High-throughput 16S rRNA Gene Sequencing Research Articles

Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling.

Intensive agriculture systems have paved the way for a growing human population. However, the abundant use of mineral fertilizers and pesticides may negatively impact nutrient cycles and biodiversity. One potential alternative is to harness beneficial relationships between plants and plant-associated rhizobacteria to increase nutrient-use efficiency and provide pathogen resistance. Plant-associated microbiota profiling can be achieved using high-throughput 16S rRNA gene amplicon sequencing. However, interrogation of these data is limited by confident taxonomic classifications at high taxonomic resolution (genus- or species level) with the commonly applied universal reference databases. High-throughput full-length 16S rRNA gene sequencing combined with automated taxonomy assignment (AutoTax) can be used to create amplicon sequence variant resolved ecosystems-specific reference databases that are superior to the traditional universal reference databases. This approach was used here to create a custom reference database for bacteria and archaea based on 987,353 full-length 16S rRNA genes from Askov and Cologne soils. We evaluated the performance of the database using short-read amplicon data and found that it resulted in the increased genus- and species-level classification compared to commonly use universal reference databases. The custom database was utilized to evaluate the ecosystem-specific primer bias and taxonomic resolution of amplicon primers targeting the V5-V7 region of the 16S rRNA gene commonly used within the plant microbiome field. Finally, we demonstrate the benefits of custom ecosystem-specific databases through the analysis of V5-V7 amplicon data to identify new plant-associated microbes for two legumes and two cereal species.

Triclosan Promotes Conjugative Transfer of Antibiotic Resistance Genes to Opportunistic Pathogens in Environmental Microbiome.

Although triclosan, as a widely used antiseptic chemical, is known to promote the transmission of antibiotic resistance to diverse hosts in pure culture, it is still unclear whether and how triclosan could affect the transmission of broad-host-range plasmids among complex microbial communities. Here, bacterial culturing, fluorescence-based cell sorting, and high-throughput 16S rRNA gene amplicon sequencing were combined to investigate contributions of triclosan on the transfer rate and range of an IncP-type plasmid from a proteobacterial donor to an activated sludge microbiome. Our results demonstrate that triclosan significantly enhances the conjugative transfer of the RP4 plasmid among activated sludge communities at environmentally relevant concentrations. High-throughput 16S rRNA gene sequencing on sorted transconjugants demonstrates that triclosan not only promoted the intergenera transfer but also the intragenera transfer of the RP4 plasmid among activated sludge communities. Moreover, triclosan mediated the transfer of the RP4 plasmid to opportunistic human pathogens, for example, Legionella spp. The mechanism of triclosan-mediated conjugative transfer is primarily associated with excessive oxidative stress, followed by increased membrane permeability and provoked SOS response. Our findings offer insights into the impacts of triclosan on the dissemination of antibiotic resistance in the aquatic environmental microbiome.

Bacterial Community Shifts in Casing Soil Before and After the Cultivation of Oudemansiella raphanipes

Casing soil is a key step in the production of Oudemansiella raphanipes. Bacterial community in casing soil plays key roles in the growth and development of edible fungi. However, a knowledge gap remains regarding the bacterial community shifts in casing soil before and after the cultivation of O. raphanipes (CSBACO). Casing soil samples before and after the cultivation of O. raphanipes (CSBC and CSAC) were collected and examined by high-throughput 16S rRNA gene sequencing technology. Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria were dominant phyla in casing soil of O. raphanipes, which accounted for 77.32% of the total abundance. After the cultivation of O. raphanipes, the alpha diversity of bacterial community and the relative abundance of some beneficial genera such as Marmoricola, Nocardioides, Sphingomonas, and Streptomyces decreased, while that of bacteria belonging to the candidate class MB-A2-108 tolerant to adverse environment significantly increased. Meanwhile, physicochemical properties of casing soil changed significantly in CSBACO. Soil ammonium nitrogen and organic matter greatly decreased in CSAC and they mainly influenced bacterial community before the cultivation of O. raphanipes. In contrast, available potassium and pH significantly increased in CSAC and mainly affected bacterial community after the cultivation of O. raphanipes. Furthermore, the relative abundance of bacteria with the function of amino acid and lipid metabolism decreased, while that of bacteria functions related to parasites and pathogens increased, which further revealed the significance of bacterial community in casing soil. Diversity, composition, and the potential function of bacterial community shifted dramatically in CSBACO. The results deepen the understanding of the bacterial community and its microecological mechanism in casing soil of O. raphanipes.

