Periodic Addition of Glucose Suppressed Cyanobacterial Abundance in Additive Lake Water Samples during the Entire Bloom Season

Previously, we showed that prophylactic addition of glucose to Harsha Lake water samples could inhibit cyanobacteria growth, at least for a short period of time. The current study tested cyanobacterial control with glucose for the entire Harsha Lake bloom season. Water samples (1000 ml) were collected weekly from Harsha Lake during the algal-bloom season starting June 9 and lasting until August 24, 2022. To each of two 7-liter polypropylene containers, 500 ml of Harsha Lake water was added, and the containers were placed in a controlled environment chamber. To one container labeled “Treated,” 0.15 g of glucose was added, and nothing was added to the container labeled “Control.” After that, three 25 ml samples from each container were collected and used for 16S rRNA gene sequencing each week. Then 1000 ml of Harsha Lake water was newly collected each week, with 500 ml added to each container, along with the addition of 0.15 g glucose to the “Treated” container. Sequencing data were used to examine differences in the composition of bacterial communities between Treated and Control containers. Treatment with glucose altered the microbial communities by 1) reducing taxonomic diversity, 2) largely eliminating cyanobacterial taxa, and 3) increasing the relative abundance of subsets of non-cyanobacterial taxa (such as Proteobacteria and Actinobacteriota). These effects were observed across time despite weekly inputs derived directly from Lake water. The addition of glucose to a container receiving weekly additions of Lake water suppressed the cyanobacterial populations during the entire summer bloom season. The glucose appears to stimulate the diversity of certain bacterial taxa at the expense of the cyanobacteria.

Alterations in gut microbiota are related to metabolite profiles in spinal cord injury

Studies have shown that gut microbiota metabolites can enter the central nervous system via the blood-spinal cord barrier and cause neuroinflammation, thus constituting secondary injury after spinal cord injury. To investigate the correlation between gut microbiota and metabolites and the possible mechanism underlying the effects of gut microbiota on secondary injury after spinal cord injury, in this study, we established mouse models of T8–T10 traumatic spinal cord injury. We used 16 S rRNA gene amplicon sequencing and metabolomics to reveal the changes in gut microbiota and metabolites in fecal samples from the mouse model. Results showed a severe gut microbiota disturbance after spinal cord injury, which included marked increases in pro-inflammatory bacteria, such as Shigella, Bacteroides, Rikenella, Staphylococcus, and Mucispirillum and decreases in anti-inflammatory bacteria, such as Lactobacillus, Allobaculum, and Sutterella. Meanwhile, we identified 27 metabolites that decreased and 320 metabolites that increased in the injured spinal cord. Combined with pathway enrichment analysis, five markedly differential amino acids(L-leucine, L-methionine, L-phenylalanine, L-isoleucine and L-valine) were screened out, which play a pivotal role in activating oxidative stress and inflammatory responses following spinal cord injury. Integrated correlation analysis indicated that the alteration of gut microbiota was related to the differences in amino acids, which suggests that disturbances in gut microbiota might participate in the secondary injury through the accumulation of partial metabolites that activate oxidative stress and inflammatory responses. Findings from this study provide a new theoretical basis for improving the secondary injury after spinal cord injury through fecal microbial transplantation.

Molecular characterization and diversity analysis of bacterial communities associated with Dialeurolonga malleswaramensis （Hemiptera： Aleyrodidae） adults using 16S rDNA amplicon pyrosequencing and FISH

Dialeurolonga malleswaramensis Sundararaj （Hemiptera： Aleyrodidae） is a phytophagous sap sucking insect. It infests Polyalthia longifolia, an important avenue tree of India, effective in alleviating noise pollution and having immense medicinal importance. Samples of this insect were collected from Polyalthia longifolia. The cytochrome c oxidase subunit I gene （mtCOl） helped in the molecular characterization of the insect. This study reports the bacterial diversity in D. malleswararnensis adults by high throughput 16S rDNA amplicon pyrosequencing. The major genera identified were Portiera and Arsenophonus. Other bacterial genera detected were uncultured alpha proteobacterium, Sphingopyxis and Methylobacterium. We also employed fluorescence in situ hybridization （FISH） in whole mount samples to confirm the presence of dominant endosymbionts Portiera and Arsenophonus to the bacteriocyte of D. malleswaramensis. This study concludes that combining techniques like 16S rDNA amplicon pyrosequencing and FISH reveal both dominant and rare bacteria. The data also predict the evolutionary position of this pest with respect to other whitefly species using a mitochondrial marker.

