Relative Abundance Of Gammaproteobacteria Research Articles

Hyposalinity elicits physiological responses and alters intestinal microbiota in Korean rockfish Sebastes schlegelii.

Global warming significantly impacts aquatic ecosystems, with changes in the salt environment negatively affecting the physiological responses of fish. We investigated the impact of hyposalinity on the physiological responses and intestinal microbiota of Sebastes schlegelii under the context of increased freshwater influx due to climate change. We focused on the osmoregulatory capacity, oxidative stress responses, and alterations in the intestinal microbiome of S. schlegelii under low-salinity conditions. Our findings revealed compromised osmoregulatory capacity in S. schlegelii under low-salinity conditions, accompanied by the activation of oxidative stress responses, indicating physiological adaptations to cope with environmental stress. Specifically, changes in Na+/K+-ATPase (NKA) activity in gill tissues were associated with decreased osmoregulatory capacity. Furthermore, the analysis of the intestinal microbiome led to significant changes in microbial diversity. Exposure to low-salinity environments led to dysbiosis, with notable decreases in the relative abundance of Gammaproteobacteria at the class level and specific genera such as Enterovibrio, and Photobacterium. Conversely, Bacilli classes, along with genera like Mycoplasma, exhibited increased proportions in fish exposed to low-salinity conditions. These findings underscore the potential impact of environmental salinity changes on the adaptive capacity of fish species, particularly in the context of aquaculture. Moreover, they highlight the importance of considering both physiological and microbial responses in understanding the resilience of aquatic organisms to environmental stress. Additionally, they highlight the importance of intestinal microbiota analyses in understanding the immune system and disease management in fish.

Multiscalar Evaluation of the Water Distribution System and Diarrheal Disease Risk in Addis Ababa, Ethiopia.

Despite growing urbanization, our understanding of the impacts of water and sanitation on human health has largely come from studies in rural sectors. To this end, we collected data at both regional (water quality measures from water treatment systems) and community (cross-sectional surveys) scales to examine determinants of enteric pathogen infection and diarrheal disease among infants in Addis Ababa, Ethiopia. Regionally, the Legedadi water treatment plant had significantly lower heterotrophic plate counts, total coliform counts, and fecal coliform counts compared with the Gefersa water treatment plant. The number of pathogen types in infant stool also differed by plant. Decreases in chlorine levels and increases in the relative abundance of Gammaproteobacteria with distance from treatment plants suggest a compromised water distribution system. In communities, infants in households that obtained water from yard pipes or public taps had significantly lower odds of diarrhea compared to households that had water piped into their dwellings (OR = 0.35, 95% CI 0.16, 0.76, and OR = 0.39, 95% CI 0.15, 1.00, respectively). Similarly, infants in households that boiled or filtered water had significantly lower odds of diarrhea compared to households that did not treat water (OR = 0.40, 95% CI 0.19, 0.86 and OR = 0.23, 95% CI 0.06, 0.84, respectively). Integrating multiscalar data better informs the health impacts of water in urban settings.

New insights into the role of soil properties in driving cadmium-induced hormesis in soil alkaline phosphatase under vegetation cover change

This study investigated the hormetic responses of soil alkaline phosphatase (ALP) to exogenous Cd under five different vegetation cover types in a typical coastal wetland, including mudflat (Mud), Phragmites australis (PA), Spartina alterniflora (SA), Metasequoia glyptostroboides (MG), and Cinnamomum camphora (CC). The results showed that the activity of soil ALP was significantly enhanced by exogenous 0.3–1.0, 0.2–0.8, 0.05–0.3, 0.05–0.6, and 0.05–0.60 mg Cd /kg in Mud, PA, SA, MG, and CC, respectively. Moreover, the Horzone (an integrated indicator of the stimulation phase) of Mud and PA was significantly higher than that of SA, MG, and CC. Multiple factor analysis revealed that soil chemical properties and soil bacteria community play an important role in the hormetic effect of soil ALP to Cd stress. Soil electric conductivity (EC) and the relative abundance of Gammaproteobacteria were also identified as key drivers of the hormetic effects of Cd on soil ALP under five vegetation cover types. These findings suggest that the soil ecosystem had better resistance to exogenous Cd stress under mudflat and native species (PA) than invasive species (SA), and artificial forests (MG and CC) when soil ALP activity was the test endpoint. Consequently, this study is beneficial for future ecological risk assessment of soil Cd contamination under divergent vegetation covers.