Heterotrophic Bioleaching of Vanadium from Low-Grade Stone Coal by Aerobic Microbial Consortium.

Bioleaching is a viable method that assists in increasing the vanadium output in an economical and environmentally friendly manner. Most bioleaching is conducted by pure cultures under autotrophic conditions, which frequently require strong acidity and produce acid wastewater. However, little is known about heterotrophic bioleaching of vanadium by mixed culture. This study investigated the bioleaching of vanadium from low-grade stone coal by heterotrophic microbial consortium. According to the results, vanadium was efficiently extracted by the employed culture, with the vanadium recovery percentage in the biosystem being 7.24 times greater than that in the control group without inoculum. The average vanadium leaching concentration reached 680.7 μg/L in the first three cycles. The kinetic equation indicated that the main leaching process of vanadium was modulated by a diffusion process. Scanning electron microscopy revealed traces of bacterial erosion with fluffy structures on the surface of the treated stone coal. X-ray photoelectron spectroscopy confirmed the reduction of the vanadium content in the stone coal after leaching. Analysis of high-throughput 16S rRNA gene sequencing revealed that the metal-oxidizing bacteria, Acidovorax and Delftia, and the heterotrophic-metal-resistant Pseudomonas, were significantly enriched in the bioleaching system. Our findings advance the understanding of bioleaching by aerobic heterotrophic microbial consortium and offer a promising technique for vanadium extraction from low-grade stone coals.

Copper and chlorpyrifos stress affect the gut microbiota of chironomid larvae (Propsilocerus akamusi).

Chironomids are characterized by their ubiquitous distribution, global diversity and tolerant ability to deal with environmental stressors. To our knowledge, this is the first study presenting the gut microbial structure of chironomid larvae and examining the microbial alteration induced by invading chlorpyrifos and copper with different dosages. Lethal bioassay displayed a significantly decreased percentage survival of Propsilocerus akamusi larvae exposed to 800mg/L copper and 50μg/L chlorpyrifos at 96h. Larvae with deficient gut microbiota exhibited a depressed level of glutathione S-transferase activity after stressful exposure. The high-throughput 16S rRNA gene sequencing was adopted to investigate the community structure and it turned out that both copper and chlorpyrifos were able to generate distinguished variations of gut microbiota in the stressor-specific and concentration-dependent manner. Of note, the relative abundance of Comamonas, Stenotrophomonas, and Yersinia remarkably elevated in the presence of copper while chlorpyrifos exposure upregulated the prevalence of certain genera (e.g. Serratia). Flavobacterium was greatly attenuated in chlorpyrifos group with lethal dosage exhibiting more severe impacts. The predicted gene functions of the gut commensals differed between normal samples and those subjected to distinct toxins. Besides, more positive associations and limited modularity of microbial interactions were observed in stressor-challenged larvae, presenting a network with impaired complexity and stability. The appearance of either copper or chlorpyrifos exhibited strong positive correlations with genera belonging to Proteobacteria and Firmicutes. Collectively, this investigation introduces a general outline of gut microbiota obtained from chironomid individuals with latent adaptive tactics to nocuous factors (heavy metal and pesticide), which could build a fundamental basis for us to further explore the protective roles of chironomid gut bacterial colonizers in defending against aquatic contaminants.

