Pore-forming aegerolysin and MACPF proteins in extremotolerant or extremophilic fungi

Aegerolysin proteins are involved in various interactions by recognising a molecular receptor in the target organism. The formation of pores in combination with larger, non-aegerolysin-like protein partners (such as membrane attack complex/perforin proteins [MACPFs]) is one of the possible responses in the presumed competitive exclusion of other organisms from the ecological niche. Bicomponent pairs are already observed at the gene level. Fungi growing under extreme conditions can be divided into ubiquitous and extremotolerant generalists which can compete with mesophilic species and rare, isolated extremophilic and extremotolerant specialists with narrow ecological amplitude that cannot compete. Under extreme conditions, there are fewer competitors, so fungal specialists generally produce less diverse and complicated profiles of specialised molecules. Since extremotolerant and extremophilic fungi have evolved in numerous branches of the fungal tree of life and aegerolysins are unevenly distributed across fungal genomes, we investigated whether aegerolysins, together with their partner proteins, contribute to the extreme survival ecology of generalists and specialists. We compiled a list of 109 thermo-, psihro-, acido-, alkali-, halo-, metallo- and polyextremo-tolerant/-philic fungal species. Several challenges were identified that affected the outcome: renaming fungal species, defining extremotolerant/extremophilic traits, identifying extremotolerant/extremophilic traits as metadata in databases and linking fungal isolates to fungal genomes. The yield of genomes coding aegerolysins or MACPFs appears to be lower in extremotolerant/extremophilic fungi compared to all fungal genomes. No candidates for pore-forming gene pairs were identified in the genomes of extremophilic fungi. Aegerolysin and MACPFs partner pairs were identified in only two of 69 species with sequenced genomes, namely in the ubiquitous metallotolerant generalists Aspergillus niger and A. foetidus. These results support the hypothesised role of these pore-forming proteins in competitive exclusion.

The spatial pattern of Populus euphratica competition based on competitive exclusion theory

Introduction

Population-level competition and spatial patterns may explain the role of competitive exclusion in communities, which is important for vegetation restoration and biodiversity conservation.

Methods

We analyzed the competitive intensity, spatial patterns, and renewal of Populus euphratica Oliv. forests in the Tarim River Basin using the Hegyi competition index and spatial point pattern analysis in a completely random model with different habitats and different forest ages.

Results

The greatest competitive distance for P. euphratica was 10 m, and the intensity of competition steadily decreased as the diameter increased. The intensity of intraspecific and interspecific competition in young, mature, and old P. euphratica forests was as follows: riverside habitat > transitional habitat > desert margin habitat. The Simpson index values for the three habitats decreased as follows: transitional > riverside > desert margin, and the Shannon-Wiener index and Pielou index values decreased as follows: riverside > transitional > desert margin. In the riverside habitat, the young P. euphratica forest experienced the greatest competitive intensity, the mature forest in the transitional habitat was the largest, and the forest in the desert margin habitat was the oldest. Competitive intensity was greatest in the young riverside P. euphratica forest, mature P. euphratica forest in the transitional habitat, and old forest in the desert margin. Riverside P. euphratica experienced strong competition from Populus pruinosa. Competitive exclusion caused P. pruinosa to disappear from the transitional and desert margin habitats. Young, mature, and old P. euphratica forests were randomly distributed along the riverside and in the transitional habitat, while mature and old P. euphratica forests were randomly distributed in the desert margin. Populus pruinosa, Tamarix ramosissima, and Tamarix hispida were mainly randomly distributed, and T. ramosissima and T. hispida were clustered at small scales. In the riverside habitat, young, mature, and old P. euphratica had no spatial correlation, and there was a significant negative correlation at small scales in the transitional habitat. The density of P. euphratica seedlings in the riverside habitat was greater than that in the transitional habitat, and greater competitive pressures on P. euphratica tree seedlings caused a lower renewal density.

Conclusions

When planting P. euphratica forests, spacing greater than 10 m can effectively reduce stand competition and thus promote seedling regeneration.

Extreme specificity in obligate mutualism-A role for competition?

