driven by physical blockage, chemical leaching, and oxidative stress, and are influenced by MPs characteristics (polymer type, shape, concentration) and plant species traits. Interestingly, low MPs levels may occasionally improve root biomass through enhanced soil aeration and water retention, reflecting the context-dependent nature of MPs impacts. Crucially, MPs alter soil microbial communities, reducing beneficial microbes, promoting pathogens, and interfering with enzymatic functions, thereby indirectly undermining soil fertility and crop productivity. Disruption of symbiotic relationships, such as mycorrhizal associations, further compounds ecological stress. This review also identifies a pressing need for standardized MPs detection and toxicity assessment protocols. Advancing analytical tools and ecologically relevant models is essential for uncovering plant molecular responses and supporting sustainable agriculture in MPs-contaminated environments.
Soil microbes play a critical role in carbon (C) cycling, yet assessing the direct impact of individual microbes and their interactions on C mineralization remains poorly understood due to confounding effects under fluctuated physicochemical and biological variables in natural soils. "Artificial soil systems" enable precise control in a uniform environment to directly quantify species-specific carbon cycling, yet it has not been sufficiently demonstrated whether they can isolate competitive dynamics and metabolic roles of individual microbes in C mineralization. This study used an artificial soil system to quantify glucose mineralization through a 14-day incubation experiment using Bacillus subtilis NBRC 101584 (B. subtilis) and Streptomyces cinnamoneus NBRC 13823 (S. cinnamoneus). In monoculture incubations, B. subtilis showed a rapid mineralization rate and high cumulative respiration, whereas S. cinnamoneus exhibited delayed and lower respiration. In co-culture incubation, cumulative respiration and DNA yields converged to that of the B. subtilis monoculture, and positively correlated with its relative abundance. In contrast, S. cinnamoneus markedly reduced soil pH despite lower respiration, highlighting a distinct ecological trade-off. These findings demonstrate that artificial soil systems provide the basis for directly evaluating species-specific mineralization patterns, competitive interactions, and microenvironmental modifications. This controlled approach provides an effective tool for elucidating microbial mechanisms regulating soil C dynamics.IMPORTANCEThe role of individual soil microorganisms in carbon dynamics has long been obscured by the extreme complexity of natural soil environments. This study utilized a controllable artificial soil system to directly quantify the glucose mineralization rate using Bacillus subtilis NBRC 101584 (B. subtilis) and Streptomyces cinnamoneus NBRC 13823 (S. cinnamoneus). As a result, B. subtilis achieved fast glucose mineralization and elevated cumulative CO2 production, in contrast to S. cinnamoneus, which demonstrated slower mineralization and reduced overall respiration. These results highlight that artificial soil systems offer a critical and enabling framework for resolving species-specific mechanisms in soil carbon cycling.
Plant-microbe interactions are key drivers of plant health and ecosystem functioning, yet their roles in marine environments remain poorly understood. The seagrass Posidonia oceanica, a foundation species in the Mediterranean Sea, forms complex associations with microbial communities that influence its development and stress tolerance. Here, we provide the first evidence of culturable bacterial and fungal endophytes inhabiting P. oceanica seeds collected from the central Mediterranean, a region representing a major center of the species' genetic diversity. Using two different marine culture media, we isolated a diverse assemblage of endophytes, predominantly affiliated with Marinomonas, Celerinatantimonas, Vibrio, Halomonas, Kocuria, Bacillus, Metabacillus, Lysobacter, and Aureimonas, along with the fungi Paecilomyces maximus and Halophytophthora sp. Most bacterial isolates displayed plant growth-promoting (PGP) traits such as indole-3-acetic acid production and nitrogen fixation, supporting their potential contribution to seed germination and early seedling establishment. The detection of Candidatus Celerinatantimonas neptuna, a nitrogen-fixing symbiont previously described in P. oceanica roots, suggests a possible route of vertical transmission. Although fungal endophytes were less frequent, their presence indicates that P. oceanica seeds may serve as a reservoir of both beneficial and potentially pathogenic taxa. These findings expand our understanding of the P. oceanica holobiont, highlight the role of seeds in the persistence and dissemination of endophytic communities and lay the groundwork for the biotechnological use of seed-associated microbes in marine plant restoration and conservation, and in crop stress tolerance.