Aged microplastics change the toxicological mechanism of roxithromycin on Carassius auratus: Size-dependent interaction and potential long-term effects

Size effects of microplastics have received extensive attention for their influence on other pollutants and harm to organisms. In this study, we investigated the uptake, elimination, tissue distribution and potential toxicity mechanism of roxithromycin (ROX) in the presence of 0.5, 5 and 50 μm of aged microplastics (AMPs) in Carassius auratus. The results showed that AMPs promoted the ROX bioaccumulation of various tissues in a size-dependent manner. AMPs and ROX significantly induced superoxide dismutase and catalase activities of liver and gut, and inhibited acetylcholinesterase activities of brain. The coexistence of smaller AMPs exacerbated pathological abnormalities in liver, gill and brain induced by ROX, while larger AMPs caused more intestinal damage. Moreover, high-throughput 16S rRNA gene sequencing indicated that the abundance of Proteobacteria in 0.5 μm AMPs and ROX joint treatments and Firmicutes and Bacteroidota in 50 μm AMPs and ROX joint treatments were significantly raised (p < 0.05). Metabolomics revealed that AMPs and ROX had a size-dependent long-term effect on gut microbial metabolites, which was mainly related to galactose metabolism, amino acid metabolism and primary bile acid biosynthesis pathways after a 7-day elimination, respectively. These results provide important insights into the relationship between the size effect of AMPs and interaction mechanism of AMPs and coexisting pollutants on aquatic organisms.

Preventive effects of the Rehmannia glutinosa Libosch and Cornus officinalis Sieb herb couple on chronic kidney disease rats via modulating the intestinal microbiota and enhancing the intestinal barrier.

CKD is a clinical syndrome with slow development and gradual deterioration of renal function. At present, modern medicine still lacks an ideal treatment method for this disease, while TCM has accumulated rich clinical experience in the treatment of CKD, which can effectively improve renal function and delay renal failure, and has unique advantages. RC is widely used in clinical practice to treat CKD, especially the “Kidney-Yin” deficiency syndrome. However, the compatibility mechanisms responsible for its effects in experimental studies, including preclinical and clinical research studies, are still not fully understood. Adenine-induced CKD rats were used to investigate the preventive effect of RC on CKD rats. Based on the high-throughput 16S rRNA gene sequencing results from Illumina, we discussed the intestinal flora abundance in rats in different treatment groups. According to a PCA and a PCoA based on a distance matrix, there was a clear separation of gut microbiome profiles between normal rats and model rats in terms of beta diversity. The abundance of Firmicutes in CKD rats was relatively increased, while that of Bacteroidetes was decreased. It is clear that the plot for the RC group was closer to that of the normal group, suggesting that the RC group had higher similarities among bacterial members with N rats. Ussing chamber, Western blot, and PCR assays were used to investigate the effects of RC on intestinal barrier function and its molecular mechanism in model animals. The results indicated that the protein expressions of ZO-1, claudin-1, and occludin-1 were decreased significantly in chronic kidney disease rats with the induction of adenine. With the treatment of RG, CO, and RC, the intestinal barrier was repaired due to the upregulated expressions of the aforementioned proteins in CKD rats. Based on our findings, RC appears to strengthen the intestinal barrier and modulate gut microbiota in adenine-induced CKD rats. This project revealed the compatibility mechanism of RC in regulating the intestinal microecology and barrier function to intervene in CKD and provided the basis and ideas for the clinical application of RC and the development of innovative drugs for CKD.

Microbial community structure and shift pattern of industry brine after a long-term static storage in closed tank.

Brine from Dingyuan Salt Mine (Anhui, China), an athalassohaline hypersaline environment formed in the early tertiary Oligocene, is used to produce table salt for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. Here, we employed cultivation and high-throughput sequencing strategies to uncover the microbial community and its shift after a long-term storage in the brine collected from Dingyuan Salt Mine. High-throughput sequencing showed (1) in the fresh brine (2021), Cyanobium_stocktickerPCC-6307 spp. (8.46%), Aeromonas spp. (6.91%) and Pseudomonas spp. (4.71%) are the dominant species in bacteria while Natronomonas spp. (18.89%), Halapricum spp. (13.73%), and Halomicrobium spp. (12.35%) in archaea; (2) after a 3-year-storage, Salinibacter spp. (30.01%) and Alcanivorax spp. (14.96%) surpassed Cyanobium_stocktickerPCC-6307 spp. (8.46%) becoming the dominant species in bacteria; Natronomonas spp. are still the dominant species, while Halorientalis spp. (14.80%) outnumbered Halapricum spp. becoming the dominant species in archaea; (3) Alcanivorax spp. and Halorientalis spp. two hydrocarbons degrading microorganisms were enriched in the brine containing hydrocarbons. Cultivation using hypersaline nutrient medium (20% NaCl) combined with high-throughput 16S rRNA gene sequencing showed that (1) the biomass significantly increased while the species diversity sharply declined after a 3-year-storage; (2) Halorubrum spp. scarcely detected from the environment total stocktickerDNA were flourishing after cultivation using AS-168 or NOM medium; (3) twelve possible new species were revealed based on almost full-length 16S rRNA gene sequence similarity search. This study generally uncovered the microbial community and the dominant halophiles in this inland athalassohaline salt mine, and provided a new insight on the shift pattern of dominant halophiles during a long-term storage, which illustrated the shaping of microorganisms in the unique environment, and the adaptation of microbe to the specific environment.