Obligate mutualisms, reciprocally obligate beneficial interactions, are some of the most important mutualisms on the planet, providing the basis for the evolution of the eukaryotic cell, the formation and persistence of terrestrial ecosystems and the establishment and expansion of coral reefs. In addition, these mutualisms can also lead to the diversification of interacting partner species. Accompanying this diversification is a general pattern of a high degree of specificity among interacting partner species. A survey of obligate mutualisms demonstrates that greater than half of these systems have only one or two mutualist species on each side of the interaction. This is in stark contrast to facultative mutualisms that can have dozens of interacting mutualist species. We posit that the high degree of specificity in obligate mutualisms is driven by competition within obligate mutualist guilds that limits species richness. Competition may be particularly potent in these mutualisms because mutualistic partners are totally dependent on each other's fitness gains, which may fuel interspecific competition. Theory and the limited number of empirical studies testing for the role of competition in determining specificity suggest that competition may be an important force that fuels the high degree of specificity. Further empirical research is needed to dissect the relative roles of trait complementarity, mutualism regulation, and competition among mutualist guild members in determining mutualism specificity at local scales.

The evolution and ecology of gigantism in terror birds (Aves, Phorusrhacidae)

Terror birds (Aves, Phorusrhacidae) were large flightless apex predators in South America during the Cenozoic. Here, we estimate a new phylogeny for phorusrhacids using Bayesian inference. We demonstrate phylogenetic evidence for a monophyletic Patagornithinae and find significant support for a distinct crown group associated with the quintessential 'terror bird' characteristics. We use this phylogeny to analyse the evolution of body size and cursoriality. Our results reveal that size overlap was rare between co-occurring subfamilies, supporting the hypothesis that these traits were important for niche partitioning. We observe that gigantism evolved in a single clade, containing Phorusrhacinae and Physornithinae. The members of this lineage were consistently larger than all other phorusrhacids. Phorusrhacinae emerged following the extinction of Physornithinae, suggesting the ecological succession of the apex predator niche. The first known phorusrhacine, Phorusrhacos longissimus, was gigantic but significantly smaller and more cursorial than any physornithine. These traits likely evolved in response to the expansion of open environments. Following the Santacrucian SALMA, phorusrhacines increased in size, further converging on the morphology of Physornithinae. These findings suggest that the evolution and displacement of body size drove terror bird niche partitioning and competitive exclusion controlled phorusrhacid diversity.

Neutral Theory and Plankton Biodiversity

The biodiversity of the plankton has been interpreted largely through the monocle of competition. The spatial distancing of phytoplankton in nature is so large that cell boundary layers rarely overlap, undermining opportunities for resource-based competitive exclusion. Neutral theory accounts for biodiversity patterns based purely on random birth, death, immigration, and speciation events and has commonly served as a null hypothesis in terrestrial ecology but has received comparatively little attention in aquatic ecology. This review summarizes basic elements of neutral theory and explores its stand-alone utility for understanding phytoplankton diversity. A theoretical framework is described entailing a very nonneutral trophic exclusion principle melded with the concept of ecologically defined neutral niches. This perspective permits all phytoplankton size classes to coexist at any limiting resource level, predicts greater diversity than anticipated from readily identifiable environmental niches but less diversity than expected from pure neutral theory, and functions effectively in populations of distantly spaced individuals.

Climate acts as an environmental filter to plant pathogens

Climate shapes the distribution of plant-associated microbes such as mycorrhizal and endophytic fungi. However, the role of climate in plant pathogen community assembly is less understood. Here, we explored the role of climate in the assembly of Phytophthora communities at >250 sites along a latitudinal gradient from Spain to northern Sweden and an altitudinal gradient from the Spanish Pyrenees to lowland areas. Communities were detected by ITS sequencing of river filtrates. Mediation analysis supported the role of climate in the biogeography of Phytophthora and ruled out other environmental factors such as geography or tree diversity. Comparisons of functional and species diversity showed that environmental filtering dominated over competitive exclusion in Europe. Temperature and precipitation acted as environmental filters at different extremes of the gradients. In northern regions, winter temperatures acted as an environmental filter on Phytophthora community assembly, selecting species adapted to survive low minimum temperatures. In southern latitudes, a hot dry climate was the main environmental filter, resulting in communities dominated by drought-tolerant Phytophthora species with thick oospore walls, a high optimum temperature for growth, and a high maximum temperature limit for growth. By taking a community ecology approach, we show that the establishment of Phytophthora plant pathogens in Europe is mainly restricted by cold temperatures.

