Bacterial fauna associating with chironomid larvae from lakes of Bengaluru city, India - A 16s rRNA gene based identification

Unveiling the Microbiome Diversity in Telenomus (Hymenoptera: Scelionidae) Parasitoid Wasps

Bacterial symbionts in insects constitute a key factor for the survival of the host due to the benefits they provide. Parasitoid wasps are closely associated with viruses, bacteria, and fungi. However, the primary symbionts and their functions are not yet known. This study was undertaken to determine the gut microbiota of six species of the Telenomus genus: T. alecto (Crawford), T. sulculus Johnson, T. fariai Costa Lima, T. remus Nixon, T. podisi Ashmead, and T. lobatus Johnson & Bin. Wasp parasitoids were collected from their hosts in different locations in Mexico. DNA was extracted from gut collection, and sequencing of bacterial 16S rRNA was carried out in Illumina® MiSeq™. Among the six species of wasps, results showed that the most abundant phylum were Proteobacteria (82.3%), Actinobacteria (8.1%), and Firmicutes (7.8%). The most important genera were Delftia and Enterobacter. Seventeen bacteria species were found to be shared among the six species of wasps. The associate microbiota will help to understand the physiology of Telenomus to promote the use of these wasp parasitoids in the management of insect pests and as potential biomarkers to target new strategies to control pests.

Chironomus riparius Larval Gut Bacteriobiota and Its Potential in Microplastic Degradation

Chironomus riparius are sediment-dwelling invertebrates in freshwater ecosystems and are used as indicators of environmental pollution. Their habitat is threatened by high levels of contaminants such as microplastics and organic matter. A promising strategy for the eco-friendly degradation of pollutants is the use of bacteria and their enzymatic activity. The aim of this study was to characterize for the first time bacteriobiota associated with the gut of C. riparius larvae from nature and laboratory samples, to compare it with sediment and food as potential sources of gut microbiota, and to assess its ability to degrade cellulose, proteins, and three different types of microplastics (polyethylene, polyvinyl chloride, and polyamide). The metabarcoding approach highlighted Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota as most abundant in both gut samples. Culturable microbiota analysis revealed Metabacillus idriensis, Peribacillus simplex, Neobacillus cucumis, Bacillus thuringiensis/toyonensis, and Fictibacillus phosphorivorans as five common species for nature and laboratory samples. Two P. simplex and one P. frigoritolerans isolates showed the ability for intensive growth on polyethylene, polyvinyl chloride, and polyamide. Both cellulolytic and proteolytic activity was observed for Paenibacillus xylanexedens and P. amylolyticus isolates. The characterized strains are promising candidates for the development of environmentally friendly strategies to degrade organic pollution and microplastics in freshwater ecosystems.

Vibrio cholerae Invasion Dynamics of the Chironomid Host Are Strongly Influenced by Aquatic Cell Density and Can Vary by Strain

Cholera has been a human scourge since the early 1800s and remains a global public health challenge, caused by the toxigenic strains of the bacterium Vibrio cholerae. In its aquatic reservoirs, V. cholerae has been shown to live in association with various arthropod hosts, including the chironomids, a diverse insect family commonly found in wet and semiwet habitats. The association between V. cholerae and chironomids may shield the bacterium from environmental stressors and amplify its dissemination. However, the interaction dynamics between V. cholerae and chironomids remain largely unknown.  In this study, we developed freshwater microcosms with chironomid larvae to test the effects of cell density and strain on V. cholerae-chironomid interactions. Our results show that chironomid larvae can be exposed to V. cholerae up to a high inoculation dose (109 cells/mL) without observable detrimental effects. Meanwhile, interstrain variability in host invasion, including prevalence, bacterial load, and effects on host survival, was highly cell density-dependent. Microbiome analysis of the chironomid samples by 16S rRNA gene amplicon sequencing revealed a general effect of V. cholerae exposure on microbiome species evenness. Taken together, our results provide novel insights into V. cholerae invasion dynamics of the chironomid larvae with respect to various doses and strains. The findings suggest that aquatic cell density is a crucial driver of V. cholerae invasion success in chironomid larvae and pave the way for future work examining the effects of a broader dose range and environmental variables (e.g., temperature) on V. cholerae-chironomid interactions. IMPORTANCE Vibrio cholerae is the causative agent of cholera, a significant diarrheal disease affecting millions of people worldwide. Increasing evidence suggests that the environmental facets of the V. cholerae life cycle involve symbiotic associations with aquatic arthropods, which may facilitate its environmental persistence and dissemination. However, the dynamics of interactions between V. cholerae and aquatic arthropods remain unexplored. This study capitalized on using freshwater microcosms with chironomid larvae to investigate the effects of bacterial cell density and strain on V. cholerae-chironomid interactions. Our results suggest that aquatic cell density is the primary determinant of V. cholerae invasion success in chironomid larvae, while interstrain variability in invasion outcomes can be observed under specific cell density conditions. We also determined that V. cholerae exposure generally reduces species evenness of the chironomid-associated microbiome. Collectively, these findings provide novel insights into V. cholerae-arthropod interactions using a newly developed experimental host system.