Characterizing free-living and particle-attached bacterial communities of a canyon river reservoir on the Yungui Plateau, China.

Revealing the composition of free-living (FL) and particle-attached (PA) bacterial communities could provide insights into their distinct roles in biogeochemical processes and algal bloom dynamics. While there is still a lack of research about the difference and interactions between FL and PA communities, especially on the Yungui plateau with underestimated diversity. This study unveiled the structure of both FL and PA bacterial communities in a canyon reservoir (Wujiangdu) on the Yungui Plateau, southern China. Water samples were collected from surface water at nine sites in the reservoir. FL and PA bacterial community structures were identified by high-throughput 16S rRNA gene sequencing. We compared the structure and diversity of FL and PA bacteria and investigated their relationship with environmental factors. Results showed that there were different structures between FL and PA bacterial communities, and the dominant FL and PA phyla were affected by different environmental variables. Moreover, diversity of PA bacteria was greater than that of FL bacteria. Both groups exhibited distance decay patterns in this reservoir with varying correlations with geographic distances. FL fraction, however, exhibited a stronger correlation with environmental factors than the PA counterpart. Both FL and PA communities were phylogenetic clustering than expected according to the mean nearest taxon distance. This study provides fundamental information on FL and PA bacteria distribution and demonstrates how specific environmental factors affected these two bacterial fractions in canyon river reservoirs.

Understanding of the interrelationship between methane production and microorganisms in high-solid anaerobic co-digestion using microbial analysis and machine learning

Co-digestion of lignocellulosic biomass and animal manure is a common approach to increase the efficiency of methane production, but the niche differentiation and microbial metabolism of the anaerobic digestion (AD) process remain to be determined. To further explore the effect of the interaction between species and their compositional niches, the methane yield and resulting microbial community were determined by machine learning (ML) and 16S rRNA gene sequencing in mixed high-solid anaerobic digestion (HS-AD) with spray-enhanced conditions to explore the internal relationship between physical and chemical parameters and microorganisms and to speculate on the enhancement mechanism of co-digestion. In this study, three ML models (extreme learning machine (ELM), artificial neural network (ANN), and random forest (RF)) were applied to analyse and model AD of dry fermentation. The results showed that the best prediction model, based on ELM, could best predict the material biogas production in this experiment with a mean absolute error (MAE/10) of 0.678 and a coefficient of determination (R2) of 0.9574, whereas the characteristic percentage analysis of the RF model showed that butyric acid, acetic acid, and pH had three important influences on the biogas production values. Meanwhile, the results of high-throughput 16S rRNA gene sequencing and PICRUSt showed that the addition of manure containing ammonia nitrogen improved the metabolism of amino acids, enriched species capable of Clostridiales and Methanosarcinales, promoted the electronic transfer of nutrient metabolism, and thus enhanced AD. Moreover, the co-occurrence network showed that seven niches were differentiated within the HS-AD system to reduce the shock of ammonia nitrogen for methanogens. Overall, microbial analysis and ML can help understand the dynamic processes of methanogenic microorganisms and predict biogas production for the efficient operation of AD.

