Biology subjects

Calixto, A.

Publications and source records attributed to Calixto, A..

6 recordsLinked to original sources

bioRxiv2026

High temperature-induced diapause transiently primes progeny for dauer formation in C. elegans.

Environmental stress during early development can have lasting effects on reproduction and developmental plasticity in Caenorhabditis elegans. Here, we compared the consequences of two dauer-inducing stressors, high temperature and crowding, on fertility, dauer formation, and intergenerational gene expression. Entry into the dauer stage protected animals from stress-induced sterility, with high-temperatureinduced diapause (HID) providing strong preservation of reproductive capacity. Remarkably, the progeny of temperature-induced post-dauers (PD-temp) displayed a twofold increase in dauer formation upon re-exposure to heat, revealing a transient intergenerational enhancement of HID. This effect was stimulus-specific, as parental heat exposure suppressed pheromone-induced dauer formation in progeny, while parental pheromone exposure did not enhance HID. This increased dauer propensity was reset after a single stress-free generation. RNA-seq across three generations identified a transient F1-specific gene expression signature associated with enhanced dauer formation upon re-exposure to heat. Functional analyses showed that snpc-1.3, F49F1.7, and Y69A2AR.12 promote HID. In parallel, vit-3 expression was selectively reduced in F1 progeny of PD-temp animals, and vit-3 mutants exhibited increased dauer formation at 27{degrees}C, suggesting that vit-3 normally restrains HID. Consistent with previous work from our group implicating RNAi pathways in environmentally induced diapause and inherited stress responses, we find that endogenous RNAi pathways also modulate HID across generations. Multiple RNAi pathway components contributed to HID, while the nuclear RNAi factor nrde-2 was specifically required for the intergenerational increase in dauer formation. Tissue-specific rescue experiments further suggest that coordinated RNAi activity across tissues contributes differently to parental HID and progeny responses. Together, these findings identify HID as a distinct stress-induced developmental program that transiently modifies progeny responses to recurring thermal stress while preserving reproductive fitness. Our results further indicate that the physiological and intergenerational consequences of dauer entry depend on the environmental cue that induces diapause.

genetics↗

bioRxiv2024

Interspecies relationships of wild amoebae and bacteria with C. elegans create environments propitious for multigenerational diapause.

The molecular and physical communication within the microworld supports the entire web of life as we know it. How organisms such as bacteria, amoeba and nematodes -all superabundant-interact to sustain their niche, however, is not known, especially how their associations generate and affect behavior of animals in fluctuating environments. To have a frame to study interactions between microbe and animal, we collected soil from a temperate semi-arid climate and isolated the culturable genus of bacteria Comamonas, Stenotrophomonas, Chryseobacterium and Rhodococcus and the amoeba Tetramitus. This ensemble was then fed in long-term experiments to the nematode C. elegans to study developmental rate, diapause entry, fertility, feeding behavior and neuronal integrity. We observed that the ensemble is long lasting and induces animals to diapause after a few generations under conditions that are not canonically pathogenic. We called this phenomenon Dauer Formation in Natural Ensembles (DaFNE). DaFNE requires the communication between live bacteria and the nematode intestine, suggesting the existence of a bidirectional interaction in the holobiont. While all bacteria from the ensemble colonize the intestine of the nematodes, Comamonas is the most represented and Rhodococcus the scarcest. The amoeba Tetramitus can be ingested by C. elegans, but it is not part of its microbiota. DaFNE depends on pheromone and nematode quorum, but high temperature in the homeostatic range, triggers diapause with fewer numbers. DaFNE increases as generations pass and is also remembered transgenerationally. The RNA interference (RNAi) pathway is needed for initiation of DaFNE, indicating the communication via RNA is crucial to execute bacterially induced behaviors in natural environments. SignificanceMicrobes have an overwhelming influence over the animals they live with, modulating development and decision making. Microscopic nematodes are the most abundant multicellular animals in the biosphere, suggesting they possess well-rehearsed successful relationships with their associated microbiota. Little is known about the modulation of nematode behavior in complex ecosystems with multiple organisms interacting. We use bacteria and amoeba from a natural ecosystem and introduce the pioneer nematode C. elegans to study behavioral parameters in long lasting experiments. The most striking response of nematodes to this natural environment is the commitment to diapause of a significant portion of the population. We call this form of hibernation Dauer Formation in Natural Ensembles or DaFNE. We propose that animals in nature may hibernate frequently, as a result of the communication with their natural biota. We find that DaFNE requires pheromone production in nematodes and also the RNA interference pathway, suggesting the RNA repertoire of both entities may be at play. Higher temperatures in the optimal range for nematode growth, require much less nematode quorum for DaFNE, indicating that a non-noxious increase in temperature favors diapause in natural environments. Nematodes respond to each bacterium in different ways when grown in monocultures and in the ensemble. This suggests that the abundance of specific species in nature may shift behavioral preferences and outputs in microscopic animals. We also show that the amoeba Tetramitus can be ingested by worms, demonstrating that C. elegans is a broader microbivore. Like worms, amoebae display specific responses to bacteria and add variability to behaviors elicited by nematodes. Finally, bacteria in the ensemble unlike in monocultures, are not exhausted during the length of the experiments even in the presence of bacterivore nematodes and amoebae.

