Bacteroidetes Group Research Articles

Integrated analysis of intestinal microbial community and muscle transcriptome profile in rabbits

Intestinal microbial community plays an important part in maintaining health and skeletal muscle development in livestock. This study is the first of its kind in the world. In order to better understand the relationship between gut microbiota and gene expression in skeletal muscle of rabbits, caecum contents and longissimus dorsi tissues of rabbits at 0 d (S1), 35 d (S2) and 70d (S3) were collected and subjected for 16S rRNA sequencing and transcriptome sequencing. Our results showed that, among three groups of rabbits, Firmicutes and Bacteroidetes were the dominant phyla at the phylum level, while Akmansia, Bacteroides and Ruminobacter were the dominant genera at the genus level, and the relative abundance of Akmansia and Bacteroides increased firstly and then decreased from 0 d to 70 d. By analyzing the transcriptome sequencing data, we identified 2866, 2446 and 4541 differentially expressed genes (DEGs) in S1 vs S2, S2 vs S3 and S1 vs S3 groups, respectively. Finally, we performed correlation analysis between gut microbiota and the expression levels of muscle development-related genes of rabbits at 0 d and 70 d. Compared with 0 day old rabbits, in 70 day old rabbits Acinetobacter and Cronbacter with decreased abundance, and Ruminococcaceae_UCG-014 and Ruminococcus_1 with increase abundance is beneficial to caecum health in rabbits. These results will lay a foundation for further re-searches about the relationship between caecum microflora and muscle development in rabbits.

Human Gut Microbiome Before and After Bariatric Surgery in Obese Patients with and Without Type 2 Diabetes.

Bariatric surgery, a significant intervention for obesity, may influence weight loss through changes in gut microbiota, particularly the Firmicutes and Bacteroidetes. This study explores these potential shifts and their metabolic implications. We conducted a cross-sectional study involving patients who had undergone bariatric surgery. Stool samples were collected at baseline, 3 months, and 6 months post-operation. We performed DNA extraction and quantified the bacterial phyla Firmicutes and Bacteroidetes to assess changes in the gut microbiota over time. Our research revealed a significant alteration in the gut microbiota following bariatric surgery. In diabetic individuals, there was a marked increase in the average number of Firmicutes bacteria at both 3 and 6 months post-operation, compared to pre-surgery levels. In contrast, non-diabetic subjects experienced a notable decrease in Firmicutes during the same timeframe. Regarding Bacteroidetes bacteria, the trend was reversed; diabetic patients showed a significant reduction, while non-diabetics exhibited an increase after the surgery. These findings highlight the dynamic changes in gut microbiota composition associated with bariatric surgery and its potential link to metabolic changes post-operation. These findings suggest that obesity alters the gut's microbial composition. The observed bacterial fluctuations, particularly in the dominant Firmicutes and Bacteroidetes groups, are likely contributors to the weight loss experienced post-surgery. This alteration in gut bacteria underscores the complex interplay between microbiota and metabolic health, highlighting potential avenues for therapeutic intervention.

Coevolution of specific gut microbiota of Min pig with host cold adaptation through enhanced vitamin B1 synthesis.

Min pigs exhibit remarkable cold tolerance, where vitamin B1 synthesis by gut microbiota is crucial for the host's energy metabolism. However, the role of this synthesis in cold adaptation of Min pigs are not yet fully understood. This study utilized 16S rRNA amplicon and metagenomic sequencing to examine seasonal variations in the gut microbiota of Min pigs. Results indicated a significant rise in microbial diversity in winter, with the Bacteroidetes group being the most notably increased. The vitamin B1 biosynthetic pathway was significantly enriched during winter, with six significantly upregulated genes (ThiC, ThiD, ThiE, ThiG, ThiH, and ThiL) showing strong evidence of purifying selection. Among the six vitamin B1 synthesis genes significantly upregulated during winter, the increase was mainly due to a marked elevation in several sequences from specific microbial species. Binding energy analysis revealed that, except for ThiL, the average substrate binding energy of the top 10 sequences with the largest seasonal differences was significantly lower than those of the 10 sequences with the smallest differences. Furthermore, most of these sequences were uniquely prevalent in Min pigs and were not found in the homologous sequences of Duroc pigs. Bacteroidetes and Bacteroidales were identified as the primary contributors to these gene sequences. This research provides valuable insights for developing innovative cold-resistant feed and probiotics.

Assessment of Lactobacillus rhamnosus mediated protection against arsenic-induced toxicity in zebrafish: a qPCR-based analysis of Firmicutes and Bacteroidetes groups and embryonic development.