Bacterial community structure of electrogenic biofilm developed on modified graphite anode in microbial fuel cell

Formation of electrogenic microbial biofilm on the electrode is critical for harvesting electrical power from wastewater in microbial biofuel cells (MFCs). Although the knowledge of bacterial community structures in the biofilm is vital for the rational design of MFC electrodes, an in-depth study on the subject is still awaiting. Herein, we attempt to address this issue by creating electrogenic biofilm on modified graphite anodes assembled in an air–cathode MFC. The modification was performed with reduced graphene oxide (rGO), polyaniline (PANI), and carbon nanotube (CNTs) separately. To accelerate the growth of the biofilm, soybean-potato composite (plant) powder was blended with these conductive materials during the fabrication of the anodes. The MFC fabricated with PANI-based anode delivered the current density of 324.2 mA cm−2, followed by CNTs (248.75 mA cm−2), rGO (193 mA cm−2), and blank (without coating) (151 mA cm−2) graphite electrodes. Likewise, the PANI-based anode supported a robust biofilm growth containing maximum bacterial cell densities with diverse shapes and sizes of the cells and broad metabolic functionality. The alpha diversity of the biofilm developed over the anode coated with PANI was the loftiest operational taxonomic unit (2058 OUT) and Shannon index (7.56), as disclosed from the high-throughput 16S rRNA sequence analysis. Further, within these taxonomic units, exoelectrogenic phyla comprising Proteobacteria, Firmicutes, and Bacteroidetes were maximum with their corresponding level (%) 45.5, 36.2, and 9.8. The relative abundance of Gammaproteobacteria, Clostridia, and Bacilli at the class level, while Pseudomonas, Clostridium, Enterococcus, and Bifidobacterium at the genus level were comparatively higher in the PANI-based anode.

Co-variance between free-living bacteria and Cochlodinium polykrikoides (Dinophyta) harmful algal blooms, South Korea

To understand the co-variance between common free-living bacteria and Cochlodinium polykrikoides harmful algal blooms (HABs) and their metabolic functions, we investigated 110 sampling sites in the Southern Sea of South Korea. These sampling sites were divided into three groups based on environmental factors and phytoplankton data with a similarity of 85% using non-metric multidimensional scaling. One group represented high-severity C. polykrikoides blooms, while the other two represented low-severity or no blooms. In high-severity HABs, inorganic phosphorous and dissolved organic carbon concentrations were strongly correlated with C. polykrikoides density (p < 0.01). This may reflect the changes in biochemical cycling due to inorganic and organic substrates released by HAB cells (or by cell destruction). Furthermore, 88 common bacterial operational taxonomic units (OTUs, with mean relative abundance > 1%) were identified. These included Gammaproteobacteria (36 OTUs), Flavobacteriia (24), Alphaproteobacteria (18), and other taxa (11). When C. polykrikoides blooms intensified, the relative abundances of Gammaproteobacteria also increased. OTU #030 (Flavicella sp., Flavobacteria, 96%) was positively correlated with C. polykrikoides abundance (r = 0.77, p < 0.001). Functional analysis based on the dominant bacterial OTUs revealed that chemoheterotrophy-related functions were more common in high-severity sites of HABs than in other groups. Therefore, the occurrence of HABs highlighted their interactions with bacteria and affected the bacterial community structure and metabolic functions.