The competitive exclusion-tolerance rule explains habitat partitioning among co-occurring species of burying beetles

Habitat partitioning among co-occurring, ecologically similar species is widespread in nature and thought to be an important mechanism for coexistence. The factors that cause habitat partitioning, however, are unknown for most species. We experimentally tested among three alternative hypotheses to explain habitat partitioning among two species of co-occurring burying beetle (Nicrophorus) that occupy forest (Nicrophorus orbicollis) and wetland (Nicrophorus hebes) habitats. Captive experiments revealed that the larger N. orbicollis (forest) was consistently dominant to N. hebes (wetland) in competitive interactions for carcasses that they require for reproduction. Transplant enclosure experiments in nature revealed that N. hebes had poor reproductive success whenever the dominant N. orbicollis was present. In the absence of N. orbicollis, N. hebes performed as well, or better, in forest versus its typical wetland habitat. In contrast, N. orbicollis performed poorly in wetlands regardless of the presence of N. hebes. These results support the competitive exclusion-tolerance rule where the competitively dominant N. orbicollis excludes the subordinate N. hebes from otherwise suitable or preferable forest habitat, while the subordinate N. hebes is uniquely able to tolerate the challenges of breeding in wetlands. Transplant experiments further showed that carcass burial depth-an important trait thought to enhance the competitive ability of the dominant N. orbicollis-is costly in wetland habitats. In the presence of N. hebes, N. orbicollis buried carcasses deeper; deeper burial is thought to provide a competitive advantage in forests but further compromised the reproductive success of N. orbicollis in wetlands. Overall, results provide evidence that the competitive exclusion-tolerance rule underlies habitat partitioning among ecologically similar species and that the traits important for competitive dominance in relatively benign environments are costly in more challenging environments, consistent with a trade-off.

Colonization of chickens with competitive exclusion products results in extensive differences in metabolite composition in cecal digesta

The concept of competitive exclusion is well established in poultry and different products are used to suppress the multiplication of enteric pathogens in the chicken intestinal tract. While the effect has been repeatedly confirmed, the specific principles of competitive exclusion are less clear. The aim of the study was to compare metabolites in the cecal digesta of differently colonized chickens. Metabolites in the cecal contents of chickens treated with a commercial competitive exclusion product or with an experimental product consisting of 23 gut anaerobes or in control untreated chickens were determined by mass spectrometry. Extensive differences in metabolite composition among the digesta of all 3 groups of chickens were recorded. Out of 1,706 detected compounds, 495 and 279 were differently abundant in the chicks treated with a commercial or experimental competitive exclusion product in comparison to the control group, respectively. Soyasaponins, betaine, carnitine, glutamate, tyramine, phenylacetaldehyde, or 3-methyladenine were more abundant in the digesta of control chicks while 4-oxododecanedioic acid, nucleotides, dipeptides, amino acids (except for glutamate), and vitamins were enriched in the digesta of chickens colonized by competitive exclusion products. Metabolites enriched in the digesta of control chicks can be classified as of plant feed origin released in the digesta by degradative activities of the chicken. Some of these molecules disappeared from the digesta of chicks colonized by complex microbiota due to them being metabolized. Instead, nucleotides, amino acids, and vitamins increased in the digesta of colonized chicks as a consequence of the additional digestive potential brought to the cecum by microbiota from competitive exclusion products. It is therefore possible to affect metabolite profiles in the chicken cecum by its colonization with selected bacterial species.

Ethanolamine enhances adhesion, promotes microcompartment formation, and modulates gene expression in Levilactobacillus brevis ATCC 14869

Ethanolamine is an abundant compound in the gastrointestinal tract and a valuable source of carbon and nitrogen for pathogenic bacteria harboring ethanolamine utilization (eut) genes. Eut-positive pathogens can consume free ethanolamine to outcompete commensal microbes, which often lack eut genes, and establish infection. Ethanolamine can also act as a host recognition signal for eut-positive pathogens to upregulate virulence genes during colonization. Therefore, reducing free ethanolamine titers may represent a novel approach to preventing infection by eut-positive pathogens. Interestingly, the commensal microorganism Levilactobacillus brevis ATCC 14869 was found to encode over 18 eut genes within its genome. This led us to hypothesize that L. brevis can compete with eut-positive pathogens by clearing free ethanolamine from the environment. Our results demonstrate that despite being unable to metabolize ethanolamine under most conditions, L. brevis ATCC 14869 responds to the compound by increasing the expression of genes encoding proteins involved in microcompartment formation and adhesion to the intestinal epithelial barrier. The improved intestinal adhesion of L. brevis in the presence of ethanolamine also enhanced the exclusion of eut-positive pathogens from adhering to intestinal epithelial cells. These findings support further studies to test whether L. brevis ATCC 14869 can counter enteric pathogens and prevent or reduce the severity of infections. Overall, the metabolic capabilities of L. brevis ATCC 14869 offer a unique opportunity to add to the armamentarium of antimicrobial therapies as well as our understanding of the mechanisms used by beneficial microbes to sense and adapt to host microenvironments.