Arsenic poses a significant health risk worldwide, impacting the gut microbiota, reproductive health, and development. To address this issue, a cost-effective method like probiotic supplementation could be beneficial. However, the interplay between arsenic toxicity, probiotics, gut microbiota, and maternal transcript modulation remains unexplored. This study investigates the impact of Lactobacillus rhamnosus (L. rhamnosus) DSM 20021 on the proportions of Firmicutes and Bacteroidetes, as well as its effects on embryonic development in zebrafish induced by arsenic trioxide (As2O3). Adult zebrafish were exposed to both high and environmentally relevant concentrations of As2O3 (10, 50, and 500ppb) for 1, 6, and 12weeks. qPCR analysis revealed increased proportions of Firmicutes and Bacteroidetes in all As2O3-exposed and As2O3 + L. rhamnosus-exposed groups, while no significant changes were observed in groups exposed only to L. rhamnosus DSM 20021. The larvae, exposed to 500ppb of As2O3 for 12weeks, exhibited low growth, decreased survival rates, and morphological deformities. However, these adverse effects were reversed upon exposure to only L. rhamnosus DSM 20021. Furthermore, the expression of DVR1 and ABCC5, which are involved in defense against xenobiotics and embryo development, decreased significantly in As2O3 (500ppb) and As2O3 (500ppb) + L. rhamnosus-exposed groups, whereas ameliorative effects were observed in only L. rhamnosus DSM 20021-exposed groups.

Effects of long-term exposure to the herbicide nicosulfuron on the bacterial community structure in a factory field

This study aims to investigate the effects of long-term nicosulfuron residue on an herbicide factory ecosystem. High-throughput sequencing was used to investigate the environmental microbial community structure and interactions. The results showed that the main contributor to the differences in the microbial community structure was the sample type, followed by oxygen content, pH and nicosulfuron residue concentration. Regardless of the presence or absence of nicosulfuron, soil, sludge, and sewage were dominated by groups of Bacteroidetes, Actinobacteria, and Proteobacteria. Long-term exposure to nicosulfuron increased alpha diversity of bacteria and archaea but significantly decreased the abundance of Bacteroidetes and Acidobateria compared to soils without nicosulfuron residue. A total of 81 possible nicosulfuron-degrading bacterial genera, e.g., Rhodococcus, Chryseobacterium, Thermomonas, Stenotrophomonas, and Bacillus, were isolated from the nicosulfuron factory environmental samples through culturomics. The co-occurrence network analysis indicated that the keystone taxa were Rhodococcus, Stenotrophomonas, Nitrospira, Terrimonas, and Nitrosomonadaceae_MND1. The strong ecological relationship between microorganisms with the same network module was related to anaerobic respiration, the carbon and nitrogen cycle, and the degradation of environmental contaminants. Synthetic community (SynCom), which provides an effective top-down approach for the critical degradation strains obtained, enhanced the degradation efficiency of nicosulfuron. The results indicated that Rhodococcus sp. was the key genus in the environment of long-term nicosulfuron exposure.

Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms

The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.

Microbial pioneers of plastic colonisation in coastal seawaters

Plastics, when entering the environment, are immediately colonised by microorganisms. This modifies their physico-chemical properties as well as their transport and fate in natural ecosystems, but whom pioneers this colonisation in marine ecosystems? Previous studies have focused on microbial communities that develop on plastics after relatively long incubation periods (i.e., days to months), but very little data is available regarding the earliest stages of colonisation on buoyant plastics in marine waters (i.e., minutes or hours). We conducted a preliminary study where the earliest hours of microbial colonisation on buoyant plastics in marine coastal waters were investigated by field incubations and amplicon sequencing of the prokaryotic and eukaryotic communities. Our results show that members of the Bacteroidetes group pioneer microbial attachment to plastics but, over time, their presence is masked by other groups – Gammaproteobacteria at first and later by Alphaproteobacteria. Interestingly, the eukaryotic community on plastics exposed to sunlight became dominated by phototrophic organisms from the phylum Ochrophyta, diatoms at the start and brown algae towards the end of the three-day incubations. This study defines the pioneering microbial community that colonises plastics immediately when entering coastal marine environments and that may set the seeding Plastisphere of plastics in the oceans.