Effects of enrichmemt planting with native tree species on bacterial community structure and potential impact on Eucalyptus plantations in southern China

Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity.However,the effects of introducing non-legume native tree species on soil nutrients and bacterial community structure remain poorly understood.This study investigated the impacts of the conversion of third generation monoculture Eucalyptus plantations to mixed systems including Eucalyptus urograndis with Cinnamomum camphora(EC)and E.urograndis with Castanopsis hystrix(EH),on soil chemical and biochemical properties and bacterial community structure,diversity and functions.First generation E.urophylla plantations were the control.Results show that planting the third generation Eucalyptus led to a significant decrease in p H,organic matter,nutrient content,enzyme activities(invertin,acid phosphataes,and urease),and bacterialα-diversity compare to the controls.However,the mixed planting showed significant improvement in soil chemical and biochemical attributes and bacterialα-diversity,although the E.urograndis and C.hystrix planting had no improvement.Chloroflexi(oligotrophic bacteria)were significantly enriched in third generation Eucalyptus and Eucalyptus+C.hystrix,while proteobacteria increased significantly in the E.urograndis with C.camphora plantings.The relative abundance of multiple metabolic pathways increased significantly in the third generation Eucalyptus plantations whereas membrane transportrelated genes were enriched in soils of the mixed systems.The changes in bacterial community structures in the two mixed systems were driven by diversity,organic matter and acid phosphatase,while bacterial functions were affected by invertase,NO_(3)^(-)-N,diversity and urease.These results suggest that the transformation of successive monoculture Eucalyptus plantations into mixed plantations reduces the depletion of soil nutrients and enhances the ecological function of soil microorganisms.

Characterization of Fe(Ⅲ)-Reducing Enrichment Cultures and Isolation of Enterobacter sp. Nan-1 from the Deep-Sea Sediment, South China Sea

To characterize the Fe(III)-reducing bacteria,enrichment cultures were initiated by inoculating deep-sea sediment from the South China Sea(SCS)into the media with hydrous ferric oxide(HFO)as the sole electron acceptor.As indicated by Meta 16S rDNA Amplicon Sequencing,the microorganisms related to Fe(III)-reduction in the enrichment cultures were mainly Shewanella and Enterobacter.A new facultative Fe(III)-reducing bacterium was obtained and identified as Enterobacter sp.Nan-1 based on its 16S rRNA gene sequence and physiological characterizations.Enterobacter sp.Nan-1 was not only a mesophilic bacterium capable of reducing HFO with a wide range of salinity(4,34,40,50 and 60 g L−1)efficiently,but also a piezotolerant bacterium that can proceed Fe(III)-reduction sustainedly at hydrostatic pressures between 0.1 and 50 MPa using glucose and pyruvate as carbon source.Furthermore,the geochemical characteristics of deep-sea sediment indicated that the microbial metabolism and iron reduction both remain active in the well-developed Fe(III)-reducing zone where the strain Nan-1 was obtained.To our knowledge,Enterobacter sp.Nan-1 could serve as a new applicative Fe(III)-reducing bacterium for future investigation on the iron biogeochemical cycle and diagenetic process of organic matter in the deep-sea environment.

