Search Results (14)

The giant freshwater prawn (Macrobrachium rosenbergii) has economic significance in the aquatic industry, but production is impacted by infectious diseases induced by various pathogens. Herein, we investigated the impact of adding feed additives to the diet of M. rosenbergii to promote health. Diets were formulated to contain different levels of Centella asiatica (L.) Urb. crude extracts (1, 5, and 10 g kg⁻¹), with growth performance and innate immune parameters assessed after 28 days of feeding. Real-time quantitative PCR (RT-qPCR) was employed to determine the mRNA levels of serine proteinase inhibitor (SPI) and alpha-2 macroglobulin (Mr-2α2M) from 12 h to 28 days of feeding. Prawns feeding at 5 and 10 g kg⁻¹ showed statistically significant differences in specific growth rate, lysozyme assay, and phenoloxidase activity. The expression levels of all the immune-related genes studied were significantly upregulated in prawns fed with supplemented diets compared to the control group. Findings revealed that the observed upregulations varied in response to alterations in feeding time and concentration. Furthermore, 16S rRNA analysis showed that the supplemented diets at 10 g kg⁻¹ supplementation increased beneficial bacteria (Lactococcus sp.) and reduced pathogenic taxa (e.g., Candidatus Hepatoplasma, Flavobacteriaceae, Weeksellaceae, Thiothrix sp.). Full article

Industrial activated sludge plants in many sectors, including the dairy industry, face sludge separation problems caused by sludge bulking. Aerobic granular sludge (AGS) could be a solution by forming well-settling granules. The key to successful granulation is the microbial selection of slow-growing glycogen-accumulating organisms (GAOs) by introducing an anaerobic feeding/reaction step. The objective of the current study was to investigate the impact of two slow feeding strategies to achieve granulation in existing sequencing batch reactors treating real dairy wastewater, by microbial selection only. The first strategy consisted of slow 90 min mixed feeding. The second strategy combined 45 min static and 45 min mixed feeding to build up a substrate gradient. The feeding strategies did not affect the effluent quality, but significantly impacted the sludge morphology, settling properties, and microbial community composition. Mixed feeding led to filamentous overgrowth by Thiothrix species, up to 45% abundance, and deteriorating settling, with sludge volume index (SVI) values up to 125 mL/g. In contrast, static feeding yielded densified sludge with SVI values below 45 mL/g and up to 35% GAO abundance. In conclusion, the results show successful granulation when using a simple static slow feeding mode, which could benefit the industrial application of AGS technology. Full article

Bacteria of the Thiothrix morphotype, comprising the genera Thiothrix, Thiolinea and Thiofilum, are frequently encountered in domestic and industrial wastewater treatment systems, but they are usually not clearly differentiated due to the marked similarity in their morphologies. Methods ranging from light microscopy, FISH and PCR to modern high-throughput sequencing are used to identify them. The development of these bacteria in wastewater treatment systems has both advantages and disadvantages. On the one hand, the explosive growth of these bacteria can lead to activated sludge bulking or clogging of the treatment system’s membranes, with a consequent decrease in the water treatment efficiency. On the other hand, members of the Thiothrix morphotype can improve the quality of granular sludge and increase the water treatment efficiency. This may be due to their capacity for sulfide oxidation, denitrification combined with the oxidation of reduced sulfur compounds, enhanced biological phosphate removal and possibly denitrifying phosphate removal. The recently obtained pangenome of the genus Thiothrix allows the explanation, at the genomic level, of the experimental results of various studies. Moreover, this review summarizes the data on the factors affecting the proliferation of representatives of the Thiothrix morphotype. Full article

Alkaline coal mine drainage represents one of the most critical issues in the coal industry, driven by complex hydro-biogeochemical processes. However, the interplay of hydrogeochemical and biogeochemical interactions in alkaline coal mine drainage is still poorly understood. To this end, water samples were systematically collected from alkaline coal mine drainage sites from five coal mining areas in Chongqing coal mining district, located in southwestern China. Hydrogeochemical analyses showed that the main water type of the coal mine drainage sample was HCO₃-SO₄~K-Na, which primarily originated from local meteoric water. The microbial community compositions in the studied alkaline coal drainage were critically associated with sulfate, bicarbonate, DOC, nitrate, and pH, and linked to three putative keystone genera via network analysis (Thiothrix, Methylophilaceae_MM1, and an unclassified genus from Comamonadaceae family). Functional predictions from FAPROTAX suggested a high abundance of metabolic pathways involving the oxidation of sulfide and sulfur compounds, potentially underscoring their importance in controlling sulfate enrichment in alkaline coal mine drainage. Interestingly, members of the Methylomonadaceae family (methanotrophs) and the Methylotenera genus (methylotrophs) had positive Spearman correlations with both ammonium and sulfate, potentially inferring that the enhanced activities of methanotrophs might help capture methane in the alkaline coal mine drainage. This study further enhances our comprehension of the intricate interplay between hydrogeochemical and biogeochemical interactions in alkaline coal mine drainage, contributing to the carbon budget. Full article