Novel microbial consortia facilitate metalliferous immobilization in non-ferrous metal(loid)s contaminated smelter soil: Efficiency and mechanisms

Exposure to toxic metals from nonferrous metal(loid) smelter soils can pose serious threats to the surrounding ecosystems, crop production, and human health. Bioremediation using microorganisms is a promising strategy for treating metal(loid)-contaminated soils. Here, a native microbial consortium with sulfate-reducing function (SRB1) enriched from smelter soils can tolerate exposures to mixtures of heavy metal(loid)s (e.g., As and Pb) or various organic flotation reagents (e.g., ethylthionocarbamate). The addition of Fe2+ greatly increased As3+ immobilization compared to treatment without Fe2+, with the immobilization efficiencies of 81.0% and 58.9%, respectively. Scanning electronic microscopy-energy dispersive spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopy confirmed that the As3+ immobilizing activity was related to the formation of arsenic sulfides (AsS, As4S4, and As2S3) and sorption/co-precipitation of pyrite (FeS2). High-throughput 16S rRNA gene sequencing of SRB1 suggests that members of Clostridium, Desulfosporosinus, and Desulfovibrio genera play an important role in maintaining and stabilizing As3+ immobilization activity. Metal(loid)s immobilizing activity of SRB1 was not observed at high and toxic total exposure concentrations (220–1181 mg As/kg or 63–222 mg Pb/kg). However, at lower concentrations, SRB1 treatment decreased bioavailable fractions of As (9.0%) and Pb (28.6%) compared to without treatment. Results indicate that enriched native SRB1 consortia exhibited metal(loid) transformation capacities under non-toxic concentrations of metal(loid)s for future bioremediation strategies to decrease mixed metal(loid)s exposure from smelter polluted soils.

Metal-free single heteroatom (N, O, and B)-doped coconut-shell biochar for enhancing the degradation of sulfathiazole antibiotics by peroxymonosulfate and its effects on bacterial community dynamics

Metal-free single heteroatom (N, O, and B)-doped coconut-shell biochar (denoted as N-CSBC, O-CSBC, and B-CSBC, respectively) were fabricated in a one-step pyrolysis process to promote peroxymonosulfate (PMS) activation for the elimination of sulfathiazole (STZ) from aquaculture water. B-CSBC exhibited remarkably high catalytic activity with 92% of STZ degradation in 30 min attributed to the presence of meso-/micro-pores and B-containing functional groups (including B–N, B–C, and B2O3 species). Radical quenching tests revealed SO4•−, HO•, and 1O2 being the major electron acceptors contributing to STZ removal by PMS over B-CSBC catalyst. The B-CSBC catalyst has demonstrated high sustainability in multiple consecutive treatment cycles. High salinity and the presence of inorganic ions such as chloride, enhanced the performance of the sulfate radical-carbon-driven advanced oxidation processes (SR–CAOPs) as pretreatment strategy that significantly facilitated the removal of STZ from aquaculture water. Furthermore, a potential sulfonamide-degrading microorganism, Cylindrospermum_stagnale, belonging to the phylum Cyanobacteria, was the dominant functional bacteria according to the results of high-throughput 16S rRNA gene sequencing conducted after the B-CSBC/PMS treatment. This study provides new insights into the SR–CAOP combined with bioprocesses for removing STZ from aqueous environments.

Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples.

Microbially mediated processes in a given habitat tend to be catalyzed by abundant populations that are ecologically adapted to exploit specific environmental characteristics. Typically, metabolic activities of rare populations are limited but may be stimulated in response to acute environmental stressors. Community responses to sudden changes in temperature and pressure can include suppression and activation of different populations, but these dynamics remain poorly understood. The permanently cold ocean floor hosts countless low-abundance microbes including endospores of thermophilic bacteria. Incubating sediments at high temperature resuscitates viable spores, causing the proliferation of bacterial populations. This presents a tractable system for investigating changes in a microbiome's community structure in response to dramatic environmental perturbations. Incubating permanently cold Arctic fjord sediments at 50°C for 216 h with and without volatile fatty acid amendment provoked major changes in community structure. Germination of thermophilic spores from the sediment rare biosphere was tracked using mass spectrometry-based metabolomics, radiotracer-based sulfate reduction rate measurements, and high-throughput 16S rRNA gene sequencing. Comparing community similarity at different intervals of the incubations showed distinct temporal shifts in microbial populations, depending on organic substrate amendment. Metabolite patterns indicated that amino acids and other sediment-derived organics were decomposed by fermentative Clostridia within the first 12–48 h. This fueled early and late phases of exponential increases in sulfate reduction, highlighting the cross-feeding of volatile fatty acids as electron donors for different sulfate-reducing Desulfotomaculia populations. The succession of germinated endospores triggered by sudden exposure to high temperature and controlled by nutrient availability offers a model for understanding the ecological response of dormant microbial communities following major environmental perturbations.