Effects of integrated multi-trophic aquaculture on microbial communities, antibiotic resistance genes, and cultured species: A case study of four mariculture systems

Aquaculture is an important protein source in many countries, including China. Integrated multitrophic aquaculture (IMTA) is widely used to reduce the environmental pressure of aquaculture and to increase profits. However, effects of IMTA on host immune and metabolic responses, the dynamics of bacterial communities, and antibiotic resistance genes (ARGs) are relatively understudied. In this study, the IMTA mariculture systems with different combinations of the hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂), the whiteleg shrimp (Litopenaeus vannamei), and the alga (Gracilaria bailinae) were constructed to evaluate the effects of different culture systems on the aquatic environment and cultured species during the initial stage of aquaculture. Results showed that G. bailinae could effectively remove inorganic nutrients accumulated in water, which in turn significantly promoted growth and enhanced non-specific immunity and glycolipid metabolism in the hybrid grouper. Although ARGs were present throughout the culture process, the relative abundance of ARGs in three of the four culture systems decreased with culture time. This was especially the case in the monoculture and the fish-algal IMTA systems, indicating that these aquaculture systems had a scavenging effect on ARGs in the environment. Correlation and network analyses indicated that ARGs were not significantly correlated with environmental factors but were closely related to bacterial communities. Approximately 25 bacterial groups of Bacteroidetes and Proteobacteria were significantly correlated with ARGs, including aminoglycoside, beta-lactamase, chloramphenicol, and multidrug resistance genes. Moreover, tnpA-07, a transposase gene, indirectly affected ARGs through its interaction with Acteroidetes and Proteobacteria. This study provides insights into further optimizing culture methods and controlling the spread and ecological risk of ARGs in IMTA systems.

Influence of selected factors on the Firmicutes, Bacteroidetes phyla and the Lactobacillaceae family in the digestive tract of sheep

In this study, we used 10 healthy sheep, which gave birth to healthy twins. Stool samples were collected from mothers and their offspring 3 times during the study (0, 28 and 56 day postpartum). Milk samples were taken from the mothers at the same time. RT PCR analysis of faeces and milk was performed in order to assess the level of bacteria from the Firmicutes and Bacteroidetes phyla including the family Lactobacillaceae (phylum Firmicutes). The composition of mother's milk was also analyzed and their BCS. The data were compiled statistically. The obtained results showed that the level of the studied groups of bacteria may change due to the change of diet. Additionally, there were significant differences between lambs and mothers in the levels of the studied groups of bacteria. Analysis also shown that in the digestive system of mothers was a smaller disproportion in the level of the studied bacterial phyla than in lambs. The results also indicated the occurrence of differences in the bacterial composition at the individual level, both in ewes and their offspring. Additionally, in the conducted experiment, there were differences in the level of Firmicutes and Bacteroidetes groups depending on the sex.

Macroalgal release of dissolved organic carbon in coral reef and its interaction with the bacteria associated with the coral Porites lutea.

Macroalgae supersede corals in the reefs worldwide, converting the coral-dominant systems into algal-dominant ones. Dissolved organic carbon (DOC) released by macroalgae play a prominent role in degrading the coral reefs by stimulating the bacterial growth and metabolism. However, the long-term remineralization of macroalgal DOC and their contribution to the carbon pool are least studied. In this study, we quantified the DOC released by five species of macroalgae that affected live corals through their physical contact and their subsequent remineralization for 100 days by coral mucus bacteria. Also, we analyzed the changes in bacterial community structure after 30 days of exposure to the macroalgal DOC. All the macroalgae released a significant amount of DOC ranging from 2.2 ± 0.17 to 8.1 ± 0.36 μmol C g-1 h-1 (mean ± SD). After 100 days, between 9.2 and 30.9% of the macroalgal DOC remained recalcitrant to bacterial remineralization. There was no apparent change in the dominant bacterial groups exposed to the DOC released by the green macroalgae Caulerpa racemosa and Halimeda sp. In comparison, the Proteobacteria group decreased with a prominent increase in the Firmicutes, Planctomycetes, and Bacteroidetes group in the samples exposed to DOC released by the brown macroalgae Turbinaria ornata, Sargassum tenerrimum, and Padina gymnospora. These inclusive data suggest that the DOC released by different species of macroalgae differed on their lability to microbial mineralization and highlight the comparable patterns in microbial responses to macroalgal exudates across different species.