microbiology↗

bioRxiv2022

The assembly of wild natural isolates define neuronal integrity and life history traits of co-inhabiting C. elegans.

Bacterivore nematodes are the most abundant animals in the biosphere, largely contributing to global biogeochemistry. The effect of environmental microbes as source of associated microbiota and natural diet on their life history traits of nematodes is likely to impact the general health of the biosphere. Caenorhabditis elegans is a unique model to study the behavioral and physiological outputs of different available microbial diets. Nonetheless, most studies are on monoaxenic cultures of laboratory bacteria while the effect of natural microbiota isolates has only recently started to be reported. Here, we quantified physiological, phenotypical and behavioral traits of worms feeding on two bacteria that co-isolated with wild nematodes and tested how combinations of these isolates with other bacteria affected the traits measured. These bacteria were identified as a putative novel species of Stenotrophomonas denominated Stenotrophomonas sp. Iso1 and a strain of Bacillus pumilus designated Iso2. The isolates induced distinctive behaviors and development patterns that changed in mixes of the two bacteria and/or the pathogen Salmonella enterica. Focusing on the degeneration rate of the touch circuit of C. elegans we show that B. pumilus alone is protective while the mix with Stenotrophomonas sp. is degenerative. The analysis of the metabolite content of each isolate and their combination identified NAD+ as potentially neuroprotective. In vivo supplementation shows that NAD+ restores neuroprotection to the mixes and also to individual non-protective bacteria. The results highlight the need to study the physiological effects of bacteria resembling native diets in a multicomponent scenario rather than using single isolates. ImportanceThe behavioral decisions of animals depend on their microbiota. In nature it is unknown how this interaction affects the health of the biosphere. To study how the nematode-bacteria relationship impacts the life history traits of these animals, we isolated bacteria found in association with wild nematodes and tested their influence as single species and consortia, in the life history traits of the model C. elegans. We identify metabolites from wild bacteria that change these traits. The bacteria isolated were identified a Stenotrophomonas sp and a B. pumilus. We find that all traits depend on the biota composition. For example, B. pumilus is neuroprotective to degenerating neurons of the touch circuit of C. elegans needed to sense and escape from predators in the wild. The co-culture with Stenotrophomonas sp. eliminates the protection. We identified NAD+ as the metabolite lost in the mix, and show that NAD+ by itself is neuroprotective.

microbiology↗

bioRxiv2021

Bacterial small RNAs and host epigenetic effectors of a transgenerational memory of pathogens in C. elegans.

The inheritance of memories is adaptive for survival. Microbes interact with all organisms challenging their immunity and triggering behavioral adaptations. Some of these behaviors induced by bacteria can be inherited although the mechanisms of action are largely unexplored. In this work, we use C. elegans and its bacteria to study the transgenerational RNA dynamics of an interspecies crosstalk leading to a heritable behavior. Heritable responses to bacterial pathogens in the nematode include avoidance and pathogen-induced diapause (PIDF), a state of suspended animation to evade the pathogen threat. We identify a small RNA RsmY, involved in quorum sensing from P. aeruginosa as required for initiation of PIDF. Histone methyltransferase SET-18/SMYD3 is also needed for PIDF initiation in C. elegans. In contrast, SET-25/EHMT2 is necessary for the maintenance of the memory of pathogen exposure in the transgenerational lineage. This work can be a starting point to understanding microbiome-induced inheritance of acquired traits.

microbiology↗

bioRxiv2020

Intergenerational pathogen-induced diapause in C. elegans is modulated by mir-243.