Distribution of microbial communities in seasonally frozen soil layers on the Tibetan Plateau and the driving environmental factors.

Large stocks of carbon and nitrogen stored in permafrost regions can potentially feed back to global biogeochemical cycles under climate warming. To understand the response of microbial communities to environmental changes, this study investigated the spatial distribution of bacterial communities in the upper layers (0-10, 10-20, and 20-30cm) of seasonally frozen soil on the Tibetan Plateau and their relationships with the environmental factors. A total of 135 soil samples were collected from the soils at depths of 0-10, 10-20, and 20-30cm in the Lhasa River and Nyang River basins, and the diversity and composition of bacterial communities in them were identified by high-throughput 16S rRNA gene sequencing. Bacterial diversity changed significantly with soil depth in the Nyang River basin (p < 0.001), while no obvious change was found in the Lhasa River basin. The whole bacterial composition exhibited small variations across different soil layers (p > 0.05). The relative abundance of aerobic bacteria, Sphingomonas and Arthrobacter, decreased with soil depth, while that of the other aerobic, facultative anaerobic, and anaerobic bacteria did not exhibit this trend. Soil pH was the key driving edaphic factor of the whole bacterial composition in all three depth layers, while vegetation also had an important influence on bacterial composition. Arthrobacter, Bradyrhizobium, and Bacillus had obvious correlations with soil nutrients or vegetation, while the other species were not significantly correlated with any environmental factors. Structural equation modeling revealed that vegetation and mean annual temperature had a key direct impact on the bacterial diversity and composition, respectively. Climate also indirectly affected bacterial communities, mainly through shaping soil pH and vegetation. These results indicate that the soil depth has a different impact on the bacterial α-diversity, whole bacterial composition, and specific taxa in the 0-30-cm surface layers of seasonally frozen soil, which were mainly determined by various environmental factors.

Effect of Ejiao (Asini Corii Colla) and Turtle Carapace Glue on Gut Microbiota in Nude Mice with Uterine Fibroids Based on High-Throughput Sequencing of 16SrRNA Gene.

Objective To observe the effects of Asini Corii Colla, turtle carapace glue, and other drugs on the intestinal flora of nude mice with uterine fibroids model, so as to provide evidence for the clinical application of drugs. Methods Set up five groups: blank control group, turtle carapace glue group, turtle carapace glue and ejiao 4 : 1 mixed group, turtle carapace glue and ejiao 1 : 1 mixed group, and turtle shell glue and Salvia miltiorrhiza (danshen) 1 : 1 mixed group. Then, the model nude mice were fed ejiao, turtle carapace glue, and other corresponding drugs. Before administration, 2 weeks after administration, and 4 weeks after administration, the feces of the model nude mice were taken respectively, subpacked into labeled cryotubes, and stored at −80°C. All samples were sent for gene sequencing after completion. The differences in gut microbiota and abundance in different groups were compared by 16SrRNA segment sequencing. Results ① There were differences in flora composition and a relative abundance among the groups, but the strains with a high relative abundance were Bacteroides, Firmicutes, and Proteobacteria; ② there were significant differences in the community structure and composition of intestinal flora between nude mice treated for 4 weeks and those not treated (p < 0.05); ③ after 4 weeks of administration, the relative abundance of Bacteroidetes in each group was higher than that before administration, and the relative abundance of Firmicutes decreased. Conclusion Asini Corii Colla, turtle carapace glue, and other drugs with different compatibility ratios can change the composition of intestinal flora in nude mice with uterine fibroids to a certain extent; the decrease in the relative abundance of Firmicutes and the increase in the relative abundance of Bacteroidetes were important structural changes of intestinal flora in nude mice at 4 weeks after administration.