Inhibitor activity of Lactiplantibacillus plantarum LP5 on thermotolerant campylobacter with different biofilm-forming capacities

AIMS

To evaluate the biofilm-forming capacity of thermotolerant Campylobacter (TC) strains from poultry production and to analyse the inhibitory capacity of Lactiplantibacillus plantarum LP5 against TC on different materials.

METHODS AND RESULTS

Biofilm-forming capacity by Campylobacter jejuni and Campylobacter coli was analysed by cell adhesion in polystyrene plates. TC were classified as non-biofilm-forming (NBF, 1.3%), weak biofilm-forming (WBF, 68.4%), moderate biofilm-forming (MBF, 27.6%), and strong biofilm-forming (SBF, 2.7%). The inhibitory capacity of L. plantarum LP5 against TC was tested on stainless-steel, nylon, aluminium, and glass disks (treated group) and compared with biofilm-forming TC (control group). Lactiplantibacillus plantarum LP5 was inoculated, and then TC. Biofilm was removed in both experimental groups and TC and LP5 bacterial counts were performed. The L. plantarum LP5 presence reduced the formation of TC biofilm (P < 0.001). The material type and strain category influenced biofilm formation, with stainless-steel and the SBF strain being the material and TC having the highest adhesion (P < 0.001). Lactiplantibacillus plantarum LP5 formed a similar biofilm on all materials (P = 0.823).

CONCLUSIONS

This trial showed very promising results; L. plantarum LP5 could be incorporated as a bio-protector of TC on different surfaces.

Draft whole-genome sequences of competitive exclusion Ligilactobacillus salivarius strains for poultry

Competitive exclusion (CE) bacteria have been used to control the colonization of chickens by major foodborne pathogens. In this article, we report draft whole-genome sequences of three Ligilactobacillus salivarius strains isolated from chicken gastrointestinal tracts and previously selected as CE for poultry. These genome sequences will provide a foundation for further characterization and understanding of their CE attributes.

Commensal Escherichia coli Strains of Bovine Origin Competitively Mitigated Escherichia coli O157:H7 in a Gnotobiotic Murine Intestinal Colonization Model with or without Physiological Stress

Cattle are a primary reservoir of enterohemorrhagic Escherichia coli (EHEC) O157:H7. Currently, there are no effective methods of eliminating this important zoonotic pathogen from cattle, and colonization resistance in relation to EHEC O157:H7 in cattle is poorly understood. We developed a gnotobiotic EHEC O157:H7 murine model to examine aspects of the cattle pathogen-microbiota interaction, and to investigate competitive suppression of EHEC O157:H7 by 18 phylogenetically distinct commensal E. coli strains of bovine origin. As stress has been suggested to influence enteric colonization by EHEC O157:H7 in cattle, corticosterone administration (±) to incite a physiological stress response was included as an experimental variable. Colonization of the intestinal tract (IT) of mice by the bovine EHEC O157:H7 strain, FRIK-2001, mimicked characteristics of bovine IT colonization. In this regard, FRIK-2001 successfully colonized the IT and temporally incited minimal impacts on the host relative to other EHEC O157:H7 strains, including on the renal metabolome. The presence of the commensal E. coli strains decreased EHEC O157:H7 densities in the cecum, proximal colon, and distal colon. Moreover, histopathologic changes and inflammation markers were reduced in the distal colon of mice inoculated with commensal E. coli strains (both propagated separately and communally). Although stress induction affected the behavior of mice, it did not influence EHEC O157:H7 densities or disease. These findings support the use of a gnotobiotic murine model of enteric bovine EHEC O157:H7 colonization to better understand pathogen-host-microbiota interactions toward the development of effective on-farm mitigations for EHEC O157:H7 in cattle, including the identification of bacteria capable of competitively colonizing the IT.