Metatranscriptomic analysis of colonic microbiota\u2019s functional response to different dietary fibers in growing pigs

BackgroundDietary fibers are widely considered to be beneficial to health as they produce nutrients through gut microbial fermentation while facilitating weight management and boosting gut health. To date, the gene expression profiles of the carbohydrate active enzymes (CAZymes) that respond to different types of fibers (raw potato starch, RPS; inulin, INU; pectin, PEC) in the gut microbes of pigs are not well understood. Therefore, we investigated the functional response of colonic microbiota to different dietary fibers in pigs through metatranscriptomic analysis.ResultsThe results showed that the microbial composition and CAZyme structure of the three experimental groups changed significantly compared with the control group (CON). Based on a comparative analysis with the control diet, RPS increased the abundance of Parabacteroides, Ruminococcus, Faecalibacterium and Alloprevotella but decreased Sutterella; INU increased the relative abundance of Fusobacterium and Rhodococcus but decreased Bacillus; and PEC increased the relative abundance of the Streptococcus and Bacteroidetes groups but decreased Clostridium, Clostridioides, Intestinibacter, Gemmiger, Muribaculum and Vibrio. The gene expression of CAZymes GH8, GH14, GH24, GH38, GT14, GT31, GT77 and GT91 downregulated but that of GH77, GH97, GT3, GT10 and GT27 upregulated in the RPS diet group; the gene expression of AA4, AA7, GH14, GH15, GH24, GH26, GH27, GH38, GH101, GT26, GT27 and GT38 downregulated in the INU group; and the gene expression of PL4, AA1, GT32, GH18, GH37, GH101 and GH112 downregulated but that of CE14, AA3, AA12, GH5, GH102 and GH103 upregulated in the PEC group. Compared with the RPS and INU groups, the composition of colonic microbiota in the PEC group exhibited more diverse changes with the variation of CAZymes and Streptococcus as the main contributor to CBM61, which greatly promoted the digestion of pectin.ConclusionThe results of this exploratory study provided a comprehensive overview of the effects of different fibers on nutrient digestibility, gut microbiota and CAZymes in pig colon, which will furnish new insights into the impacts of the use of dietary fibers on animal and human health.

Protective effect of Bacteroides fragilis LPS on Escherichia coli LPS-induced inflammatory changes in human monocytic cells and in a rheumatoid arthritis mouse model

It has been reported that patients with rheumatoid arthritis (RA) have significantly less bacteria belonging to the Bacteroides group in their microbiota. We speculate that inhibition of cytokine production is impaired in patients with RA owing to their low levels of intestinal bacteria belonging to the Bacteroidetes group. Here we investigated the effect of Bacteroides fragilis lipopolysaccharide (B-LPS) on cytokine production in vitro and on the development of collagen antibody-induced arthritis (CAIA) in DBA/1 mice, an animal model of RA. in vitro culture experiments showed that Escherichia coli LPS (E-LPS)-induced cytokine production from THP-1 monocytic cells and peripheral blood mononuclear cells was significantly suppressed by B-LPS in a dose-dependent manner. A decrease in TNF-α and IL-1β production was also observed in LPS-tolerized macrophages induced by B-LPS at concentrations equal to and higher than that of E-LPS. Similar results were obtained when autoclaved feces were used to induce cytokine production instead of E-LPS. In in vivo experiments using CAIA models, B-LPS had no adverse effects even when administered at 10 times the concentration of E-LPS, which elicits severe arthritis. In addition, simultaneous administration of high dose B-LPS with E-LPS or administration of B-LPS prior to E-LPS significantly suppressed arthritis development in CAIA model animals when compared with administration of E-LPS alone. These results suggest that increasing certain bacterial groups such as Bacteroides is an effective strategy for preventing arthritis development in patients with RA.

Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond

In the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA genes showed the relative abundance of Delta-Proteobacteria and Bacteroidetes groups performing sulphur respiration and organic matter degradation, archaeal groups of anaerobic sulphur respiring Crenarchaeotae, and chemolithoautotrophic ammonia oxidizers belonging to Thaumarchaeota. The presence of these diverse bacterial and archaeal communities denotes their significant roles in the cycling the carbon, nitrogen, and sulphur thereby bringing out efficient bioremediation in the bioaugmented zero-water exchange shrimp culture pond. Similarly, the functional gene-specific study showed the predominance of Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrosopumilus maritimus (ammonia-oxidizing archaea), and Candidatus Kuenenia (anaerobic ammonia-oxidizing bacteria) in the system, which points to their importance in the removal of accumulated ammonia. Thus, this study paves the way for understanding the microbial communities, specifically the ammonia oxidizers responsible for maintaining healthy and optimal environmental conditions in the bioaugmented zero-water exchange shrimp culture pond.