High peatland methane emissions following permafrost thaw: enhanced acetoclastic methanogenesis during early successional stages

Abstract. Permafrost thaw in northern peatlands often leads to increased methane (CH4) emissions, but the underlying controls responsible for increased emissions and the duration for which they persist have yet to be fully elucidated. We assessed how shifting environmental conditions affect microbial communities and the magnitude and stable isotopic signature (δ13C) of CH4 emissions along a thermokarst bog transect in boreal western Canada. Thermokarst bogs develop following permafrost thaw when dry, elevated peat plateaus collapse and become saturated and dominated by Sphagnum mosses. We differentiated between a young and a mature thermokarst bog stage (∼ 30 and ∼ 200 years since thaw, respectively). The young bog located along the thermokarst edge was wetter, warmer, and dominated by hydrophilic vegetation compared to the mature bog. Using high-throughput 16S rRNA gene sequencing, we show that microbial communities were distinct near the surface and converged with depth, but fewer differences remained down to the lowest depth (160 cm). Microbial community analysis and δ13C data from CH4 surface emissions and dissolved gas depth profiles show that hydrogenotrophic methanogenesis was the dominant pathway at both sites. However, mean δ13C-CH4 signatures of both dissolved gas profiles and surface CH4 emissions were found to be isotopically heavier in the young bog (−63 ‰ and −65 ‰, respectively) compared to the mature bog (−69 ‰ and −75 ‰, respectively), suggesting that acetoclastic methanogenesis was relatively more enhanced throughout the young bog peat profile. Furthermore, mean young bog CH4 emissions of 82 mg CH4 m−2 d−1 were ∼ 3 times greater than the 32 mg CH4 m−2 d−1 observed in the mature bog. Our study suggests that interactions between the methanogenic community, hydrophilic vegetation, warmer temperatures, and saturated surface conditions enhance CH4 emissions in young thermokarst bogs but that these favourable conditions only persist for the initial decades after permafrost thaw.

Combined Oral Contraceptive Treatment Does Not Alter the Gut Microbiome but Affects Amino Acid Metabolism in Sera of Obese Girls With Polycystic Ovary Syndrome.

Background: The gut microbiome is altered in obese adolescents with polycystic ovary syndrome (PCOS), and is associated with free testosterone, metabolic markers, and insulin resistance. Combined oral contraceptives (OCP) are a primary treatment for PCOS and decrease testosterone, but the effect on the serum metabolome or gut microbiome in obese adolescents with PCOS is unknown. Objective: Contrast gut microbiome profiles, targeted serum metabolomics, hormone levels, and metabolic measures in adolescents with PCOS and obesity with and without OCP treatment. Methods: Adolescent girls with obesity and PCOS underwent stool and fasting blood collection and MRI for hepatic fat fraction. Fecal bacteria were profiled by high-throughput 16S rRNA gene sequencing and fasting serum metabolomics performed with high resolution mass spectrometry. Groups were contrasted using t-tests and principle least squares discrimination analysis (PLS-DA). Associations between bacterial taxa, baseline metabolic measures, hormone levels and the metabolome were conducted using Spearman analysis. Analyses were adjusted for false discovery rate. Results: 29 adolescents with obesity [Untreated N = 21, 16 ± 1.2 years, BMI%ile 36.5 ± 3.0; OCP N = 8, 15.5 ± 0.9 years, BMI%ile 32.5 ± 3.9] participated. Of the untreated adolescents, N = 14 contributed serum for metabolomic analysis. Participants on OCP therapy had lower free testosterone and free androgen index (p < 0.001) and higher sex hormone binding globulin. There was no difference in measures of fasting glucose, insulin, lipids or HOMA-IR between groups. PLS-DA of serum metabolomics showed discrimination between the groups, secondary amino acid changes. Untreated and OCP had similar stool microbiome α-diversity based on evenness (p = 0.28), richness (p = 0.39), and Shannon diversity (p = 0.24) and global microbial composition (β-diversity, p = 0.56). There were no differences in % relative abundance at any level. Bacterial α-diversity was negatively associated with serum long chain fatty acids and branched chain amino acids. A higher %relative abundance of family Ruminococcaceae was significantly associated with serum bile acids and HOMA-IR. Conclusion: Despite hormone and serum amino acid differences, girls treated with OCP had similar metabolic and gut microbiome profiles compared to the untreated PCOS group. The association between bacterial α-diversity, Ruminococcaceae, clinical markers and long chain fatty acids suggests a potential role of the gut microbiome in the pathogenesis of the metabolic comorbidities in PCOS.