Homologous genes shared between probiotics and pathogens affect the adhesion of probiotics and exclusion of pathogens in the gut mucus of shrimp

Clarifying mechanisms underlying the selective adhesion of probiotics and competitive exclusion of pathogens in the intestine is a central theme for shrimp health. Under experimental manipulation of probiotic strain (i.e., Lactiplantibacillus plantarum HC-2) adhesion to the shrimp mucus, this study tested the core hypothesis that homologous genes shared between probiotic and pathogen would affect the adhesion of probiotics and exclusion of pathogens by regulating the membrane proteins of probiotics. Results indicated that the reduction of FtsH protease activity, which significantly correlated with the increase of membrane proteins, could increase the adhesion ability of L. plantarum HC-2 to the mucus. These membrane proteins mainly involved in transport (glycine betaine/carnitine/choline ABC transporter choS, ABC transporter, ATP synthase subunit a atpB, amino acid permease) and regulation of cellular processes (histidine kinase). The genes encoding the membrane proteins were significantly (p < 0.05) up-regulated except those encoding ABC transporters and histidine kinases in L. plantarum HC-2 when co-cultured with Vibrio parahaemolyticus E1, indicating that these genes could help L. plantarum HC-2 to competitively exclude pathogens. Moreover, an arsenal of genes predicted to be involved in carbohydrate metabolism and bacteria-host interactions were identified in L. plantarum HC-2, indicating a clear strain adaption to host's gastrointestinal tract. This study advances our mechanistic understanding of the selective adhesion of probiotics and competitive exclusion of pathogens in the intestine, and has important implications for screening and applying new probiotics for maintaining gut stability and host health.

Phylogenetic and functional trait-based community assembly within Pacific Cyrtandra (Gesneriaceae): Evidence for clustering at multiple spatial scales

Tropical rainforest communities are often characterized by a small number of species-rich genera that contribute disproportionately to the alpha diversity in these habitats. In the Pacific Basin, there are nearly 200 species of Cyrtandra, most of which are white-flowered woody shrubs that are single-island endemics. Within these island communities, multiple Cyrtandra species are commonly observed to occur sympatrically in wet forest understories, forming swarms of what appear to be ecologically similar taxa. The aim of this study was to determine whether species of these plants are randomly assembled with respect to phylogenetic relatedness and traits that are ecologically relevant. I examined assembly patterns across three Pacific archipelagoes using a combination of 10 functional traits and a well-resolved phylogeny comprising 34 species of Cyrtandra. Coexisting species were found to be more closely related and more phenotypically similar than would be expected by chance. This pattern was observed at both regional (island) and local (site) spatial scales. The retention of phylogenetic signal in floral traits and the strong influence of these traits on the observed degree of phylogenetic clustering may indicate that generalist insect pollinators act as a biotic filter on oceanic islands, driving selection for similar floral morphology among closely related species of Pacific Cyrtandra. Phylogenetic signal was also detected in leaf size, which contributed to niche clustering at both spatial scales. Coupled with a propensity for long-distance dispersal, and the restricted distribution of Cyrtandra to rainforest understories, this finding suggests that environmental filtering along this trait axis may be more important than dispersal limitation in determining species assemblages. This study supports the theory that plant species are not randomly assembled, and instead, that niche-based processes structure biodiversity at regional and local spatial scales in diverse congeneric species assemblages.

Niche breadth of Amazonian trees increases with niche optimum across broad edaphic gradients