As modern populations spend the majority of their time indoors, understanding indoor microbial ecology is crucial for public health. While research has addressed abiotic pollutants, the ecological dynamics of surface-associated mycobiomes remain insufficiently understood. This study assessed fungal communities across 25 types of public facilities in South Korea to evaluate the relative influence of environmental parameters and human-driven factors. A total of 327 surface samples from six surface types (handles, tables, chairs, walls, pillars, floors) were analyzed using internal transcribed spacer (ITS) sequencing, yielding 27 million reads and 31,721 amplicon sequence variants (ASVs). Although temperature and humidity significantly correlated with airborne fungal concentration, they exerted minimal influence on community diversity and structure. Instead, the intensity of human contact with indoor surfaces emerged as a primary driver of fungal community composition. We found that the relative abundance of the human-associated genus Malassezia is strongly associated with two distinct ecological states of indoor surface mycobiomes; high-Malassezia samples exhibited significantly distinct communities (ANOSIM R = 0.217, p < 0.001) and dense co-occurrence networks among genera of potential clinical relevance, with strong correlations between Malassezia and both Aspergillus and Cladosporium (|corr| = 0.81). These Malassezia-associated patterns persisting across diverse facilities demonstrate that human-driven microbes are the primary ecological drivers of surface mycobiomes in public spaces, providing foundational evidence for human contact-based microbial assessments in public health monitoring and hygiene-conscious environment design.
More than 99% of microorganisms in the natural environment are not readily culturable using standard laboratory techniques. These microbes can be reservoirs of novel metabolites and biomolecules having pharmaceutical applications against bacterial infections, chronic diseases, and antibiotic resistance. Given this, our work is a comprehensive synthesis of recent advances in understanding, detection, and cultivation of "yet-to-be cultured" (YTBC) microbes. We highlight physiological traits that restrict their domestication under standard laboratory conditions. Some of the factors that may influence are their metabolic dormancy, specialized nutrient demands, siderophore-mediated iron acquisition, microbial signaling, and interspecies interactions. The review discusses various strategies, such as simulated natural environments, co-culture, and advanced bioreactor systems, which can be implemented to cultivate them. We reviewed recent metagenomic approaches and single-cell isolation methods, including label-based techniques (e.g. fluorescence in situ hybridization), label-free approaches such as Raman-activated cell sorting, and high-throughput tools like flow cytometry. We also examined culture-dependent approaches, including co-cultivation with helper strains with a special emphasis on bioreactor-based systems, diffusion chamber, hollow-fiber membrane chamber, high-throughput isolation chip (iChip), and encapsulation. Overall, this review provides a roadmap to unlock the biotechnological potential of YTBC microbes by outlining new technologies, methodological trends, and important knowledge gaps.
Microbiomes and their host environments form complex, interconnected ecosystems. The microbial species within a microbiome, on the one hand, compete for resources, while on the other hand, they exchange vital metabolites to support their survival. These interactions are influenced by the microbial genetic repertoire, environmental conditions, and availability of nutrients. We developed EcoGS (http://www.github.com/KaletaLab/EcoGS), a metabolic modeling tool designed to predict the ecological interactions between pairs of microbes. Applying EcoGS to the microbiomes of two distinct human cohorts revealed a shift from collaborative to exploitative ecological interactions associated with increased dietary intake of simple sugars (glucose and fructose) in diabetic individuals and those living industrialized lifestyles. On the other hand, the consumption of cobalamin (vitamin B12), phylloquinone (vitamin K1), and biotin (vitamin B7), among other compounds, was associated with increased collaboration in the gut microbiome. We conclude that the abundance of simple sugars as an energy source reduces the necessity for microbes to cooperate, thereby increasing competition and hostility among microbiome members. Moreover, our study proposes multiple compounds, such as urate, deoxyadenosine, deoxyguanosine, and hypoxanthine, for in vitro validation tests as dietary interventions that have the potential to restore the ecological balance within the community. EcoGS serves as a valuable tool for exploring microbiome dynamics and their connections to environmental changes and disease.