The amendment of Organic matters enhances the anaerobic dechlorination of Polychlorinated Biphenyls in Paddy Soil.

The toxicity of high-chlorinated polychlorinated biphenyls (PCBs) can be efficiently reduced through anaerobic dechlorination. However, this approach suffers a lot in face of in situ microbial remediations, like a shortage of biomass. In this study, we showed that the amendment of organic matters could help microbiota in paddy soil with anaerobic dechlorination and greatly shortened the lag period. The presence of organic matters offered a better environment for dechlorinating bacteria. They provided not only a more strictly anaerobic milieu but also copious carbon sources. By using high-throughput 16S rRNA gene sequencing, genera Dehalobacter, Dehalobacterium, and Desulfitobacterium capable of dechlorination were identified in enriched cultures. Taken together, this study proved that extra organic matters can promote anaerobic dechlorination in paddy soil slurry microcosm systems, which provides new insights into the bioremediation of PCB-contaminated soils.

Specific characteristics of the microbial community in the groundwater fluctuation zone.

Groundwater level fluctuation is a common natural phenomenon that causes alternate changes in oxygen, moisture, and biogeochemical processes in sediments. Microbes are sensitive to these environmental changes. Therefore, a specific microbial community is proposed to form in the groundwater fluctuation zone (GFZ). The vertical distributions of microbial abundance, diversity, and functional microbes and genes in sediment profiles were investigated, focusing on the GFZ, using high-throughput 16S rRNA gene sequencing, qPCR, and the Functional Annotation of Prokaryotic Taxa (FAPROTAX) approach. The relationships between chemical variables and microbial community structure were investigated by redundancy analysis (RDA). Results showed that the microbial abundance and microbial community richness and diversity were higher in the sediments of the GFZ. The nitrate reducers prefer to stay just below the groundwater level in the GFZ. The predominant microbes in the GFZ functioned as nitrifiers and Fe-oxidizers. The specific community in the GFZ is mainly related to NO3- and Fe(III) in the sediment. Consequently, the biochemical processes nitrification and Fe- and Mn-oxidation sequentially happen above the nitrate-reduction zone near the groundwater level in the GFZ. These results provide new knowledge in the biogeochemistry cycle of the GFZ and its disturbance on the vertical distribution and transport of biogenic elements and contaminants.

Community Vertical Composition of the Laguna Negra Hypersaline Microbial Mat, Puna Region (Argentinean Andes).

Simple SummaryThe Laguna Negra is a high-altitude hypersaline lake located in the Puna region in Argentina, hosting microbial mats and modern stromatolites, microbially formed rocks found throughout the geological record. Some recent studies have shown the relevance of the lakes in this region for (i) the discovery of new extremophiles, particularly those tolerant to high UV and, furthermore, (ii) the study of biosignatures in stromatolites. In this work, a detailed survey, layer by layer, of the microbial diversity of the most widespread microbial mat in the Laguna Negra was reported, to unravel the spatial arrangement of the microbial community. The results reveal the vertical distribution of the main prokaryotic microbial taxa, and underline abundant Deinococcus-Thermus at the top of the microbial mat with high amounts of deinoxanthin, which may help the total community to cope with high UV radiation. This study allows a better understanding of the community strategies to thrive under environmental stressors in the Laguna Negra and its counterparts in the Altiplano-Puna region. The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region.