Understanding how biotic interactions and environmental filtering mediated by soil properties shape plant community assembly is a major challenge in ecology, especially when studying complex and hyper-diverse ecosystems like tropical forests. To shed light on the influence of both factors, we examined how the edaphic optimum of species (their niche position) relates to their edaphic range (their niche breadth) along different environmental gradients, and how this translates into functional strategies. Here we test four scenarios describing the shape of the niche breadth - niche position relationship, including one neutral scenario and three scenarios proposing different relative influences of abiotic and biotic factors on community assembly along a soil resource gradient. To do so, we used soil concentration data for five key nutrients (N, P, Ca, Mg and K), along with accurate measurements of 14 leaf, stem and root traits for 246 tree species inventoried in 101 plots located across Eastern (French Guiana) and Western (Peru) Amazonia. We found that species niche breadth increased linearly with species niche position along each soil nutrient gradient. This increase was associated with more resource acquisitive traits in the leaves and the roots for soil N, Ca, Mg and K concentration, while it was negatively associated with wood density for soil P concentration. These observations agreed with one of our hypothetical scenarios in which species with resource conservation traits are confined to the most nutrient-depleted soils (abiotic filter), but they are outperformed by faster-growing species on more fertile conditions (biotic filter). Our results refine and strengthen support for niche theories of species assembly, while providing an integrated approach to improve forest management policies.

Darwinian evolution as a dynamical principle

Darwinian evolution (DE)-biology's powerful process of adaptation-is remarkably different from other known dynamical processes. It is antithermodynamic, driving away from equilibrium; it has persisted for 3.5 billion years; and its target, fitness, can seem like "Just So" stories. For insights, we make a computational model. In the Darwinian Evolution Machine (DEM) model, resource-driven duplication and competition operate inside a cycle of search/compete/choose. We find the following: 1) DE requires multiorganism coexistence for its long-term persistence and ability to cross fitness valleys. 2) DE is driven by resource dynamics, like booms and busts, not just by mutational change. And, 3) fitness ratcheting requires a mechanistic separation between variation and selection steps, perhaps explaining biology's use of separate polymers, DNA and proteins.

Linking resource- and disturbance-based models to explain tree-grass coexistence in savannas

Savannas cover a significant fraction of the Earth's land surface. In these ecosystems, C₃ trees and C₄ grasses coexist persistently, but the mechanisms explaining coexistence remain subject to debate. Different quantitative models have been proposed to explain coexistence, but these models make widely contrasting assumptions about which mechanisms are responsible for savanna persistence. Here, we show that no single existing model fully captures all key elements required to explain tree-grass coexistence across savanna rainfall gradients, but many models make important contributions. We show that recent empirical work allows us to combine many existing elements with new ideas to arrive at a synthesis that combines elements of two dominant frameworks: Walter's two-layer model and demographic bottlenecks. We propose that functional rooting separation is necessary for coexistence and is the crux of the coexistence problem. It is both well-supported empirically and necessary for tree persistence, given the comprehensive grass superiority for soil moisture acquisition. We argue that eventual tree dominance through shading is precluded by ecohydrological constraints in dry savannas and by fire and herbivores in wet savannas. Strong asymmetric grass-tree competition for soil moisture limits tree growth, exposing trees to persistent demographic bottlenecks.

Phenotypic characterization and genome analysis reveal the probiotic potential of a banyan endophyte Bacillus velezensis K1

AIM

The current study aimed to scrutinize the probiotic traits and safety aspects of Bacillus velezensis K1 through experimental and supporting genome studies.

METHODS AND RESULTS

The seven cultures previously isolated from the aerial roots of Ficus benghalensis were initially screened for their antibacterial activity as well as acid and bile tolerance. The isolate K1 was found to be the most potent and was further investigated for probiotic traits and safety. K1 showed tolerance to simulated digestive juices and 0.3% bile. It showed notable aggregation, cell surface hydrophobicity, and adherence to HT-29 cells. K1 significantly prevented the adhesion of E. coli O157: H7 and S. enterica ATCC 13076 to HT-29 in cell culture assays. K1 could hydrolyze phytate and complex polysaccharides. The genes related to stress tolerance, adhesion, antimicrobial activity, and production of vitamins, viz. thiamine, riboflavin, pyridoxine, pantothenic acid, folate, and biotin were annotated in the K1 genome. K1 was found to be non-hemolytic, noncytotoxic, as well as susceptible to antibiotics. No virulence or toxin-encoding genes were identified in its genome.

CONCLUSIONS

B. velezensis K1 is a prospective probiotic with the ability to tolerate gastrointestinal stress, adhere to intestinal surfaces, and inhibit enteropathogens.