Characterization of virulence and antimicrobial resistance genes of Aeromonas media strain SD/21-15 from marine sediments in comparison with other Aeromonas spp

Aeromonas media is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen associated with diarrhea in humans and skin ulceration in fish. In this study, we used whole genome sequencing to profile all antimicrobial resistance (AMR) and virulence genes found in A. media strain SD/21-15 isolated from marine sediments in Denmark. To gain a better understanding of virulence and AMR genes found in several A. media strains, we included 24 whole genomes retrieved from the public databanks whose isolates originate from different host species and environmental samples from Asia, Europe, and North America. We also compared the virulence genes of strain SD/21-15 with A. hydrophila, A. veronii, and A. salmonicida reference strains. We detected Msh pili, tap IV pili, and lateral flagella genes responsible for expression of motility and adherence proteins in all isolates. We also found hylA, hylIII, and TSH hemolysin genes in all isolates responsible for virulence in all isolates while the aerA gene was not detected in all A. media isolates but was present in A. hydrophila, A. veronii, and A. salmonicida reference strains. In addition, we detected LuxS and mshA-Q responsible for quorum sensing and biofilm formation as well as the ferric uptake regulator (Fur), heme and siderophore genes responsible for iron acquisition in all A. media isolates. As for the secretory systems, we found all genes that form the T2SS in all isolates while only the vgrG1, vrgG3, hcp, and ats genes that form parts of the T6SS were detected in some isolates. Presence of bla MOX-9 and bla OXA-427 β-lactamases as well as crp and mcr genes in all isolates is suggestive that these genes were intrinsically encoded in the genomes of all A. media isolates. Finally, the presence of various transposases, integrases, recombinases, virulence, and AMR genes in the plasmids examined in this study is suggestive that A. media has the potential to transfer virulence and AMR genes to other bacteria. Overall, we anticipate these data will pave way for further studies on virulence mechanisms and the role of A. media in the spread of AMR genes.

Aeromonas species isolated from aquatic organisms, insects, chicken, and humans in India show similar antimicrobial resistance profiles

Aeromonas species are Gram-negative bacteria that infect various living organisms and are ubiquitously found in different aquatic environments. In this study, we used whole genome sequencing (WGS) to identify and compare the antimicrobial resistance (AMR) genes, integrons, transposases and plasmids found in Aeromonas hydrophila, Aeromonas caviae and Aeromonas veronii isolated from Indian major carp (Catla catla), Indian carp (Labeo rohita), catfish (Clarias batrachus) and Nile tilapia (Oreochromis niloticus) sampled in India. To gain a wider comparison, we included 11 whole genome sequences of Aeromonas spp. from different host species in India deposited in the National Center for Biotechnology Information (NCBI). Our findings show that all 15 Aeromonas sequences examined had multiple AMR genes of which the Ambler classes B, C and D β-lactamase genes were the most dominant. The high similarity of AMR genes in the Aeromonas sequences obtained from different host species point to interspecies transmission of AMR genes. Our findings also show that all Aeromonas sequences examined encoded several multidrug efflux-pump proteins. As for genes linked to mobile genetic elements (MBE), only the class I integrase was detected from two fish isolates, while all transposases detected belonged to the insertion sequence (IS) family. Only seven of the 15 Aeromonas sequences examined had plasmids and none of the plasmids encoded AMR genes. In summary, our findings show that Aeromonas spp. isolated from different host species in India carry multiple AMR genes. Thus, we advocate that the control of AMR caused by Aeromonas spp. in India should be based on a One Health approach.

