Bacterial Resuscitation from Starvation-Induced Dormancy Results in Phenotypic Diversity Coupled with Translational Activity Depending on Carbon Substrate Availability.

Dormancy is a survival strategy of stressed bacteria inhabiting a various environment. Frequent dormant-active transitions owing to environmental changes play an important role in functional redundancy. However, a proper understanding of the phenotypic changes in bacteria during these transitions remains to be clarified. In this study, orthogonal approaches, such as electron microscopy, flow cytometry, and Raman spectroscopy, which can evaluate phenotypic heterogeneity at the single-cell level, were used to observe morphological and molecular phenotypic changes in resuscitated cells, and RNA sequencing (RNASeq) was used to determine the genetic characteristics associated with phenotypes. Within 12 h of the resuscitation process, morphological (cell size and shape) and physiological (growth and viability) characteristics as well as molecular phenotypes (cellular components) were found to be recovered to the extent that they were similar to those in active cells. The recovery rate and detailed phenotypic properties of the resuscitated cells differed significantly depending on the type or concentration of carbon sources. RNASeq analysis revealed that genes related to translation were significantly upregulated under all resuscitation conditions. The simpler the carbon source (e.g., glucose), the higher the expression of genes involved in cellular repair, and the more complex the carbon source (e.g., beef extract), the higher the expression of genes associated with increased energy production associated with cellular aerobic respiration. This study of phenotypic plasticity of resuscitated cells provides fundamental insight into understanding the adaptive fine-tuning of the microbiome in response to environmental changes and the functional redundancy resulting from phenotype heterogeneity.

Prediction of groundwater quality index to assess suitability for drinking purpose using averaged neural network and geospatial analysis.

Groundwater quality management is pivotal for ensuring public health and ecological resilience. However, the conventional water quality indices often face challenges related to parameter selection, geographic coverage, and scalability. The integration of machine learning and spatial analysis represents a promising methodological shift, allowing for high accuracy and adaptive management strategies. The Safe Groundwater Project in Unsupplied Areas (2017-2020) employed a comprehensive Groundwater Quality Index (GQI) to evaluate potable groundwater quality across South Korea, utilizing a large dataset comprising 28 water quality parameters and 3552 wells. This study revealed that over 50 % of the evaluated wells (Total 8326 wells) were inappropriate as sources of drinking water, indicating a pressing need for policy revision. The averaged neural network model achieved a high predictive accuracy of approximately 95 % for GQI grades, outperforming other classification models. The introduction of 2D spatial analysis in conjunction with machine learning algorithms notably increased the predictive accuracy for unevenly distributed groundwater samples. Moreover, this combined approach enabled the intuitive visualization of groundwater vulnerability across various regions, which can inform targeted interventions for effective resource allocation and management. This research represents a methodologically robust, interdisciplinary approach that holds significant implications for a framework for future groundwater quality management and vulnerability assessment.

Continuous operation of fungal wheel reactor based on solid-state fermentation for the removal of pharmaceutical and personal care products.

Wood-rotting fungi and their enzymatic systems represent promising biocatalysts for the removal of pharmaceuticals and personal care products (PPCPs) from wastewater. We designed a fungal wheel reactor (FWR) based on solid-state fermentation (SSF) of Trametes versicolor and a lignocellulosic substrate, which was used as an immobilization carrier for fungal biomass and the sole initial nutrient source for producing fungal oxidative enzymes. Three pharmaceutical and personal care products, acetaminophen, bisphenol A and carbamazepine, were spiked into the synthetic wastewater and the treatment was carried out under non-sterile conditions. Acetaminophen was completely removed from the FWR until laccase was observed. The acetaminophen removal efficiency was retrieved by replacing the fungal wheel with fresh SSF products. Bisphenol A and carbamazepine were removed via enzymatic activity and adsorption. When the fungal wheel was replaced, acetaminophen began to be completely removed, even after laccase depletion. The microbial community analysis indicated that the continuous removal of acetaminophen was mainly due to the high proportion of T. versicolor. The relative abundance of the co-occurring microbial community might be responsible for the divergence in acetaminophen removal between two of fungal wheel-replaced reactors. Overall, FWRs are promising tools for the removal of PPCPs by highly reactive enzymatic mechanisms as well as adsorption on the carrier surface. By replacing SSF and settled microbial communities, FWRs may continuously contribute to bioremediation over a long-term period.