Carbon-sequestering microorganisms play an important role in the carbon cycle of wetland ecosystems. However, the response mechanism of carbon-sequestering microbial communities to wetland type changes and their relationship with soil carbon remain unclear. To explore these differences and identify the main influencing factors, this study selected marsh wetlands, river wetlands and lakeside wetlands around Qinghai Lake as research subjects. High-throughput sequencing was employed to analyze the functional gene cbbM of carbon-sequestering microorganisms. The results revealed that the alpha diversity of cbbM carbon-sequestering microorganisms mirrored the trend in total carbon content, with the highest diversity observed in marsh wetlands and the lowest in lakeside wetlands. The dominant bacterial phylum was Proteobacteria, with prevalent genera including Thiothrix, Acidithiobacillus, and Thiodictyon. Acidithiobacillus served as a biomarker in lakeside wetlands, while two other genera were indicative of marsh wetlands. The hierarchical partitioning analysis indicated that the diversity of cbbM carbon-fixing microorganisms was primarily influenced by the total nitrogen content, while the community structure was significantly affected by the soil total carbon content. Moreover, an increased soil temperature and humidity were found to favor the carbon fixation processes of Thiomicrospira, Thiomonas, Polaromonas, and Acidithiobacillus. In summary, changes in wetland types seriously affected the characteristics of cbbM carbon sequestration in microbial communities, and a warm and humid climate may be conducive to wetland carbon sequestration. Full article

Currently, the phylogeny of the genus Thiothrix is based on comparative whole genome analysis because of the high homology of the 16S ribosomal RNA gene sequences within the genus. We analyzed the possibility of using various conservative genes as phylogenetic markers for the genus Thiothrix. We found that the levels of similarity of the nucleotide sequences of the tRNA(Ile)-lysidine synthase (tilS) and the β subunit of RNA polymerase (rpoB) genes are in good agreement with the average nucleotide identity (ANI) values between the genomes of various representatives of the genus Thiothrix. The genomes of Thiothrix strains MK1, WS, DNT52, DNT53, and H33 were sequenced. Taxonomic analysis using both whole genomes and the tilS gene consistently showed that MK1 and WS belong to Thiothrix lacustris, while DNT52, DNT53, and H33 belong to Thiothrix subterranea. The tilS gene fragments were subjected to high-throughput sequencing to profile the Thiothrix mat of a sulfidic spring, which revealed the presence of known species of Thiothrix and new species-level phylotypes. Thus, the use of tilS and rpoB as phylogenetic markers will allow for rapid analyses of pure cultures and natural communities for the purpose of phylogenetic identification of representatives of the genus Thiothrix. Full article

Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1–55.6%). We proposed to assign GKL-01 to a new species and genus ‘Candidatus Thiocaldithrix dubininis’ gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name ‘Candidatus Thiothrix putei’ sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na⁺-ATPases and H⁺-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically. Full article

The structure and diversity of microbial communities developing in the combined gradient of temperature (44–19 °C), as well as concentration of oxygen (0–10 mg/L) and hydrogen sulfide (33–0.7 mg/L), were studied in the thermal sulfide spring on the coast of Northern Lake Baikal. The predominance of bacteria participating in sulfur and nitrogen cycles and significant changes in the composition of microbial communities were noted at changing physicochemical conditions. Thiovirga sp. (sulfur-oxidizing bacteria, up to 37%) and Azonexus sp. (nitrogen-fixing bacteria, up to 43%) were dominant at high temperatures and concentrations of hydrogen sulfide in two hydrotherms. In addition, a significant contribution of the Rhodocyclaceae family (up to 51%) which is involved in the denitrification processes, and Acetoanaerobium sp. (up to 20%) fixing carbon oxide were found in the spring water. In the stream, mainly oxygenic cyanobacteria (up to 56%) developed at a temperature of 33 °C, in the presence of hydrogen sulfide and oxygen. In addition, sulfur bacteria of the genus Thiothrix (up to 48%) found in epibiotic communities of benthic animals of Lake Baikal were present here. Thiothrix sp. formed massive fouling in the zone of mixing lake and thermal waters with a significant contribution of hydrogen-oxidizing bacteria of the genus Hydrogenophaga (up to 22.5%). As well as chemolitho- and phototrophic bacteria, chemoorganotrophs (phyla Firmicutes, Chloroflexi, Desulfobacterota, Nitrospirota, Fibrobacterota, etc.) have been identified in all communities. The chemical parameters of water in spring and coastal zones indicate a significant change in the composition of thermal waters occurring with the participation of diverse microbial communities that contribute to the assimilation of inorganic components of mineral thermal waters. Full article

