Chironomus ramosus Larval Microbiome Composition Provides Evidence for the Presence of Detoxifying Enzymes

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.

History of the Study of the Genus Thiothrix: From the First Enrichment Cultures to Pangenomic Analysis

Representatives of the genus Thiothrix are filamentous, sulfur-oxidizing bacteria found in flowing waters with counter-oriented sulfide and oxygen gradients. They were first described at the end of the 19th century, but the first pure cultures of this species only became available 100 years later. An increase in the number of described Thiothrix species at the beginning of the 21st century shows that the classical phylogenetic marker, 16S rRNA gene, is not informative for species differentiation, which is possible based on genome analysis. Pangenome analysis of the genus Thiothrix showed that the core genome includes genes for dissimilatory sulfur metabolism and central metabolic pathways, namely the Krebs cycle, Embden–Meyerhof–Parnas pathway, glyoxylate cycle, Calvin–Benson–Bassham cycle, and genes for phosphorus metabolism and amination. The shell part of the pangenome includes genes for dissimilatory nitrogen metabolism and nitrogen fixation, for respiration with thiosulfate. The dispensable genome comprises genes predicted to encode mainly hypothetical proteins, transporters, transcription regulators, methyltransferases, transposases, and toxin–antitoxin systems.

Accumulation of nylon microplastics and polybrominated diphenyl ethers and effects on gut microbial community of Chironomus sancticaroli

Microplastics (MP) are emerging contaminants with the capacity to bind and transport hydrophobic organic compounds of environmental concern, such as polybrominated diphenyl ethers (PBDEs). The aim of this study was to investigate the ingestion of nylon (polyamide) MP alone and when associated with PBDEs and their effects on Chironomus sancticaroli larvae survival and microbiome structure. Survival, PBDE uptake and microbial community composition were measured in fourth instar larvae exposed for 96 h to BDEs- 47, 99, 100 and 153 in the presence and absence of 1% w/w MP in sediment. Microbiome community structures were determined through high throughput sequencing of 16S small subunit ribosomal RNA gene (16S rRNA). Initial experiments showed that larvae ingested MP faster at 0.5% w/w MP, while depuration was more efficient at 1% w/w MP, although retention of MP was seen even after 168 h depuration. No mortality was observed as a result of PBDEs and MP exposure. MP had a negative effect on PBDE concentration within larvae (η² = 0.94) and a negative effect on sediment concentrations (η² = 0.48). In all samples, microbial communities were dominated by Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Gammaproteobacteria. Bacterial alpha diversity was not significantly affected by PBDEs or MP exposure. However, the abundance of discrete bacterial taxa was more sensitive to MP (X² = 45.81, p = 0.02), and PBDE exposure. Our results highlight that C. sancticaroli showed no acute response to MPs and PBDEs, but that MPs influenced bacterial microbiome structure even after only short-term acute exposure.

Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and ‘Candidatus Thiothrix sulfatifontis’ sp. nov

The metagenome of foulings from sulfidic spring “Serovodorodny” (Tatarstan, Russia), where members of the genus Thiothrix was observed, was sequenced. Representatives of the phyla Gammaproteobacteria, Cyanobacteria and Campilobacteriota dominated in the microbial community. The complete genome of Thiothrix sp. KT was assembled from the metagenome. It displayed 93.93–99.72% 16S rRNA gene sequence identity to other Thiothrix species. The average nucleotide identity (ANI) и digital DNA-DNA hybridization (dDDH) showed that the genome designated KT represents a new species within the genus Thiothrix, ‘Candidatus Thiothrix sulfatifontis’ sp. nov. KT. The taxonomic status has been determined of the strain Thiothrix sp. CT3, isolated about 30 years ago and not assigned to any of Thiothrix species due to high 16S rRNA gene sequence identity with related species (i.e., 98.8–99.4%). The complete genome sequence of strain CT3 was determined. The ANI between CT3 and other Thiothrix species was below 82%, and the dDDH values were less than 40%, indicating that strain CT3 belongs to a novel species, Thiothrix winogradskyi sp. nov. A genome analysis showed that both strains are chemo-organoheterotrophs, chemolithotrophs (in the presence of hydrogen sulfide and thiosulfate) and chemoautotrophs. For the first time, representatives of Thiothrix showed anaerobic growth in the presence of thiosulfate.

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.

The Chironomid Microbiome Plays a Role in Protecting Its Host From Toxicants

Organisms are assemblages of the host and their endogenous bacteria, which are defined as microbiomes. The host and its microbiome undergo a mutual evolutionary process to adapt to changes in the environment. Chironomids (Diptera; Chironomidae), are aquatic insects that grow and survive in polluted environments; however, the mechanisms that protect them under these conditions are not fully understood. Here we present evidence that the chironomids’ microbiome enables them to survival in polluted environments. It has been demonstrated that about 40% of the microbiota that inhabit Chironomus transvaalensis egg masses and larvae has the potential to detoxify different toxicants. Metagenomic analysis of Chironomus ramosus larvae demonstrated the presence of genes in the insects’ microbiome that can help the insects to survive in hostile environments. A set of experiments demonstrated that short exposure of C. transvaalensis larvae to metals significantly changed their microbiota composition in comparison to unexposed larvae. Another experiment, that followed Koch’s postulates, demonstrated that disinfected C. transvaalensis larvae can survive toxic lead and chromium exposure when they are recolonized with bacteria that can detoxify these toxic metals. This accumulating research, points to the conclusion that the chironomid microbiome plays a role in protecting its host from toxicants.

Comparative Microbiota Composition Across Developmental Stages of Natural and Laboratory-Reared Chironomus circumdatus Populations From India

Chironomids are aquatic insects that undergo a complete metamorphosis of four life stages. Here we studied, for the first time, the microbiota composition of Chironomus circumdatus, a tropical midge species, both from the Mula and Mutha Rivers in Pune, India and as a laboratory-reared culture. We generated a comparative microbial profile of the eggs, larvae and pupae, the three aquatic life stages of C. circumdatus. Non-metric multidimensional scaling analysis (NMDS) demonstrated that the developmental stage had a more prominent effect on the microbiota composition compared to the sampling location. Notably, the microbiota composition of the egg masses from the different sampling points clustered together and differed from laboratory culture larvae. Proteobacteria was the dominant phylum in all the environmental and laboratory-reared egg masses and pupal samples, and in the laboratory-reared larvae, while Fusobacteria was the dominant phylum in the larvae collected from the field environment. The most abundant genera were Cetobacterium, Aeromonas, Dysgonomonas, Vibrio, and Flavobacterium. The ten amplicon sequence variants (ASVs) that most significantly contributed to differences in microbiota composition between the three sampled locations were: Burkholderiaceae (ASVs 04 and 37), C39 (Rhodocyclaceae, ASV 14), Vibrio (ASV 07), Arcobacter (ASV 21), Sphaerotilus (ASV 22), Bacteroidia (ASVs 12 and 28), Flavobacterium (ASV 29), and Gottschalkia (ASV 10). No significant differences were found in the microbial richness (Chao1) or diversity (Shannon H’) of the three sampled locations. In contrast, significant differences were found between the microbial richness of the three life stages. Studying the microbiota of this Chironomus species may contribute to a better understanding of the association of C. circumdatus and its microbial inhabitants.