Fecal microbiome of growing pigs fed a cereal based diet including chicory(Cichorium intybus L.) or ribwort(Plantago lanceolata L.) forage

Background： The purpose of this study was to investigate how inclusion of chicory forage or ribwort forage in a cereal-based diet influenced the fecal microbial community（microbiome） in newly weaned（35 days of age） piglets.The piglets were fed a cereal-based diet without（B） and with inclusion（80 and 160 g/kg air-dry forage） of vegetative shoots of chicory（C） and leaves of ribwort（R） forage in a 35-day growth trial. Fecal samples were collected at the start（D0）, 17（D17） and 35（D35） days after weaning and profiles of the microbial consortia were generated using terminal restriction fragment length polymorphism（T-RFLP）. 454-FLX pyrosequencing of 16 S r RNA gene amplicons was used to analyze the microbial composition in a subset of the samples already analyzed with T-RFLP.Results： The microbial clustering pattern was primarily dependent on age of the pigs, but diet effects could also be observed. Lactobacilli and enterobacteria were more abundant at D0, whereas the genera Streptococcus, Treponema,Clostridium, Clostridiaceae1 and Coprococcus were present in higher abundances at D35. Pigs fed ribwort had an increased abundance of sequences classified as Treponema and a reduction in lactobacilli. However, the abundance of Prevotellaceae increased with age in on both the chicory and the ribwort diet. Moreover, there were significant correlations between the abundance of Bacteroides and the digested amount of galactose, uronic acids and total non-starch polysaccharides, and between the abundance of Bacteroidales and the digested amount of xylose.Conclusion： This study demonstrated that both chicory and ribwort inclusion in the diet of newly weaned pigs influenced the composition of the fecal microbiota and that digestion of specific dietary components was correlated with species composition of the microbiota. Moreover, this study showed that the gut will be exposed to a dramatic shift in the microbial community structure several weeks after weaning.

Influence of group B streptococcus and vaginal cleanliness on the vaginal microbiome of pregnant women

BACKGROUND The vaginal microbiome plays a critical role in the health of pregnant women and their newborns.Group B Streptococcus(GBS)and vaginal cleanliness significantly affect the vaginal microecosystem and are closely associated with vaginal diseases.AIM To explore the effects of GBS status and vaginal cleanliness on vaginal microecosystems.METHODS We collected 160 vaginal swabs from pregnant women and divided them into the following four groups based on GBS status and vaginal cleanliness:GBS-positive+vaginal cleanliness I–II degree,GBS-negative+vaginal cleanliness I–II degree,GBS-positive+vaginal cleanliness III–IV degree,and GBS-negative+vaginal cleanliness III–IV degree.Samples were subjected to 16S rRNA gene amplicon sequencing.RESULTS Alpha diversity analysis showed that the Shannon index did not significantly differ between the four groups.We identified significant variation in taxa abundance between the GBS-positive and GBS-negative groups and between the vaginal cleanliness I–II degree and III–IV degree groups.Principal coordinate analysis and non-metric multidimensional scaling analysis further confirmed the microbial diversity of the four groups.Moreover,the linear discriminant analysis demonstrated that Lactobacillus jensenii and Actinobacteria were strongly associated with GBS-positive status,and Lactobacillus iners,Lactobacillaceae,Lactobacillus,Lactobacillales,Bacilli and Firmicutes were closely correlated with GBS-negative status.CONCLUSION GBS status and vaginal cleanliness significantly affect vaginal microbiome differences in pregnant women.Our findings provide instructional information for clinical antibiotic treatment in pregnant women with different GBS statuses and vaginal cleanliness degrees.

Spatiotemporal dynamics of the microbial diversity on salt-preserved goatskins assessed by culturing and 16S rRNA gene amplicon sequencing