Polarization- and Electrode-Optimized Polyvinylidene Fluoride Films for Harsh Environmental Piezoelectric Nanogenerator Applications.

While piezoelectric nanogenerators have demonstrated the effective conversion of tiny mechanical vibrations to electricity, their performances are rarely examined under harsh environmental conditions. Here, a multilayered polyvinylidene fluoride (PVDF) film-based piezoelectric nanogenerator (ML-PENG) is demonstrated to generate considerable and stable power outputs even at extremely low temperatures and pressures, and under strong UV. Up-/down-polarized PVDF films are alternately stacked, and Ag electrodes are intercalated between the two adjacent films. At -266 °C and 10-5  Torr, the ML-PENG generates an open-circuit voltage of 1.1 V, a short-circuit current density of 8 nA cm-2 , and a power density of 4.4 nW cm-2 . The piezoelectric outputs are quite stable against prolonged illumination of UV, large temperature- and pressure-variations, and excessive mechanical vibrations. The piezoelectric power density is greatly enhanced above the freezing and glass transition temperatures of PVDF and recorded to be 10, 105, and 282 nW cm-2 at -73, 0, and 77 °C, respectively. The ML-PENG generates sufficient power to operate five light-emitting diodes by harvesting biomechanical energy under simulated Martian conditions. This work suggests that polarization- and electrode-optimized ML-PENG can serve as a reliable and economic power source in harsh and inaccessible environments like polar areas of Earth and extraterrestrial Mars.

Role of Algal Community Stability in Harmful Algal Blooms in River-Connected Lakes.

Harmful algal blooms (HABs) in freshwater produce toxins that pose a threat to public health and aquatic ecosystems. Although algal communities have been studied globally to understand the characteristics of HABs, the occurrence of toxic cyanobacteria in freshwater ecosystems is rarely understood. Unlike abiotic factors, the effects of biotic factors (e.g., interaction, dominance, and variability) on the occurrence of toxic cyanobacteria were overlooked due to the intricate interaction of microorganisms under different environmental conditions. To address this problem, a comprehensive ecological concept stability, which encompasses variations in species or communities due to changing biological interactions or environmental fluctuations, was applied in this study. The algal communities in six river-connected lakes in the North Han River, South Korea, were classified into high and low stability groups. The algal species belonging to diatoms and green algae groups played a major role in the interaction within the algal community in highly stable lakes, but the frequency of Microcystis led the interaction within the algal community at the center of the network in low-stability lakes. These results indicate that the interaction within the cluster is easily changed by Microcystis, where the abundance explosively increases in lakes with low algal community stability. Water quality is more strongly associated with the occurrence of toxic cyanobacteria (Microcystis and Dolichospermum). In low-stability lakes, more diverse water quality indicators are correlated with the development of toxic algae than in high-stability lakes. This paper is the first report on the importance of algal community stability in freshwater in the occurrence of toxic cyanobacteria and offers a new perspective on Microcystis monitoring and management.

Short-Term Legacy Effects of Mercury Contamination on Plant Growth and nifH-Harboring Microbial Community in Rice Paddy Soil.

Methylmercury (MeHg), which is formed in rice paddy soil, exhibits strong neurotoxicity through bioaccumulation in the food chain. A few groups of microorganisms drive both mercury methylation and nitrogen fixation in the rhizosphere. Little is known about how the shifted soil microbial community by Hg contamination affects nitrogen fixation rate and plant growth in paddy soil. Here, we examined how stimulated short-term Hg amendment affects the nitrogen fixing microbial community and influences plant-microbe interactions. Soil was treated with low (0.2 mg/kg) and high (1.1 mg/kg) concentrations of Hg for 4 weeks; then, rice (Oryza sativa) was planted and grown for 12 weeks. The nitrogen-fixation rate and rice growth were measured. The diversity and structure of the microbial community were analyzed by sequencing the nifH gene before and after rice cultivation. Hg treatments significantly decreased the nitrogen fixation rate and dry weight of the rice plants. The structure of the nifH-harboring community was remarkably changed after rice cultivation depending on Hg treatments. Iron- or sulfate-reducing bacteria, including Desulfobacca, Desulfoporosimus, and Geobacter, were observed as legacy response groups; their abundances increased in the soil after Hg treatment. The high abundance of those groups were maintained in control, but the abundance drastically decreased after rice cultivation in the soil treated with Hg, indicating that symbiotic behavior of rice plants changes according to the legacy effects on Hg contamination. These results suggested that Hg contamination can persist in soil microbial communities, affecting their nitrogen-fixation ability and symbiosis with rice plants in paddy soil.