Mining the diversity and functional profile of bacterial symbionts from the larvae of Chironomus circumdatus (bloodworms)

Chironomids are the most abundant aquatic insects in freshwater habitats that can survive in extreme conditions. In this study, as the microbiome provides extended genotype to the host to perform various functions, we explored the microbiota of the Chironomus circumdatus larvae to find out the putative role played by the symbiotic bacteria for the host. The metabarcoding analyses of the larvae revealed that the insect harbors 1771 phylotypes. Out of the various microbial communities found, the majority corresponded to the phyla Proteobacteria (52.59%) and Actinobacteria (20.56%), respectively. The midges also harbored Klebsiella (2.57%), Enterobacter (1.32%), Bacillus (2.29%), and Acinetobacter (2.13%) genera that are involved in detoxification of xenobiotics present in the water. The presence of radiation-resistant genera like Deinococcus, including bacterial species like radiodurans, a highly radiation-resistant bacterium, indicates its potential to support the host's ability to sustain in adverse environments. The functional profiling of the bacteria showed the relative abundance of many enzyme groups, such as transferases (40.62%), oxidoreductases (23.49%), and hydrolases (3.77%). The results indicate that the larvae harbor a considerable variety of bacteria that help the host adapt and survive in the polluted waters. The present study provides thorough insights into the microbiome of the C. circumdatus larvae that can be exploited for the bioremediation of certain pollutants through biomimetic strategies. It also gives us a wake-up call to take a good look at the guts of these disease-carrying insects' inabilities to spread deadly human diseases.

Single and combined effects of microplastics, pyrethroid and food resources on the life-history traits and microbiome of Chironomus riparius

There is growing evidence of widespread contamination of freshwater ecosystems with microplastics. However, the effects of chronic microplastic ingestion and its interaction with other pollutants and stress factors on the life-history traits and the host-microbiome of aquatic invertebrates are not well understood. This study investigates the effects of exposure to sediment spiked with 1 μm polystyrene-based latex microplastic spheres, an environmentally realistic concentration of a pyrethroid pesticide (esfenvalerate), and a combination of both treatments on the life-history traits of the benthic-dwelling invertebrate, Chironomus riparius and its microbial community. The chironomid larvae were also exposed to two food conditions: abundant or limited food in the sediment, monitored for 28 and 34 days respectively. The microplastics and esfenvalerate had negative effects on adult emergence and survival, and these effects differed between the food level treatments. The microbiome diversity was negatively affected by the exposure to microplastics, while the relative abundances of the four top phyla were significantly affected only in the high food level treatment. Although the combined exposure to microplastics and esfenvalerate showed some negative effects on survival and emergence, there was little evidence for synergistic effects when compared to the single exposure. The food level affected all life-history traits and the microbiota, and lower food levels intensified the negative effects of the exposure to microplastics, esfenvalerate and their combination. We argue that these pollutants can affect crucial life-history traits such as successful metamorphosis and the host-microbiome. Therefore, it should be taken into consideration for toxicological assessment of pollutant acceptability. Our study highlights the importance of investigating possible additive and synergic activities between stressors to understand the effects of pollutants in the life story traits and host-microbiome.

Characterization of an Esterase Producing Bacterium from the Gut of Chironomus circumdatus (Bloodworms) and its Ability to Use Modified Phthalates

Insects harbor bacteria that are a rich source of enzymes that can be utilized for various industrial and biotechnological applications. It is predicted that during evolution these detoxifying enzymes have been acquired by insects through bacteria. However, the role of host insect detoxification enzymes has already been extensively studied but only a few resistance development studies have been focused on the enzymes derived from gut bacteria. Thus in this study, two bacterial isolates were found in the gut of Chironomous circumdatus larvae having esterase activity, out of which one bacterium was molecular characterized and it was found to be Enterobacter mori designated as strain BI1245. Further, crude extract from the bacterium was characterized and it was observed that it showed maximum activity at pH 8 and temperature 60 °C. Moreover, the crude extract showed 0.26 mM and 290 U/mg of protein as K_m and V_max value when p-nitrophenyl acetate was used as a substrate. Thereafter, the bacterial isolate was incubated in minimal salts medium containing modified phthalates and it was found that bacterium could utilize shorter alkyl-chain phthalic acid esters faster as compared to long alkyl chains thereby indicating that side chain of the substrates has a significant effect on the utilization of phthalic acid esters. Thus the gut flora present in insects may play an important role in providing resistance to the host to live in phthalate polluted water.

Identification of chironomid species as natural reservoirs of toxigenic Vibrio cholerae strains with pandemic potential