Research Note: A mixture of Bacteroides spp. and other probiotic intestinal anaerobes reduces colonization by pathogenic E. coli strain O78:H4-ST117 in newly hatched chickens

An experimental group of one-day-old chicken from a commercial hatchery was given a defined mixture of 7 gut anaerobes. The next day the chicks were inoculated by an APEC strain O78:H4-ST117 resistant to ciprofloxacin, alongside with the control group and monitored for 4 wk after the inoculation for the presence of the colonizing strains and ciprofloxacin-resistant E. coli. Significant reduction of colonization rates in the first 2 wk was recorded in the experimental group for the numbers of ciprofloxacin-resistant E. coli. The results show that colonization of chicken by defined anaerobic mixtures may provide a decisive protection during the critical period of the chicken intestinal microflora development.

Genetic and phenotypic assessment of the antimicrobial activity of three potential probiotic lactobacilli against human enteropathogenic bacteria

Introduction

Lactobacilli are avid producers of antimicrobial compounds responsible for their adaptation and survival in microbe-rich matrices. The bactericidal or bacteriostatic ability of lactic acid bacteria (LAB) can be exploited for the identification of novel antimicrobial compounds to be incorporated in functional foodstuffs or pharmaceutical supplements. In this study, the antimicrobial and antibiofilm properties of Lactiplantibacillus pentosus L33, Lactiplantibacillus plantarum L125 and Lacticaseibacillus paracasei SP5, previously isolated form fermented products, were examined, against clinical isolates of Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Enteritidis and Escherichia coli.

Methods

The ability of viable cells to inhibit pathogen colonization on HT-29 cell monolayers, as well as their co-aggregation capacity, were examined utilizing the competitive exclusion assay. The antimicrobial activity of cell-free culture supernatants (CFCS) was determined against planktonic cells and biofilms, using microbiological assays, confocal microscopy, and gene expression analysis of biofilm formation-related genes. Furthermore, in vitro analysis was supplemented with in silico prediction of bacteriocin clusters and of other loci involved in antimicrobial activity.

Results

The three lactobacilli were able to limit the viability of planktonic cells of S. aureus and E. coli in suspension. Greater inhibition of biofilm formation was recorded after co-incubation of S. enterica with the CFCS of Lc. paracasei SP5. Predictions based on sequence revealed the ability of strains to produce single or two-peptide Class II bacteriocins, presenting sequence and structural conservation with functional bacteriocins.

Discussion

The efficiency of the potentially probiotic bacteria to elicit antimicrobial effects presented a strain- and pathogen-specific pattern. Future studies, utilizing multi-omic approaches, will focus on the structural and functional characterization of molecules involved in the recorded phenotypes.

Parapatric speciation of Meiothermus in serpentinite-hosted aquifers in Oman

The factors that control the distribution and evolution of microbial life in subsurface environments remain enigmatic due to challenges associated with sampling fluids from discrete depth intervals via boreholes while avoiding mixing of fluids. Here, using an inflatable packer system, fracture waters were isolated and collected from three discrete depth intervals spanning >130 m in a borehole intersecting an ultramafic rock formation undergoing serpentinization in the Samail Ophiolite, Sultanate of Oman. Near surface aquifer waters were moderately reducing and had alkaline pH while deeper aquifer waters were reduced and had hyperalkaline pH, indicating extensive influence by serpentinization. Metagenomic sequencing and analysis of DNA from filtered biomass collected from discrete depth intervals revealed an abundance of aerobes in near surface waters and a greater proportion of anaerobes at depth. Yet the abundance of the putatively obligate aerobe, Meiothermus, increased with depth, providing an opportunity to evaluate the influence of chemical and spatial variation on its distribution and speciation. Two clades of Meiothermus metagenome assembled genomes (MAGs) were identified that correspond to surface and deep populations termed Types I (S) and II (D), respectively; both clades comprised an apparently Oman-specific lineage indicating a common ancestor. Type II (D) clade MAGs encoded fewer genes and were undergoing slower genome replication as inferred from read mapping. Further, single nucleotide variants (SNVs) and mobile genetic elements identified among MAGs revealed detectable, albeit limited, evidence for gene flow/recombination between spatially segregated Type I (S) and Type II (D) populations. Together, these observations indicate that chemical variation generated by serpentinization, combined with physical barriers that reduce/limit dispersal and gene flow, allowed for the parapatric speciation of Meiothermus in the Samail Ophiolite or a geologic precursor. Further, Meiothermus genomic data suggest that deep and shallow aquifer fluids in the Samail Ophiolite may mix over shorter time scales than has been previously estimated from geochemical data.

Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River

Ciliates are a group of phagotrophic protists found in a wide variety of ecosystems. This study builds on recent studies of ciliates in the Krka river and investigates changes in the phylogenetic and functional diversity of ciliates in biofilm to predict the phylogenetic and functional structure of ciliates in other karstic rivers. Biofilm samples were collected from four representative locations: upstream (Krka spring), midstream (Marasovine), and downstream (Roški slap, Skradinski buk) of the Krka river to test for differences in phylogenetic and functional diversity of ciliates in relation to location and positioning on tufa stones (light/dark-exposed side of tufa stone). Our results showed that Krka spring had higher phylogenetic species variability, lower phylogenetic diversity, and lower functional richness than Skradinski buk, suggesting phylogenetic overdispersal at Krka spring. This could be due to environmental filtering, competitive exclusion, or a combination of these factors. As the first study of its kind in the Mediterranean, our results shed light on the phylogenetic and functional diversity of ciliates in karst ecosystems and provide a basis for future ecological and conservation efforts.

Towards Understanding the Function of Aegerolysins

Aegerolysins are remarkable proteins. They are distributed over the tree of life, being relatively widespread in bacteria and fungi, but also present in some insects, plants, protozoa, and viruses. Despite their abundance in cells of certain developmental stages and their presence in secretomes, only a few aegerolysins have been studied in detail. Their function, in particular, is intriguing. Here, we summarize previously published findings on the distribution, molecular interactions, and function of these versatile aegerolysins. They have very diverse protein sequences but a common fold. The machine learning approach of the AlphaFold2 algorithm, which incorporates physical and biological knowledge of protein structures and multisequence alignments, provides us new insights into the aegerolysins and their pore-forming partners, complemented by additional genomic support. We hypothesize that aegerolysins are involved in the mechanisms of competitive exclusion in the niche.

An integrated belowground trait-based understanding of nitrogen-driven plant diversity loss

Belowground plant traits play important roles in plant diversity loss driven by atmospheric nitrogen (N) deposition. However, the way N enrichment shapes plant microhabitats by patterning belowground traits and finally determines aboveground responses is poorly understood. Here, we investigated the rhizosheath trait of 74 plant species in seven N-addition simulation experiments across multiple grassland ecosystems in China. We found that rhizosheath formation differed among plant functional groups and contributed to changes in plant community composition induced by N enrichment. Compared with forb species, grass and sedge species exhibited distinct rhizosheaths; moreover, grasses and sedges expanded their rhizosheaths with increasing N-addition rate which allowed them to colonize belowground habitats. Grasses also shaped a different microenvironment around their roots compared with forbs by affecting the physicochemical, biological, and stress-avoiding properties of their rhizosphere soil. Rhizosheaths act as a "biofilm-like shield" by the accumulation of protective compounds, carboxylic anions and polysaccharides, determined by both plants and microorganisms. This enhanced the tolerance of grasses and sedges to stresses induced by N enrichment. Conversely, forbs lacked the protective rhizosheaths which renders their roots sensitive to stresses induced by N enrichment, thus contributing to their disappearance under N-enriched conditions. This study uncovers the processes by which belowground facilitation and trait matching affect aboveground responses under conditions of N enrichment, which advances our mechanistic understanding of the contribution of competitive exclusion and environmental tolerance to plant diversity loss caused by N deposition.

Type VI secretion systems of pathogenic and commensal bacteria mediate niche occupancy in the gut

The type VI secretion system (T6SS) is a contractile nanomachine widely distributed among pathogenic and commensal Gram-negative bacteria. The T6SS is used for inter-bacterial competition to directly kill competing species; however, its importance during bacterial infection in vivo remains poorly understood. We report that the murine pathogen Citrobacter rodentium, used as a model for human pathogenic Escherichia coli, harbors two functional T6SSs. C. rodentium employs its T6SS-1 to colonize the murine gastrointestinal tract by targeting commensal Enterobacteriaceae. We identify VgrG1 as a C. rodentium T6SS antibacterial effector, which exhibits toxicity in E. coli. Conversely, commensal prey species E. coli Mt1B1 employs two T6SSs of its own to counter C. rodentium colonization. Collectively, these data demonstrate that the T6SS is a potent weapon during bacterial competition and is used by both invading pathogens and resident microbiota to fight for a niche in the hostile gut environment.