Wet-salted skin,as a special artificial high-salt environment,is rich in protein,fat,collagen and other nutrient substrates,and is a rich resource of halotolerant and halophilic microorganisms.However,knowledge gaps regarding the microbial community structure and inter taxa associations of wet-salted skin are large.In this study,the spatiotemporal dynamics and community structure of microorganisms present on wet-salted goatskins were investigated using 16S rRNA gene amplicon sequencing and culturable technique.Alpha diversity analysis based on Sobs,Chao,Ace and Shannon indices revealed that microbial diversity on the wet-salted goatskins exhibited a trend of‘down→up→down→flat’with time.During preservation,genera belonging to the bacteria domain such as Aci-netobacter,Weissella and Streptococcus were slowly dying out,whereas those belonging to halophilic archaea such as Natrialba and Haloterrigena were gradually flourishing.Moreover,to resist high-salt stress,microorganisms on the wet-salted goatskin gradually migrated from the outside to the inside,eventually leading to the microbial diversity inside the skin being the same as or even higher than that on the skin surface.Venn diagram analysis revealed that the strains of some genera,including Psychrobacter,Salimicrobium,Salinicola,Ornithinibacillus,Halomonas,Bacillus and Chromohalobacter,were distributed throughout the interior and exterior of the wet-salted goatskin and existed during various periods.Accordingly,45 protease-producing halophilic or halotolerant microorganisms were isolated and screened from the wet-salted goatskin using the gradient dilution plate method.Importantly,16S rRNA genes of some bacteria exhibited less than 99.5%similarity to valid published species,indicating that they likely are novel spe-cies and have a good potential for application.

Catalog of operational taxonomic units and unified amplicon sequencing data for the microbiomes of medicinal plant roots

China has a rich history of cultivating medicinal plants,whose root microbial communities closely interact with the medicinal plants,thereby influencing their growth,health,and medicinal properties.Currently,researchers widely use 16S rRNA gene amplicon sequencing to study these root microbial communities.However,publicly available sequence datasets often lack essential sample information or contain errors,impeding the reuse of the datasets in the future.In this study,we aimed to create a united,reliable,and readily usable source of 16S rRNA gene sequences for medicinal plant root microbiomes.We compiled a catalog of 1392 microbiome samples for 58 medicinal plants from 58 studies,and manually provided essential sample information based on the experimental setup described in the associated papers.We then processed the sequences using a custom pipeline,generating a united catalog of operational taxonomic units(OTUs)and conducting taxonomic classification.We also pre-dicted the ecological functions of the communities for each sample.Finally,we used this dataset,to compare the rhizosphere bacterial communities of Pseudostellaria heterophylla from Fujian and Guizhou Provinces,revealing significant differences in the community composition of the same plant from different geographic locations.By providing a comprehensive and united catalog of amplicon sequences and OTUs for medicinal plant root bacterial communities,this study offers an invaluable resource for future comparative studies and data mining.

Characteristics of microbial communities in water from CBM wells and biogas production potential in eastern Yunnan and western Guizhou, China

The study of microbial communities in the produced water of coalbed methane(CBM)wells is an important aspect of microbial-enhanced methane production.Water produced from 15 CBM wells in four synclines in eastern Yunnan and western Guizhou was collected.Through the use of 16S ribosomal RNA(16S rRNA)amplicon sequencing and realtime fluorescence quantitative polymerase chain reaction(PCR),the characteristics of bacterial and archaeal communities before and after enrichment culture were studied.The methanogenic pathways of secondary biogas were discussed,and potential microbial-enhanced methane production was preliminarily evaluated.The results showed that the bacterial DNA content in uncultured produced water was low,so it is difficult to detect.After enrichment,the dominant bacteria phyla were Proteobacteria,Bacteroidetes,and Firmicutes.A total of seven phyla were detected in the uncultured produced water,and the dominant archaeal phylum was Euyarchaeota.Methanogens were the main component of archaea.The dominant archaeal genera were Methanobacterium,Methanoculleus and Methanobrevibacter.The community structure of the archaea changed noticeably after four days of enrichment culture.The relative abundance of Euryarchaeota increased to 99%in most samples after enrichment culture.It was found that there was a transition from Methanoregula to Methanobacterium within genera.The relative abundance of Methanobacterium increased,which can produce hydrogenotrophic methane.Combined with the isotopic composition of the produced water and gas,it is considered that the CBM in the Tucheng and Enhong synlines consists of a mixture of thermogenic gas and biogas.The proportion of secondary biogas in the Tucheng and Enhong synlines are estimated to range from 10.89% to 49.62%.There are mainly hydrogentrophic methanogens in the study area,and CO_(2) reduction is the main way of microbial gas production.After enrichment culture of produced water in the study area,the hydrogenotrophic methanogens were enriched.These two areas have strong potential for microbial-enhanced methane production.