Influence of Temperature on Denitrification and Microbial Community Structure and Diversity: A Laboratory Study on Nitrate Removal from Groundwater

Temperature is an extremely important environmental condition in the application of microbial denitrification for nitrate removal from groundwater. Understanding the nitrate removal efficiency of groundwater and the diversity, composition, and structure of microbial communities under different temperature conditions is of great significance for effective mitigation of groundwater nitrate pollution. This study investigated the effects of temperature on denitrification at 15 °C, 25 °C, 40 °C, and 45 °C. Moreover, the characteristics of microbial community structure and diversity were analyzed by combining high-throughput sequencing and polymerase chain reaction methods in order to fully clarify the denitrification efficiency under different temperature conditions. According to laboratory batch experiments and the findings of previous research, glucose was set as the carbon source and changes in “three nitrogen” indicators of the four temperature systems were mainly tested to clarify the effectiveness of nitrate removal. The maximum removal rates of nitrate nitrogen at 15 °C, 25 °C, 40 °C, and 45 °C were 44.05%, 87.03%, 99.26%, and 92.79%, respectively. Therefore, the most efficient nitrate removal can be achieved at 40℃. The Chao abundance indexes in the denitrification systems at 15 °C, 25 °C, 40 °C, and 45 °C were 1873, 352, 466, and 640, respectively. Therefore, the highest species richness was observed at 15 °C, but there were only a few dominant bacteria species. The composition of the bacterial community and the most dominant phylum varied at different temperatures. Among them, Gammaproteobacteria in Proteobacteria phylum plays an important role in the degradation of nitrate nitrogen. The relative abundance of Gammaproteobacteria at 15 °C, 25 °C, 40 °C, and 45 °C were 25.32%, 66.56%, 72.83%, and 3.47%. Tolumonas belongs to Gammaproteobacteria. The relative abundance of Tolumonas at 15 °C, 25 °C, 40 °C, and 45 °C were 9.41%, 65.47%, 62.49%, and 0.03%, respectively. The results of this study show that different temperature conditions affect the diversity, composition, and structure of the microbial community, thereby affecting the efficiency of denitrification for nitrate removal from groundwater.

Potential involvement of the microbiota-gut-brain axis in the neurotoxicity of triphenyl phosphate (TPhP) in the marine medaka (Oryzias melastigma) larvae

Triphenyl phosphate (TPhP), a prevalent pollutant in the aquatic environment, has been reported to induce neurotoxicity (e.g., a suppression in locomotor activity) in fish larvae, posing a great threat to fish populations. However, the underlying mechanism was not fully revealed. In this study, the Oryzias melastigma larvae (21 dph) were exposed to waterborne TPhP (20 and 100 μg/L) for 7 days and a decreased locomotor activity was found. After exposure, the brain transcriptome and communities of gut microbiota were investigated to explore the potential mechanism underlying the suppressed locomotor activity by TPhP. The results showed that 1160 genes in the brain were dysregulated by TPhP, of which 24 genes were identified as being highly associated with the neural function and development (including nerve regeneration, neuronal growth and differentiation, brain ion homeostasis, production of neurotransmitters and etc), suggesting a general impairment in the central nervous system. Meanwhile, TPhP caused disorders in the gut microbiota. The relative abundance of Gammaproteobacteria and Alphaproteobacteria, which can influence the brain functions of host via the microbiota-gut-brain axis, were significantly altered by TPhP. Furthermore, the Redundancy analysis (RDA) revealed positive correlations between the intestinal genera Ruegeria, Roseivivax and Nautella and the dysregulated brain genes by TPhP. These results suggest that TPhP might impair the central nervous system of the O. melastigma larvae not only directly but also through the microbiota-gut-axis (indirectly), contributing to the suppressed locomotor activity. These findings enrich our mechanistic understanding of the toxicity of TPhP in fish larvae and shed preliminary light on the involvement of microbiota-gut-brain axis in the neurotoxicity of environmental pollutants.

Processed Animal Proteins from Insect and Poultry By-Products in a Fish Meal-Free Diet for Rainbow Trout: Impact on Intestinal Microbiota and Inflammatory Markers.

Sustainability of aquaculture is tied to the origin of feed ingredients. In search of sustainable fish meal-free formulations for rainbow trout, we evaluated the effect of Hermetia illucens meal (H) and poultry by-product meal (P), singly (10, 30, and 60% of either H or P) or in combination (10% H + 50% P, H10P50), as partial replacement of vegetable protein (VM) on gut microbiota (GM), inflammatory, and immune biomarkers. Fish fed the mixture H10P50 had the best growth performance. H, P, and especially the combination H10P50 partially restored α-diversity that was negatively affected by VM. Diets did not differ in the Firmicutes:Proteobacteria ratio, although the relative abundance of Gammaproteobacteria was reduced in H and was higher in P and in the fishmeal control. H had higher relative abundance of chitin-degrading Actinomyces and Bacillus, Dorea, and Enterococcus. Actinomyces was also higher in H feed, suggesting feed-chain microbiome transmission. P increased the relative abundance of protein degraders Paeniclostridium and Bacteroidales. IL-1β, IL-10, TGF-β, COX-2, and TCR-β gene expression in the midgut and head kidney and plasma lipopolysaccharide (LPS) revealed that the diets did not compromise the gut barrier function or induce inflammation. H, P, and H10P50 therefore appear valid protein sources in fishmeal-free aquafeeds.

Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean.

Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5TM XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator’s impact throughout the Caribbean.

Influence of Pelvic Intensity-Modulated Radiation Therapy With Concurrent Cisplatin-Based Chemotherapy of Cervical Cancer on the Vaginal Microbiome.

Pelvic intensity-modulated radiation therapy (IMRT) combined with concurrent chemotherapy is an effective treatment for cervical cancer; however, radiation resistance impairs its clinical benefit. The vaginal microbiome plays an important but poorly understood role in cancer radiochemotherapy. In this study, we investigated the effects of treatment on the overall composition and alteration of the vaginal microbiome in patients receiving pelvic IMRT with concurrent cisplatin-based chemotherapy. We collected samples from twenty patients with cervical cancer and six healthy controls and performed 16S rRNA sequencing. Vaginal microbial composition analysis revealed significant differences between the two groups, but no significant differences between radiation treatment time points. However, the relative abundances of Gammaproteobacteria, Gemmatimonadetes, Gemmatimonadales, Pseudomonadales, Gemmatimonadaceae, Rikenellaceae, Acinetobacter, Desulfovibrio, Prevotella 9, Rikenellaceae RC9 gut group, Turicibacter, and the metagenome increased with time. The results encourage further study into the effects of the vaginal microbiome on cervical cancer treatment strategies, especially radiochemotherapy. Better understanding of these effects could inform new therapeutic approaches to enhance the efficacy of radiochemotherapy.

Oral and intestinal microbial features in pregnant women with hypothyroidism and their correlations with pregnancy outcomes

The purpose of this study was to explore the characteristics of oral and intestinal microbiota of pregnant women with hypothyroidism during pregnancy, and to find the correlations between the changes of flora and pregnancy outcome of pregnant women with hypothyroidism during pregnancy. In this study, oral and intestinal microbial composition was surveyed by using the 16S rRNA sequencing approach in 61 pregnant women (30 with hypothyroidism and 31 normal controls). Sequentially, we validated the differential microbial features by using the quantitative real-time PCR (qPCR) approach in 10 randomly selected pregnant women (5 with hypothyroidism and 5 normal controls). Furthermore, general clinical data and serological indices were added to the analysis to examine the links between oral and intestinal microbiota and pregnancy outcomes. The 16S rRNA results showed that the relative abundances of Gammaproteobacteria were higher in pregnant women in the hypothyroidism group than in those in the control group, whereas the levels of Firmicutes were higher in the control group than in the hypothyroidism group. The serum C-reactive protein level, the weight gain during pregnancy, and the incidence of fetal distress were higher in the hypothyroidism group than in the control group. The QPCR results also showed the same changes of the intestinal microbiota in the two groups. There were significant differences in the oral and intestinal microbiota between pregnant women with hypothyroidism and normal pregnant women. The changes of microbiota is one of the factors influencing the occurrence and development of hypothyroidism during pregnancy.

Utilization of carbon sources in the rice rhizosphere and nonrhizosphere soils with different long-term fertilization management.