The aerobic granulation, pollutant removal, and microbial community in real textile wastewater (TWW) treatment were compared using conventional activated sludge (CAS) and preformed aerobic granular sludge (AGS) in synthetic wastewater as seed in two reactors, reactor-1 (R1) and reactor-2 (R2), respectively. The results showed that complete granulation was achieved in R1 (sludge volume index at 5 min (SVI₅) and 30 min (SVI₃₀): 19.4 mL/g; granule size: 210 μm) within 65 days, while it only required 28 days in R2 (SVI₅ and SVI₃₀: 27.3 mL/g; granule size: 496 μm). The removal of COD, NH₄⁺-N and TN in R1 (49.8%, 98.8%, and 41.6%) and R2 (53.6%, 96.9%, and 40.8%) were comparable in 100% real TWW treatment, but stable performance was achieved much faster in R2. The real TWW had an inhibitory effect on heterotrophic bacteria activity, but it had no inhibition on ammonia-oxidizing bacteria activity. AGS with a larger particle size had a higher microbial tolerance to real TWW. Furthermore, filamentous Thiothrix in the AGS in R2 disappeared when treating real TWW, leading to the improvement of sludge settleability. Thus, seeding preformed AGS is suggested as a rapid start-up method for a robust AGS system in treating real TWW. Full article

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. Full article

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. Full article

Chironomids (Diptera; Chironomidae) are aquatic insects that are abundant in freshwater. We aimed to study the endogenous microbiota composition of Chironomus ramosus larvae that were sampled from the Mutha River and a laboratory culture in India. Furthermore, we performed a metagenomic analysis of the larval microbiome, sampled from the Mutha River. Significant differences were found between the bacterial community composition of C. ramosus larvae that were sampled from the Mutha River and the laboratory culture. A total of 54.7% of the amplicon sequence variants (ASVs) that were identified in the larvae from the Mutha River were unique, compared to only 12.9% of unique ASVs that were identified from the laboratory-reared larvae. The four most abundant phyla across all samples were: Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes, while the nine most abundant genera were: Aeromonas, Alkanindiges, Breznakia, Cetobacterium, Chryseobacterium, Desulfovibrio, Dysgonomonas, Thiothrix, and Vibrio. Moreover, in the metagenomic analysis, we detected bacterial genes and bacterial pathways that demonstrated the ability to degrade different toxic compounds, detoxify metal, and confer resistance to antibiotics and UV radiation, amongst other functions. The results illuminate the fact that there are detoxifying enzymes in the C. ramosus larval microbiome that possibly play a role in protecting the insect in polluted environments. Full article

Two metagenome-assembled genomes (MAGs), obtained from laboratory-scale enhanced biological phosphorus removal bioreactors, were analyzed. The values of 16S rRNA gene sequence identity, average nucleotide identity, and average amino acid identity indicated that these genomes, designated as RT and SSD2, represented two novel species within the genus Thiothrix, ‘Candidatus Thiothrix moscowensis’ and ‘Candidatus Thiothrix singaporensis’. A complete set of genes for the tricarboxylic acid cycle and electron transport chain indicates a respiratory type of metabolism. A notable feature of RT and SSD2, as well as other Thiothrix species, is the presence of a flavin adenine dinucleotide (FAD)-dependent malate:quinone oxidoreductase instead of nicotinamide adenine dinucleotide (NAD)-dependent malate dehydrogenase. Both MAGs contained genes for CO₂ assimilation through the Calvin–Benson–Bassam cycle; sulfide oxidation (sqr, fccAB), sulfur oxidation (rDsr complex), direct (soeABC) and indirect (aprBA, sat) sulfite oxidation, and the branched Sox pathway (SoxAXBYZ) of thiosulfate oxidation to sulfur and sulfate. All these features indicate a chemoorganoheterotrophic, chemolithoautotrophic, and chemolithoheterotrophic lifestyle. Both MAGs comprise genes for nitrate reductase and NO-reductase, while SSD2 also contains genes for nitrite reductase. The presence of polyphosphate kinase and exopolyphosphatase suggests that RT and SSD2 could accumulate and degrade polyhosphates during the oxic-anoxic growth cycle in the bioreactors, such as typical phosphate-accumulating microorganisms. Full article