Removal of pharmaceuticals and personal care products using native fungal enzymes extracted during the ligninolytic process.

Significant concentrations of pharmaceuticals and personal care products (PPCPs) have been detected in aquatic environment. Fungal enzymatic processes can oxidize these persistent PPCPs; thus, these processes have attracted considerable attention from the scientific community. Here, we evaluated the efficacy of the removal of PPCPs using native fungal enzymes derived from Bjerkandera spp. TBB-03 under various conditions. Among the eight lignocellulosic substrates, ash, which showed the highest laccase production, was selected as the sole enzyme inducer. TBB-03 laccase was found to exhibit remarkable stability under varied pH and temperature conditions. Acetaminophen and bisphenol A were effectively removed by TBB-03 laccase under various conditions, except at pH 8. Although TBB-03 laccase could not efficiently remove single-state sulfamethoxazole directly, a 22% of improvement in sulfamethoxazole removal was observed in the presence of acetaminophen. Overall, our proposed approach showed that Bjerkandera adusta TBB-03 can be potentially applied for further research regarding PPCP remediation.

Bacillus-Dominant Airborne Bacterial Communities Identified During Asian Dust Events.

Asian dust (AD) events have received significant attention due to their adverse effects on ecosystems and human health. However, detailed information about airborne pathogens associated with AD events is limited. This study monitored airborne bacterial communities and identified AD-specific bacteria and the potential hazards associated with these bacteria during AD events. Over a 33-month period, 40 air samples were collected under normal atmospheric conditions (non-AD events; n = 34) and during AD events (n = 6). The airborne bacterial communities in the air samples collected during non-AD events (non-AD sample) and AD events (AD sample) were evaluated using both culture-dependent and culture-independent methods. The bacterial diversity increased significantly, along with the 16S rRNA gene copy number, in AD samples (p < 0.05) and was positively correlated with PM10 concentration. High throughput sequencing of the 16S rRNA gene revealed that the relative abundance of the phylum Firmicutes increased substantially in AD samples (44.3 ± 5.0%) compared with non-AD samples (27.8 ± 4.3%). Within the phylum Firmicutes, AD samples included a greater abundance of Bacillus species (almost 23.8%) than non-AD samples (almost 13.3%). Both culture-dependent and culture-independent methods detected common predominant species closely related to Bacillus cereus during AD events. Subsequent multilocus sequence typing (MLST) and enterotoxin gene assays confirmed the presence of virulence factors in B. cereus isolates from AD samples. Furthermore, the abundance of bceT, encoding enterotoxin in B. cereus, was significantly higher in AD samples (p < 0.05). The systematic characterization of airborne bacterial communities in AD samples in this study suggests that B. cereus pose risks to public health.

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells.

Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.

A comparison study of the potential risks induced in arable land and forest soils by carcass-derived pollutants.

Improper decisions concerning animal carcass disposal sites pose grave threats to environmental biosecurity. However, only a few studies have focused on the effects of different land-use types on the composition of carcass-derived pollutants and microbial responses to the disturbances. This study was conducted using soil microcosms with minced pork built from arable land and forest soils for 5 weeks. To compare the risk induced from different land-use types by carcass burial, the soil properties, the microbial community, and multiple-antibiotic-resistant bacteria were evaluated for microcosm containing 0, 1.5 and 7.5 g of minced pork. The abiotic properties, including pH, organic carbon, nitrogen and phosphorus compounds, significantly increased, regardless of the land-use types and applied load masses. The microbial diversity indices of the forest soil were reduced, whereas those of the arable land remained relatively stable. The disturbances produced from carcass-derived pollutants altered the bacterial community structures differently for the different land-use types. The treatment increased multiple-antibiotic-resistant bacteria in the both soil samples, although the increase in the forest soil was significantly less compared to the arable land soils.