Carbon (C) plays an important role in the interaction between plant and rhizosphere microbial communities, but there is still limited information about how C source utilization soil microbial structure responds to soil fertility changes under the double-cropping rice (Oryza sativa L.) system in Southern China paddy fields. Therefore, the effects of long-term (33 years) fertilizer regimes on the characteristics of C utilization in both rhizosphere and nonrhizosphere soils under double-cropping rice fields in Southern China were investigated by using the metagenome sequencing technology. The experiment began in 1986, and included five fertilizer treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic matter, and 70% chemical fertilizer (LOM), and 60% organic matter and 40% chemical fertilizer (HOM). The results showed that the relative abundance of Gemmatimonadetes and Planctomycetia in both the rhizosphere and nonrhizosphere soils was increased by application of rice straw residue and organic manure, whereas the relative abundance of Gammaproteobacteria and Nitrospira was promoted by application of inorganic fertilizers. The largest group of clusters of orthologous groups of proteins categories was "amino acid transport and metabolism" with 16.46% unigenes, followed by "general function prediction only" (12.23%). Regarding the gene ontology categories, biological process were the largest category (174 949, 46.40%), followed by cellular component (126 766, 33.62%), and molecular function (110 353, 29.26%). The principal coordinate analysis indicated that different parts of the root zone were the most important factors affecting the variation of C source utilization bacteria community, and the different fertilizer treatments were the second important factor affecting the variation of C source utilization bacteria community. As a result, the application of fertilization practices had significant effects on the abundance and community composition of C source utilization microbes in paddy soils. The results showed that the combined application of rice straw residue or organic manure with chemical fertilizer practices significantly increases the C source utilization of soil microorganisms in double-cropping rice fields.

Effect of inorganic nutrients on bacterial community composition in oil-bearing sandstones from the subsurface strata of an onshore oil reservoir and its potential use in Microbial Enhanced Oil Recovery.

Microbial Enhanced Oil Recovery (MEOR) is a promising strategy to improve recovery of residual oil in reservoirs, which can be performed by promoting specific indigenous microorganisms. In this study, we performed preliminary evaluation of the possibility of conducting MEOR at Mae Soon reservoir, an onshore reservoir in Northern Thailand. The reservoir’s physicochemical characteristics, including the characteristics of the wells, the oil-bearing sandstone cores, and the reservoir’s produced water, were determined. The microbiological characteristics of the oil wells in the reservoir were also investigated by submerging the reservoir’s sandstone core samples, obtained from 6 oil wells, in the reservoir’s produced water and in the produced water added with inorganic nutrients (KNO3 and NaH2PO4). The uncultured bacteria in both treatments were determined, using tagged 16S rRNA gene amplicon with Ion Torrent Sequencing Analysis. The effects of inorganic nutrients and the reservoir’s parameters on the bacterial communities were analysed. A total number of 16,828 OTUs were taxonomically classified into 89 classes and 584 genera. In the controls (sandstone cores submerged in the produced water), the dominant bacterial populations were related to Deinococcus-Thermus, and Betaproteobacteria; while in the nutrient treated samples, there was a marked increase in the relative abundance of Gammaproteobacteria in three samples. Thermus, Acinetobacter, and Pseudomonas were the most abundant genera, and these are potential microorganisms for MEOR. Analysis of correlations between physiochemical properties of the reservoir and bacterial genera, using spearman’s correlation analysis, suggested that some of the reservoir’s properties, especially of the well and the rock, could influence some bacterial genera. To our knowledge, this is the first demonstration of the effect of inorganic nutrients on alteration of bacterial communities attached to reservoir’s rock, and how the bacterial, physical, and chemical properties of a reservoir were co-analysed to serve as a basis for designing a MEOR process.

Roots and Panicles of the C4 Model Grasses Setaria viridis (L). and S. pumila Host Distinct Bacterial Assemblages With Core Taxa Conserved Across Host Genotypes and Sampling Sites.

Virtually all studied plant tissues are internally inhabited by endophytes. Due to their relevance for plant growth and health, bacterial microbiota of crop plants have been broadly studied. In plant microbiome research the root is the most frequently addressed environment, whereas the ecology of microbiota associated with reproductive organs still demands investigation. In this work, we chose the model grasses Setaria viridis and Setaria pumila to better understand the drivers shaping bacterial communities associated with panicles (representing a reproductive organ) as compared to those associated with roots. We collected wild individuals of both grass species from 20 different locations across Austria and investigated the bacterial assemblages within roots and ripe grain-harboring panicles by 16S rRNA gene-based Illumina sequencing. Furthermore, plant samples were subjected to genotyping by genetic diversity-focused Genotyping by Sequencing. Overall, roots hosted more diverse microbiota than panicles. Both the plant organ and sampling site significantly shaped the root and panicle-associated microbiota, whereas the host genotype only affected root communities. In terms of community structure, root-specific assemblages were highly diverse and consisted of conserved bacterial taxa. In contrast, panicle-specific communities were governed by Gammaproteobacteria, were less diverse and highly origin-dependent. Among OTUs found in both plant tissues, relative abundances of Gammaproteobacteria were higher in panicles, whereas Rhizobiales dominated root communities. We further identified core and non-core taxa within samples of both Setaria species. Non-core taxa included members of the Saccharibacteria and Legionelalles, while core communities encompassed eleven OTUs of seven bacterial orders, together with a set of ten panicle-enriched OTUs. These communities were widespread across root and panicle samples from all locations, hinting toward an evolved form of mutualism through potential vertical transmission of these taxa within Setaria species.