Throughout their life cycle, plants associate with diverse and complex microbial communities collectively known as their microbiota. These microbiota contribute to plant performance and health by enhancing nutrient acquisition, modulating immunity, and providing a microbial barrier against pathogens. To successfully colonize their hosts, pathogens must overcome not only plant immune defenses but also this microbial barrier. For example, the soil-borne fungal pathogen Verticillium dahliae secretes the antimicrobial effector Ave1 to suppress antagonistic microbes and facilitate infection. Although many plant pathogens, including V. dahliae, inhabit both plant-associated and soil environments, how antimicrobial effectors contribute to pathogen establishment across these diverse ecological contexts remains poorly understood. To explore this question, we assembled a collection of natural soils differing in physicochemical properties and microbiota composition. Using three host plant species-barley, tomato, and cotton-we found that root-associated bacterial and fungal communities were primarily shaped by type of soil, whereas phyllosphere microbiota were mainly determined by plant species identity. On tomato, we further observed that the effector Ave1 differentially contributed to V. dahliae virulence depending on the soil of origin. While Ave1 consistently altered tomato-associated microbiota across all soils tested, the specific microbial taxa affected varied between soils. Our findings demonstrate that the impact of the antimicrobial effector Ave1 on microbiota composition and pathogen virulence is context-dependent, influenced by the specific soil-derived microbial community that assembles on the host. This work highlights the ecological complexity of effector functions and suggests that pathogen success in natural environments depends on dynamic interactions with both the plant host and its microbiota. Video Abstract.
Pseudomonas protegens, a member of the P. fluorescens complex, is a key biocontrol bacterium with well-documented potential to protect plants against diverse pathogens. Although P. protegens strains have been widely exami-ned globally, those originating from Japan have not been well described. In this study, we isolated and characterized a new P. protegens strain, GSF-73, from the rhizosphere of Allium fistulosum in Gifu, Japan, and assessed its performance against several major plant diseases. Draft genome sequencing produced a 7.13-Mbp assembly, and average nucleotide identity values of 97.81-98.26% with reference strains (Cab75, CHA0, and Pf-5) confirmed its species identity. A comparative genomic anal-ysis showed that GSF-73 possessed a larger genome than the reference strains, containing eight conserved biosynthetic gene clusters for antimicrobial compounds and an expanded set of strain-specific genes related to metabolism, regulation, mobilome functions, and secretion. GSF-73 exhibited broad-spectrum antagonistic activity in vitro against fungal, oomycete, and bacterial pathogens. In biocontrol assays, GSF-73 significantly suppressed spinach Fusarium wilt, cucumber anthracnose on detached cotyledons, tomato bacterial wilt, and cucumber downy mildew. In contrast, root and/or seed treatments enhanced Pythium root rot in spinach and anthracnose in pot-grown cucumbers, indicating pathosystem-dependent efficacy. Despite these contrasting outcomes, GSF-73 shows strong biocontrol potential and merits further study to elucidate the mechanisms underlying both beneficial and adverse effects for its optimized use as a locally adapted biocontrol agent for Japanese agriculture.
This study investigates the archaeal lipid distribution in freshwater springs with a particular focus on lipidomic profiles as ecological indicaters. Cultivation-independent approaches were employed to analyze organisms that had not yet been cultivated in the laboratory. Shotgun lipidomics of 21 springs in western and central part of Slovakia revealed more than 100 characteristic archaeal lipids, from which three biomarker groups were selected: (i) core lipids containing archaeol and glycerol dialkyl glycerol tetraethers (GDGT), including their mono and dihydroxy derivatives; (ii) mono- to tetra-glycosides of archaeol and GDGTs; and (iii) six phosphoarchaeols (archaeol-based phospholipids). Statistical analyses classified springs into three categories: cold (temperature < 20 °C), warm (> 30 °C), and radioactive (a subset of cold springs with ˃100 Bq/L radioactivity). Significant shifts in the ratios of archaeal lipids were correlated with the temperature and radioactivity, demonstrating the sensitivity of lipidomic profiling to environmental parameters. Moreover, tandem mass spectrometry identified a previously undescribed metabolite, archaeol-based dimethylphosphatidylethanolamine. The applied method provides rapid and highly sensitive tools for screening the presence of archaea, detecting as few as several thousand cells per liter, and offers new insights into the ecology of archaeal communities in groundwater environments.