Molecular approaches for the detection and monitoring of microbial communities in bioaerosols: A review.

Bioaerosols significantly affect atmospheric processes while they undergo long-range vertical and horizontal transport and influence atmospheric chemistry and physics and climate change. Accumulating evidence suggests that exposure to bioaerosols may cause adverse health effects, including severe disease. Studies of bioaerosols have primarily focused on their chemical composition and largely neglected their biological composition and the negative effects of biological composition on ecosystems and human health. Here, current molecular methods for the identification, quantification, and distribution of bioaerosol agents are reviewed. Modern developments in environmental microbiology technology would be favorable in elucidation of microbial temporal and spatial distribution in the atmosphere at high resolution. In addition, these provide additional supports for growing evidence that microbial diversity or composition in the bioaerosol is an indispensable environmental aspect linking with public health.

The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability.

The number of functional traits of a wastewater treatment plant (WWTP) microbial community (i.e. functional richness) is thought to be an important determinant of its overall functional performance, but the ecological factors that determine functional richness remain unclear. The number of taxa within a community (i.e. taxonomic richness) is one ecological factor that might be important. Communities that contain more taxa are more likely to have more functional traits, and a positive association is therefore expected between functional and taxonomic richness. Empirical tests for this positive association among WWTP communities, however, are lacking. We address this knowledge gap by measuring the functional and taxonomic richness of 10 independent WWTP communities. We demonstrate that functional and taxonomic richness are positively associated with each other. We further demonstrate that functional and taxonomic richness are negatively associated with the effluent NH4 -N and BOD5 concentrations. This led us to hypothesize that correlated variation in functional and taxonomic richness is likely related to variation in ambient nitrogen and carbon availability. We finally demonstrate that this hypothesis is consistent with the functional and taxonomic attributes of the WWTP communities. Together, our results improve our basic understanding of the ecology and functioning of WWTP communities.

Association of biodiversity with the rates of micropollutant biotransformations among full-scale wastewater treatment plant communities.

Biodiversities can differ substantially among different wastewater treatment plant (WWTP) communities. Whether differences in biodiversity translate into differences in the provision of particular ecosystem services, however, is under active debate. Theoretical considerations predict that WWTP communities with more biodiversity are more likely to contain strains that have positive effects on the rates of particular ecosystem functions, thus resulting in positive associations between those two variables. However, if WWTP communities were sufficiently biodiverse to nearly saturate the set of possible positive effects, then positive associations would not occur between biodiversity and the rates of particular ecosystem functions. To test these expectations, we measured the taxonomic biodiversity, functional biodiversity, and rates of 10 different micropollutant biotransformations for 10 full-scale WWTP communities. We have demonstrated that biodiversity is positively associated with the rates of specific, but not all, micropollutant biotransformations. Thus, one cannot assume whether or how biodiversity will associate with the rate of any particular micropollutant biotransformation. We have further demonstrated that the strongest positive association is between biodiversity and the collective rate of multiple micropollutant biotransformations. Thus, more biodiversity is likely required to maximize the collective rates of multiple micropollutant biotransformations than is required to maximize the rate of any individual micropollutant biotransformation. We finally provide evidence that the positive associations are stronger for rare micropollutant biotransformations than for common micropollutant biotransformations. Together, our results are consistent with the hypothesis that differences in biodiversity can indeed translate into differences in the provision of particular ecosystem services by full-scale WWTP communities.

Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review.

Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.

Determinants of microbial colonization on microplastics through wastewater treatment processes: The role of polymer type and sequential treatment.