Long-term effects of legume mulching on soil chemical properties and bacterial community composition and structure

Applying legumes as green manure has been reported to improve soil fertility and alter soil bacterial community structure. Few studies have been conducted to determine the effects of Chamaecrista rotundifolia and Arachis pintoi mulching on soil bacterial communities in orchards. In this study, we described the bacterial community in the 0–20 cm soil profile under long-term (approximate 20 years) C. rotundifolia and A. pintoi mulching of persimmon orchards in subtropical and tropical China. The experiment included three treatments: (1) terraced persimmon orchard with A. pintoi mulching (TPA), (2) terraced persimmon orchard with C. rotundifolia mulching (TPC), and (3) terraced persimmon orchard with no vegetation mulching (TPN, CK). Soil chemical properties were significantly altered by long-term A. pintoi and C. rotundifolia mulching. Concentrations of total phosphorus (TP), available nitrogen (AN), soluble organic carbon (SOC), total soluble carbon (TSC), and organic matter (OM) were significantly higher in TPA and TPC soils than in TPN soils; TN and NH4+-N were highest in TPA soils and NO3−-N was highest in TPC soils. Soluble organic nitrogen (SON) and total soluble nitrogen (TSN) concentrations were significantly lower in mulched soils than in TPN soil. Illumina-based sequencing showed that soil bacterial community composition and structure were significantly altered by C. rotundifolia and A. pintoi mulching (TPC and TPA), and the changes in the dominant soil bacterial communities were demonstrated as reductions in the Simpson and Shannon indices. Proteobacteria (relative abundance 37.55%–50.94%) and Acidobacteria (relative abundance 9.47%–12.02%) were enriched in TPA and TPC soils, while Firmicutes (relative abundance 15.74%–22.00%) were higher in TPN soil. Further taxonomic analyses of Proteobacteria revealed that the relative abundance of Gammaproteobacteria and Deltaproteobacteria in PTA and TPC were significantly higher than in TPN, while the Betaproteobacteria in TPA and TPC were significantly lower than in TPN. Genus Phenylobacterium and Escherichia were enriched in TPC, Rhodoplanes and Escherichia were enriched in TPA, while, Kaistobacter, Sphingomonas, Burkholderia, and Enterobacter were enriched in TPN. Family Koribacteraceae classified as Acidobacteria was significantly higher in TPA than in TPN and TPC, and the genus Candidatus Koribacer of Acidobacteria was significantly higher in TPA and TPC than in TPN. In-depth taxonomic analyses of Firmicutes showed the relative abundance of family Bacillaceae, and Streptococcaceae and genus Bacillus and Lactococcus were lower in TPA and TPC than in TPN, while those of family Leuconostocaceae and Lactobacillaceae and genus Pediococcus were higher in TPA and TPC than in TPN. The genus Weissella was only observed in TPC and TPA. Our results indicate that long-term C. rotundifolia and A. pintoi mulching significantly influences the soil chemical properties and bacterial communities of persimmon orchards in subtropical and tropical China.