Metagenome and analysis of metabolic potential of the microbial community in pit mud used for Chinese strong-flavor liquor production

Complex microbiomes of pit mud (PM) play significant roles in imbuing flavors and qualities of Chinese strong-flavor liquor (CSFL) during fermentation. However, understanding both of the taxonomic and functional diversity of the whole microorganisms in PM still remain a major challenge. Here, PM microbiomes were investigated based on metagenomic sequencing, assembly and binning. Metagenomic data revealed that Euryarchaeota was the predominant phylum, followed by Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. For further functional exploration, 703 metagenome-assembled genomes (MAGs), including 304 novel strains, 197 novel species, and 94 novel genera were reconstructed. Three primary groups of Firmicutes (n = 406), Euryarchaeota (n = 130) and Bacteroidetes (n = 74), particularly genus of them Syntrophomonas, Thermacetogenium and Clostridium, methanogens (Methanobacterium, Methanoculleus, and Methanosarcina), Proteiniphilum and Prevotella, contained most of metabolic potential genes. Additionally, Chloroflexi was firstly reported to have potential to be involved in the caproic acid (CA) production. Bacteroidetes could be the key phylum to synthesize terpenes, and Armatimonadetes, Firmicutes, Ignavibacteriae and Verrucomicrobia may possess the same metabolic potential as well. Overall, this study will significantly improve our understanding of the diverse PM microbiome and help guide the future exploration of microbial resources for modifying PM fermentation processes.

Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey

Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%) groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.

Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids

Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol-1-phosphate (G1P), while Bacteria/Eukarya produce membranes consisting of fatty acids ester-bound to glycerol-3-phosphate (G3P). This dichotomy in membrane lipid composition (i.e., the ‘lipid divide’) is believed to have arisen after the Last Universal Common Ancestor (LUCA). A leading hypothesis is that LUCA possessed a heterochiral ‘mixed archaeal/bacterial membrane’. However, no natural microbial representatives supporting this scenario have been shown to exist today. Here, we demonstrate that bacteria of the Fibrobacteres–Chlorobi–Bacteroidetes (FCB) group superphylum encode a putative archaeal pathway for ether-bound isoprenoid membrane lipids in addition to the bacterial fatty acid membrane pathway. Key genes were expressed in the environment and their recombinant expression in Escherichia coli resulted in the formation of a ‘mixed archaeal/bacterial membrane’. Genomic evidence and biochemical assays suggest that the archaeal-like lipids of members of the FCB group could possess either a G1P or G3P stereochemistry. Our results support the existence of ‘mixed membranes’ in natural environments and their stability over a long period in evolutionary history, thereby bridging a once-thought fundamental divide in biology.

Effect of Bacillus pumilus 3-19 protease on growth parameters and gut microbiome of broiler chickens

The objective of the study was to determine the effect of adding protease obtained from the Bacillus pumilus 3-19 strain to the diet of Hubboard broiler chickens on the growth indicators of poultry and the composition of the cecum microbiota of broiler chickens. As a result of metagenomic analysis of 16S rRNA genes in the contents of the cecum of chickens, it was shown that the control and experimental groups formed two separate clusters, which indicates differences in microbial communities in these two groups. Analysis of alpha diversity showed an increase in species richness in the group of chickens that received protease as a feed additive. On day 35, both groups were dominated by bacterium of Firmicutes (21.13 — 49.01%) and Bacteroidetes (37.68 — 67.72%) groups. It was shown that in the group of chickens receiving protease as a feed additive, the average daily gain in live weight was higher than in the control group by 0.5 kg (P < 0.05). The introduction of protease resulted in an increased F/B ratio, which was positively correlated with chicken body weight. Thus, the addition of B. pumilus 3-19 protease to broiler feed leads to improved feed intake and digestibility, which is of great importance for reducing the cost of the final product. The use of protease regulates the cecum microbiota of broiler chickens and increases microbial diversity on 35 day of chicken growth.

Evidence for positive response of soil bacterial community structure and functions to biosynthesized silver nanoparticles: An approach to conquer nanotoxicity?