This study examines the microbial colonization characteristics of microplastics (MPs) in wastewater treatment plants (WWTPs), focusing on polymer types (High-Density Polyethylene (HDPE) and Polyethylene Terephthalate (PET)) and various stages of wastewater treatments. Through individual and sequential deployment approaches, the research aimed to identify the determinants of bacterial colonization on MPs, whether they were introduced at each stage of treatment individually or in sequence from primary to tertiary stages. The study revealed that the stage of wastewater treatment profoundly influenced bacterial colonization on the polymer types MPs, with bacterial attachment being largely niche-specific. HDPE showed increased sensitivity to wastewater composition, leading to selective biofilm formation. For instance, in HDPE, Firmicutes accounted for 25.1 ± 0.04 % during primary treatment, while Alphaproteobacteria increased significantly in the tertiary treatment to 19.8 ± 0.1 %. Conversely, PET exhibited a stochastic pattern of bacterial colonization due to differences in surface hydrophilicity. Additionally, in sequential deployments, a notable shift towards stochastic bacterial attachment on MPs, particularly with HDPE was observed. The Shannon diversity values for MP biofilms were consistently higher than those for wastewater across all stages, with PET showing an increase in diversity in sequential deployments (Shannon diversity: 5.01 ± 0.03 for tertiary stage). These findings highlight the critical role of MPs as carriers of diverse bacteria, emphasizing the necessity for strategies to mitigate their impact in WWTPs. This study presents a significant advancement in our understanding of the interactions between MPs and microbial populations in WWTP environments.

Environmental consequences of transformation products from an antibiotic mixture and their mitigation in a wastewater microbiome using an HCl-modified adsorbent.

This study enhanced our understanding of antibiotic mixtures' occurrence, transformation, toxicity, and ecological risks. The role of acid-modified biochar (BC) in treating antibiotic residues was explored, shedding light on how BC influences the fate, mobility, and environmental impact of antibiotics and transformation products (TPs) in an activated sludge (AS) microbiome. A mixture of oxytetracycline and sulfamethoxazole was found to synergistically (or additively) inhibit cell growth of AS and disrupt the microbiome structure, species richness/diversity, and function. The formation of TPs with potentially higher toxicity and persistence than the original compounds was identified, explaining the microbiome disruption. Agricultural waste-derived BC was optimized for contaminant adsorption, leading to a reduction in toxicity when added to AS by sequestering TPs on its surface. This work highlighted adsorbents as a practical engineering strategy for mitigating liquid-phase contaminants' toxicological consequences, proactively controlling the fate and effects of antibiotics and TPs.

The impact of bioaerosol trajectories on microbial community assembly and physicochemical dynamics in the atmosphere.

This study explored the assembly mechanisms and physicochemical dynamics of microbial communities within atmospheric bioaerosols, focusing on the influence of different aerial trajectories. Over two years, samples near Seoul were classified into 'North', 'Southwest', and 'Others' categories based on their aerial trajectories. Physicochemical analysis of the PM2.5 particles revealed distinct ion compositions for each cluster, reflecting diverse environmental influences. Microbial community analysis revealed that shared dominant bacterial phyla were present in all clusters. However, distinct taxonomic profiles and biomarkers were also evident, such as coastal bacteria in the 'Southwest' cluster correlating with wind speed, and arid soil-originated bacteria in the 'North' cluster correlating with cations. These findings demonstrate that biomarkers in each cluster are representative of the distinct environments associated with their aerial trajectories. Notably, cluster 'Southwest' the highest microbial diversity and a strong alignment with the neutral community model, suggesting a large influence of passive dispersal from marine environments. Contrarily, 'North' and 'Others' were more influenced by niche-dependent factors. This study highlights the complex interplay between environmental factors and microbial dynamics in bioaerosols and provides important insights for environmental monitoring and public health risk assessment.

Assessing long-term ecological impacts of PCE contamination in groundwater using a flow cytometric fingerprint approach.