Effects of Lactobacillus acidophilus on gut microbiota composition in broilers challenged with Clostridium perfringens

This study shows the effects of dietary supplementation with Lactobacillus acidophilus on the gut microbiota of broiler chickens challenged with Clostridium perfringens infection during a 21-day period according to pyrosequencing of the 16S ribosomal RNA gene. In a 2 × 2 factorial arrangement of treatments, 308 1-day-old male Arbor Acres broiler chicks were analyzed for the effects of the probiotic (groups without or with L. acidophilus supplementation), pathogen challenge (groups without or with C. perfringens), and the effects of interaction. The infection decreased the number of Observed species, Chao1, and ACE of ileal microbiota and increased Chao1 of cecal microbiota of broilers, whereas L. acidophilus supplementation decreased the Shannon index of the ileal microbiota. Shannon index and Simpson indices were lower in the ileal microbiota than in the cecal microbiota. In the ileal microbiota, the control group had higher relative abundance of Lachnospiraceae and Ruminococcaceae in comparison with the other groups; however, the relative abundance of Gammaproteobacteria was significantly higher in the challenge group than in the other groups. C. perfringens infection tended to increase lactate concentration and decreasedconcentrations of formate, acetate and propionate in the ileum; decreased isobutyrate concentration; and tended to decrease isovalerate concentration in the cecum. Besides, L. acidophilus supplementation increased the concentration of lactate and butyrate and decreased concentrations of formate and propionate in the ileum, and increased concentrations of lactate and valerate in the cecum. In conclusion, C. perfringens infection and/or dietary supplementation with L. acidophilus modulated the relative abundance of some bacteria taxa, and the L. acidophilus supplementation helped to restore the microbial community disrupted by C. perfringens infection.

Microbial richness and composition independently drive soil multifunctionality

Abstract Soil microbes provide multiple ecosystem functions such as nutrient cycling, decomposition and climate regulation. However, we lack a quantitative understanding of the relative importance of microbial richness and composition in controlling multifunctionality. This knowledge gap limits our capacity to understand the influence of biotic attributes in the provision of services and functions on which humans depend. We used two independent approaches (i.e. experimental and observational), and applied statistical modelling to identify the role and relative importance of bacterial richness and composition in driving multifunctionality (here defined as seven measures of respiration and enzyme activities). In the observational study, we measured soil microbial communities and functions in both tree‐ and bare soil‐dominated microsites at 22 locations across a 1,200 km transect in southeastern Australia. In the experimental study we used soils from two of those locations and developed gradients of bacterial diversity and composition through inoculation of sterilized soils. Microbial richness and the relative abundance of Gammaproteobacteria, Actinobacteria, and Bacteroidetes were positively related to multifunctionality in both the observational and experimental approaches; however, only Bacteroidetes was consistently selected as a key predictor of multifunctionality across all experimental approaches and statistical models used here. Moreover, our results, from two different approaches, provide evidence that microbial richness and composition are both important, yet independent, drivers of multiple ecosystem functions. Overall, our findings advance our understanding of the mechanisms underpinning relationships between microbial diversity and ecosystem functionality in terrestrial ecosystems, and further suggest that information on microbial richness and composition needs to be considered when formulating sustainable management and conservation policies, and when predicting the effects of global change on ecosystem functions. A plain language summary is available for this article.

Characterization of the Gastric Microbiota in a Pediatric Population According to Helicobacter pylori Status.

Helicobacter pylori colonizes the human stomach of approximately 50% of the world's population, and increases the risk of several gastric diseases. The goal of this study is to compare the gastric microbiota in pediatric patients with and without H. pylori colonization. We studied 51 children who underwent gastric endoscopy because of dyspeptic symptoms (18 H. pylori positive and 33 negative). Gastric biopsies were obtained for rapid urease test, culture, histology and DNA extraction. H. pylori was quantified by quantitative polymerase chain reaction and the gastric microbiome studied by V4-16S ribosomal RNA gene high-throughput sequencing. Bacterial richness and diversity of H. pylori-positive specimens were lower than those of negative, and both groups were clearly separated according to beta diversity. Taxonomic analysis confirmed that H. pylori-positive subjects had a higher relative abundance of Helicobacter genus (66.3%) than H. pylori-negative subjects (0.45%). Four phyla (proteobacteria, bacteroidetes, firmicutes and actinobacteria) accounted for >97% of all reads in both groups. Within proteobacteria, gamma- and betaproteobacteria were the most abundant for H. pylori-negative patients, whereas epsilonproteobacteria was for H. pylori positive. H. pylori-positive patients were associated with low body mass index. In the group of underweight patients (body mass index, <18.5), there were 46.1% of H. pylori-positive patients compared with 24% in the nonunderweight group (P = 0.049). Patients with active superficial gastritis in H. pylori-positive patients had the lowest alpha diversity (P = 0.035). We characterized the gastric microbiota for the first time in children with and without H. pylori and observed that when H. pylori is present, it tends to dominate the microbial community. In the H. pylori-negative patients, there was more relative abundance of gammaproteobacteria, betaproteobacteria, bacteroidia and clostridia classes and a higher bacterial richness and diversity.