The interaction and communication between bacteria and their hosts modulate many aspects of animal physiology and behavior. Dauer entry as a response to chronic exposure to pathogenic bacteria in Caenorhabditis elegans is an example of a dramatic survival response. This response is dependent on the RNAi machinery, suggesting the involvement of sRNAs as effectors. Interestingly, dauer formation occurs after two generations of interaction with two unrelated moderately pathogenic bacteria. Therefore, we sought to discover the identity of C. elegans RNAs involved in pathogen-induced diapause. Using transcriptomics and differential expression analysis of coding and long and small non-coding RNAs, we found that mir-243-3p is the only transcript continuously upregulated in animals exposed to both, P. aeruginosa or S. enterica for two generations. Phenotypic analysis of mutants showed that mir-243 is required for dauer formation under pathogenesis but not under starvation. Moreover, DAF-16, a master regulator of defensive responses in the animal and required for dauer formation was found to be necessary for mir-243 expression. This work highlights the role of a small non-coding RNA in the intergenerational defensive response against pathogenic bacteria and inter-kingdom communication. ImportancePersistent infection of the bacterivore nematode C. elegans with bacteria such as P. aeruginosa and S. enterica makes the worm diapause or hibernate. By doing this, the worm closes its mouth avoiding infection. This response takes two generations to be implemented. In this work, we looked for genes expressed upon infection that could mediate the worm diapause triggered by pathogens. We identify mir-243-3p as the only transcript commonly upregulated when animals feed on P. aeruginosa and S. enterica for two consecutive generations. Moreover, we demonstrate that mir-243-3p is required for pathogen-induced dauer formation, a new function that has not been previously described for this miRNA. We also find that the transcriptional activators DAF-16, PQM-1 and CRH-2 are necessary for the expression of mir-243 under pathogenesis. Here we establish a relationship between a small RNA and a developmental change that ensures the survival of a percentage of the progeny.

microbiology↗

bioRxiv2019

Bacterially produced GABA protects neurons from degeneration

Caenorhabditis elegans and its cognate bacterial diet comprise a reliable, widespread model to study diet and microbiota effects on host physiology. Nonetheless, how diet influences the rate at which neurons die remains largely unknown. A number of models have been used in C. elegans as surrogates for neurodegeneration. One of these is a C. elegans strain expressing a neurotoxic allele of the MEC-4(d) DEG/ENaC channel which causes the progressive degeneration of the touch receptor neurons (TRNs). Using such model, this study evaluated the effect of various dietary bacteria on neurodegeneration dynamics. While degeneration of TRNs was steadily carried and completed at adulthood in the strain routinely used for C. elegans maintenance Escherichia coli OP50, it was significantly reduced in environmental and other laboratory bacterial strains. Strikingly, neuroprotection reached more than 40% in the E. coli HT115 strain. HT115 protection was long lasting well into old age of animals and not restricted to the TRNs. Small amounts of HT115 on OP50 bacteria as well as UV-killed HT115 were still sufficient to produce neuroprotection. Early growth of worms in HT115 protected neurons from degeneration during later growth in OP50. HT115 diet promoted the nuclear translocation of the DAF-16/FOXO transcription factor, a phenomenon previously reported to underlie neuroprotection caused by downregulation of the insulin receptor in this system. Moreover, a daf-16 loss of function mutation abolishes HT115-driven neuroprotection. Comparative genomics, transcriptomics and metabolomics approaches pinpointed the neurotransmitter {gamma}-aminobutyric acid (GABA) as a metabolite differentially produced between E. coli HT115 and OP50. HT115 mutant lacking glutamate decarboxylase enzyme genes (gad), which catalyze the conversion of GABA from glutamate, lost the ability to produce GABA and also to stop neurodegeneration. Moreover, in situ GABA supplementation or heterologous expression of glutamate decarboxylase in E. coli OP50 conferred neuroprotective activity to this strain. Specific C. elegans GABA transporters and receptors were required for full HT115-mediated neuroprotection. Together, these results demonstrate that bacterially produced GABA exerts an effect of neuroprotection in the host, highlighting the role of neuroactive compounds of the diet in nervous system homeostasis.

microbiology↗