The environmental impacts of biosynthesized nanoparticles on the soil bacterial community assemblage and functions are not sufficiently understood. Given the broad application of silver nanoparticles (AgNPs), the present study aims to reveal the effects of biosynthesized AgNPs (~12 nm) on the soil bacterial community structure and functions. Specifically, we used a quantitative real-time PCR (qPCR) approach to quantify the relative abundance of bacterial taxon/group and representative functional genes (AOA, AOB, NirK, NirS, NosZ, and PhoD). Results showed high relative abundance of Actinobacteria (1.53 × 107, p = 0.000) followed by Alphaproteobacteria (1.18 × 106, p = 0.000) and Betaproteobacteria (2.01 × 106, p = 0.000) in the soil exposed to biosynthesized AgNPs (100 mg/kg soil) after 30 days of treatment. Bacteroidetes group was observed to be negatively affected by AgNPs treatment. In the case of functional genes abundance, more pronounced impact was observed after 30 days of application. The biosynthesized AgNPs treatment accounted for significant increase in the relative abundance of all targeted functional genes except NirS. We conclude that the biosynthesized AgNPs did not cause toxic effects on nitrifiers, denitrifiers and organic phosphorus metabolizing bacterial community. While AgNO3 caused higher toxicity in the soil bacterial community structure and function. Based on our findings, we propose two key research questions for further studies; (i) is there any adaptation strategy or silver resistance embraced by the soil microbial community? and (ii) are biosynthesized nanoparticles environmentally safe and do not pose any risk to the soil microbial community? There is a necessity to address these questions to predict the environmental safety of biosynthesized AgNPs and to apply appropriate soil management policies to avoid nanotoxicity. Since this study provides preliminary evidence for the positive response of the soil bacterial community structure and functions to biosynthesized AgNPs, additional investigations under different soil conditions with varying soil physico-chemical properties are required to authenticate their environmental impact.

Impact of Anthropogenic Organic Matter on the Distribution Patterns of Sediment Microbial Community from the Yangtze River, China

How microbes respond to substantial and increasing anthropogenic disturbance remains an open question in river systems. We tested the hypothesis that the source and distribution of anthropogenic organic matter (OM) were significant factors affecting the spatial variation of the microbial community composition of the Yangtze River sediments. Bulk geochemical proxies and lignin phenols suggested a general decrease of terrestrial C3 plants or soil OM input from the middle to the lower reaches. Fecal sterols inferred higher sewage contamination levels in the middle reaches. Polycyclic aromatic hydrocarbons (PAHs) distribution indicated a dominant biomass and coal combustion signal in the middle reaches, whereas a mixed source including petroleum combustion in the lower reaches. Phylogenetic analysis revealed a large portion of Methanobacteria and Verrucomicrobia enriched in the middle reaches, whereas OM-degrading bacteria, including Flavobacteria, Acidobacteria, and Alphaproteobacteria were dominant in the lower reaches. Quantitative PCR analyses and multivariate analysis further demonstrated that sources and distribution of OM had combined effects in shaping alpha and beta-diversity of sediment microbial communities. Sewage discharge and incomplete OM combustion, respectively, were associated with Methylococcaceae, Chloroflexi, and Bacteroidetes groups. This study provides a foundation for further understanding of the river sediment microbial composition, considering the continued increase of anthropogenic influences.

Response of fermenting bacterial and methanogenic archaeal communities in paddy soil to progressing rice straw degradation

Rice straw is one of the major organic materials introduced to rice field soils and its incorporation strongly enhances the emission of CH4. We incubated unamended and straw-amended Italian paddy soil under anaerobic conditions and studied the functional (carbon source, rate, pathway) and structural (abundance, taxonomic composition) responses of methanogenic microbial communities progressively in samples taken after 0, 30, 60, 90, and 120 days. Initially, rice straw significantly enhanced CH4 production rates. Later on, the values strongly decreased with the progress of rice straw degradation. The contribution of rice straw to CH4 production decreased with progressing anaerobic incubation. This decrease was paralleled by an increase of the contribution of hydrogenotrophic methanogenesis to CH4 production indicating a change in the network of bacterial and archaeal microbial communities. The methanogenic and bacterial communities indeed strongly responded to rice straw amendment and exhibited a distinct succession over the subsequent degradation periods. Network analysis of both 16S rRNA and Methyl coenzyme M reductase (mcrA) genes showed apparent co-occurrence of fermenting bacteria and CH4-producing archaea belonging to distinct operational taxonomic units (OTU) demonstrating strong functional and structural responses of methanogenic microbial communities to progressing rice straw degradation. Clostridiales, Fibrobacterales, and two Bacteroidetes groups (WCHB1-32 and Sphingobacteriales), as well as Anaerolineales and Bacteroidetes environmental group vadinHA17 were important bacterial taxa. Acetoclastic Methanosarcina and Methanothrix (‘Methanosaeta’) as well as hydrogentrophic Methanocella were important archaeal taxa involved in rice straw degradation.