Vertical sleeve gastrectomy reduces blood pressure and hypothalamic endoplasmic reticulum stress in mice.

ABSTRACTBariatric surgery, such as vertical sleeve gastrectomy (VSG), causes remarkable improvements in cardiometabolic health, including hypertension remission. However, the mechanisms responsible remain undefined and poorly studied. Therefore, we developed and validated the first murine model of VSG that recapitulates the blood pressure-lowering effect of VSG using gold-standard radiotelemetry technology. We used this model to investigate several potential mechanisms, including body mass, brain endoplasmic reticulum (ER) stress signaling and brain inflammatory signaling, which are all critical contributors to the pathogenesis of obesity-associated hypertension. Mice fed on a high-fat diet underwent sham or VSG surgery and radiotelemeter implantation. Sham mice were fed ad libitum or were food restricted to match their body mass to VSG-operated mice to determine the role of body mass in the ability of VSG to lower blood pressure. Blood pressure was then measured in freely moving unstressed mice by radiotelemetry. VSG decreased energy intake, body mass and fat mass. Mean arterial blood pressure (MAP) was reduced in VSG-operated mice compared with both sham-operated groups. VSG-induced reductions in MAP were accompanied by a body mass-independent decrease in hypothalamic ER stress, hypothalamic inflammation and sympathetic nervous system tone. Assessment of gut microbial populations revealed VSG-induced increases in the relative abundance of Gammaproteobacteria and Enterococcus, and decreases in Adlercreutzia. These results suggest that VSG reduces blood pressure, but this is only partly due to the reduction in body weight. VSG-induced reductions in blood pressure may be driven by a decrease in hypothalamic ER stress and inflammatory signaling, and shifts in gut microbial populations.

Bacterial succession along a long-term chronosequence of paddy soil in the Yangtze River Delta, China

Conversion of tidal wetlands into paddy soils is an ancient and prevalent agricultural practice to meet increasing demand of food in the Yangtze River Delta of China, a coastal region where paddy soils originated. However, the impacts of tidal wetland reclamation and continuous rice cultivation at long time scales on soil bacterial communities remains poorly understood. In this study, we investigated temporal dynamics of bacterial communities using 16S rRNA gene pyrosequencing to delineate the patterns and drivers of soil bacterial succession along a long-term (2000 years) chronosequence of paddy field since reclamation from tidal wetlands. The results exhibited orderly changes in soil physicochemical characteristics and bacterial community composition with increasing rice cultivation time, indicating the occurrence of paddy soil development and bacterial succession since reclamation from tidal wetlands. Soil bacterial diversity significantly increased after reclamation of tidal wetlands. Succession of bacterial community composition was primarily linked with significant decrease in the relative abundances of Gammaproteobacteria and Planctomycetes and increase in those of Alphaproteobacteria and Firmicutes. Further analysis showed that long-term rice cultivation led to the enrichment of certain populations such as Rhodospirillaceae (within the class Alphaproteobacteria) and Clostridiaceae (within the phylum Firmicutes), which are potentially beneficial to higher rice yields. Canonical correspondence analysis indicated that at the time scale of millennia, the shift of bacterial community structure was mainly driven by the changes of soil physicochemical properties, especially cation exchange capacity and pH during paddy soil development. Overall, we demonstrate an orderly shift of soil bacterial communities towards higher productivity along with a 2000-year development of paddy soils after the tidal wetland reclamation, which was primarily associated with soil physicochemical alterations with time, and suggest that such chronosequence of paddy soils can serve as a test bed to delineate the relationship between microbial community and soil functions, particularly crop productivity.