Vibrio cholerae causes the fatal cholera diarrhea. Chironomids (Diptera; Chironomidae) are abundant in freshwater aquatic habitats and estuaries and are natural reservoirs of V. cholerae. Until now, only the non-O1/O139 serogroups of V. cholerae were identified in chironomids. Here, we explored whether chironomids are natural reservoirs of V. cholerae O1/O139 serogroups, which are associated with cholera endemics and pandemics. All four life stages of chironomids were sampled from two rivers, and a laboratory culture in Pune, India, and from a pond in Israel. In total, we analyzed 223 chironomid samples. The presence of V. cholerae O1/O139 serogroups was verified using molecular tools. Nine chironomid species were identified; of them, Chironomus circumdatus was the most abundant. The presence of V. cholerae serogroup O1 and the cholera toxin genes were detected in samples from all chironomid species. However, serogroup O139 was detected in only two chironomid species. Besides PCR to detect specific genes, a metagenomic analysis that was performed in three selected C. ramosus larvae, identified a list of virulence genes associated with V. cholerae. The findings provide evidence that chironomids are natural reservoirs of toxigenic V. cholerae O1/O139. Chironomid populations and V. cholerae show biannual peak patterns. A similar pattern is found for cholera epidemics in the Bengal Delta region. Thus, we hypothesize that monitoring chironomids in endemic areas of the disease may provide a novel tool for predicting and preventing cholera epidemics. Moreover, serogroup O139 was detected only in two chironomid species that have a restricted distribution in the Indian subcontinent, possibly explaining why the distribution of the O139 serogroup is limited.

Seasonal dynamics of Chironomus transvaalensis populations and the microbial community composition of their egg masses

Chironomids (Diptera; Chironomidae) are the most abundant insects in freshwater environments and are considered natural reservoirs of Vibrio cholerae. We monitored the annual dynamics of chironomid populations along with their microbiota in order to better understand host–microbiota interactions. Chironomus transvaalensis populations peaked biannually in August and May–June. The composition of the endogenous bacterial communities of their egg masses clustered in two groups according to the sampling periods August–November and May–July. Nevertheless, a core bacterial community (43%) was present in all egg-mass samples. The most abundant phyla were: Proteobacteria, Firmicutes, Cyanobacteria and Bacteroidetes. The abundance of several genera (e.g. Rheinheimera and Pseudomonas) was positively correlated with C. transvaalensis population dynamics, while a predator–prey interaction was observed between the relative abundance of Vibrio OTUs and C. transvaalensis population size. Chironomids are known to tolerate toxic and stress conditions, and our results demonstrated that bacterial genera that may protect the insect under these conditions are present in the egg masses. After hatching, the first larval meal is the gelatinous matrix that surrounds the eggs. This meal contains a probiotic consortium that may protect the larva during its metamorphosis. The results provide important insights into the host–microbe interactions of chironomids.

The Relative Abundance of Benthic Bacterial Phyla Along a Water-Depth Gradient in a Plateau Lake: Physical, Chemical, and Biotic Drivers

Water-depth biodiversity gradient, one of the typical biogeographical patterns on Earth, is understudied for bacteria in freshwater ecosystems, and thus left the underlying mechanisms poorly understood especially for benthic bacteria. Here, we investigated the water-depth distribution of surface sediment bacterial phyla and their driving factors in Lake Lugu, a plateau lake in Southwest China. Our results revealed that the relative abundance of 11 dominant bacterial phyla showed various water-depth patterns, such as increasing, decreasing, hump-shaped, and U-shaped patterns. These patterns across phyla were consistent with their different niche positions of water depth, while the occupancy-abundance relationships were not dependent on phylum attributes. Consistently, phylum abundance was best explained by water depth; other physical and chemical factors, such as metal ion concentrations, SiO₂, and pH, can also explain the variations in some bacterial phyla. Chemical variables were the main drivers of the dominant bacterial phyla. However, biotic variables also showed substantial importance for some phyla, such as Planctomycetes, Actinobacteria, and WS3. This work could provide new insights into the general water-depth patterns and underlying mechanisms of the relative abundance of bacterial phyla in freshwater ecosystems.

Bacterial flora analysis of coliforms in sewage, river water, and ground water using MALDI-TOF mass spectrometry

The aim of this study was to rapidly and effectively analyze coliforms, which are the most fundamental indicators of water quality for fecal pollution, using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Coliform bacteria were isolated from municipal sewage, river water, and groundwater. For each sample, 100 isolates were determined by MALDI-TOF MS. In addition, these same 100 isolates were also identified via 16S rRNA gene sequence analysis. Obtained MALDI-TOF MS data were compared with the 16S rRNA sequencing analysis, and the validity of MALDI-TOF MS for classification of coliform bacteria was examined. The concordance rate of bacterial identification for the 100 isolates obtained by MALDI-TOF MS analysis and 16S rRNA gene sequence analysis for sewage, river water, and ground water were 96%, 74%, and 62% at the genus level, respectively. Among the sewage, river water, and ground water samples, the coliform bacterial flora were distinct. The dominant genus of coliforms in sewage, river water, and groundwater were Klebsiella spp., Enterobacter spp., and Serratia spp., respectively. We determined that MALDI-TOF MS is a rapid and accurate tool that can be used to identify coliforms. Therefore, without using conventional 16S rRNA sequencing, it is possible to rapidly and effectively classify coliforms in water using MALDI-TOF MS.