This study aims to develop and validate a comprehensive method for assessing ecological disturbances in groundwater ecosystems caused by tetrachloroethylene (PCE) contamination, utilizing flow cytometry (FCM) fingerprint approach. We hypothesized that the ecological disturbance resulting from PCE contamination would exhibit 'press disturbance', persisting over extended periods, and inducing notable phenotypic differences in the microbial community compared to undisturbed groundwater. We collected 40 groundwater samples from industrial district with a history of over twenty years of PCE contamination, along with 56 control groundwater from the national surveillance groundwater system. FCM revealed significant alterations in the phenotypic diversity of microbial communities in PCE-contaminated groundwater, particularly during the dry season. The presence of specific dechlorinating bacteria (Dehalococcoides, Dehalogenimonas, and Geobacter) and their syntrophic partners was identified as an indicator of contamination. Phenotypic diversity measures provided clearer and more direct reflections of contamination impact compared to taxonomic diversity measures. This study establishes FCM fingerprinting as a simple, robust, and accurate method for evaluating ecological disturbances, with potential applications in early warning systems and continuous monitoring of groundwater contamination. The findings not only underscore the sensitivity of FCM in detecting phenotypic variations induced by environmental stressors but also highlight its utility in understanding the complex dynamics of microbial communities in contaminated groundwater ecosystems.

Case report: Intrathecal baclofen therapy improved gait pattern in a stroke patient with spastic dystonia.

Background: Intrathecal baclofen (ITB) therapy, a viable alternative for unsuitable candidates of conventional spasticity medications, is a preferred method of administration over the oral route. Owing to its enhanced bioavailability, ITB ensures a more effective delivery at the target site. Objective: There is a lack of conclusive evidence regarding the use of ITB treatment in managing ambulatory patients with spastic dystonia. Before ITB pump implantation, patients commonly undergo an ITB bolus injection trial to rule out potential adverse reactions and verify the therapeutic effects on hypertonic issues. In this report, we highlight a case of spastic dystonia, particularly focusing on an ambulatory patient who demonstrated significant improvement in both the modified Ashworth scale (MAS) score and gait pattern following the ITB injection trial. Case report: This case report outlines the medical history of a 67-year-old male diagnosed with left-side hemiplegia and spastic dystonia, resulting from his second episode of intracranial hemorrhage in the right thalamus. An ITB injection trial was initiated because the patient was not suitable for continued botulinum toxin injections and oral medications. This was due to the persistent occurrence of spastic dystonia in both the upper and lower extremities. The patient underwent a four-day ITB injection trial with progressively increasing doses, resulting in improved MAS scores and gait parameters, including cadence, step length, step time, stride length, and stride time were increased. Particularly, kinematic gait analysis demonstrates a substantial improvement of increased knee flexion in the swing phase in stiff knee gait pattern. These findings indicated a gradual reduction in spasticity-related symptoms, signifying the positive effect of the ITB injection trial. The patient eventually received an ITB pump implantation. Conclusion: In this post-stroke patient with spastic dystonia, ITB therapy has demonstrated effective and substantial management of spasticity, along with improvement in gait patterns.

A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory.

The complex interplay between an animal and its surrounding environment requires constant attentive observation in natural settings. Moreover, how ecological interactions are affected by an animal's genes is difficult to ascertain outside the laboratory. Genetic studies with the bacterivorous nematode Caenorhabditis elegans have elucidated numerous relationships between genes and functions, such as physiology, behaviors, and lifespan. However, these studies use standard laboratory culture that does not reflect C. elegans true ecology. C. elegans is found growing in nature and reproduced in large numbers in soils enriched with rotting fruit or vegetation, a source of abundant and diverse microbes that nourish the thriving populations of nematodes. We developed a simple mesocosm we call soil-fruit-natural-habitat that simulates the natural ecology of C. elegans in the laboratory. Apples were placed on autoclaved potted soils, and after a soil microbial solution was added, the mesocosm was subjected to day-night, temperature, and humidity cycling inside a growth chamber. After a period of apple-rotting, C elegans were added, and the growing worm population was observed. We determined optimal conditions for the growth of C. elegans and then performed an ecological succession experiment observing worm populations every few days. Our data showed that the mesocosm allows abundant growth and reproduction of C. elegans that resembles populations of the nematode found in rotting fruit in nature. Overall, our study presents a simple protocol that allows the cultivation of C. elegans in a natural habitat in the laboratory for a broad group of scientists to study various aspects of animal and microbial ecology.