Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.However,there is an urgent need to study...Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.However,there is an urgent need to study the function of the gut microbiome at the genome level using metagenome-assembled genomes.Here,we conducted single-sample metagenomic binning analysis using shotgun metagenomic sequencing data and retrieved 2837 metagenome-assembled genomes to explore the gut microbiota profile at the genome level.Reconstructing microbial genomes from metagenomic sequences greatly enriched the diversity and number of microbial genomes,especially those of uncultivable strains.By integrating the analysis of metagenome-assembled genomes with clinical parameters,we observed higherα-diversity indexes and a very different composition of microbial communities in patients with Parkinson’s disease.We also identified microbial species and metagenome-assembled genomes that were significantly associated with clinical characteristics,including disease severity,medication,motor complications,and non-motor symptoms.The genes of Parkinson’s disease severity-associated metagenome-assembled genomes were distributed across multiple pathways,such as carbon metabolism,phosphonate metabolism,carbohydrate metabolism,amino acid metabolism,fatty acid metabolism,bile acid metabolism,metabolism of cofactors and vitamins,neuroprotective molecules,immunogenic components,toxic metabolites,translation,and bacterial secretion.Our work provides a comprehensive resource for investigating the gut microbiota-Parkinson’s disease relationship at the genome level,which may enhance our comprehension of the underlying mechanisms of this disease.展开更多
The anaerobic/anoxic/oxic（A2O） process is globally one of the widely used biological sewage treatment processes. This is the first report of a metagenomic analysis using Illumina sequencing of full-scale A2O sludge ...The anaerobic/anoxic/oxic（A2O） process is globally one of the widely used biological sewage treatment processes. This is the first report of a metagenomic analysis using Illumina sequencing of full-scale A2O sludge from a municipal sewage treatment plant.With more than 530,000 clean reads from different taxa and metabolic categories, the metagenome results allow us to gain insight into the functioning of the biological community of the A2O sludge. There are 51 phyla and nearly 900 genera identified from the A2O activated sludge ecosystem. Proteobacteria, Bacteroidetes, Nitrospirae and Chloroflexi are predominant phyla in the activated sludge, suggesting that these organisms play key roles in the biodegradation processes in the A2O sewage treatment system.Nitrospira, Thauera, Dechloromonas and Ignavibacterium, which have abilities to metabolize nitrogen and aromatic compounds, are most prevalent genera. The percent of nitrogen and phosphorus metabolism in the A2O sludge is 2.72% and 1.48%, respectively. In the current A2O sludge, the proportion of Candidatus Accumulibacter is 1.37%, which is several times more than that reported in a recent study of A2O sludge. Among the four processes of nitrogen metabolism, denitrification related genes had the highest number of sequences（76.74%）, followed by ammonification（15.77%）, nitrogen fixation（3.88%） and nitrification（3.61%）. In phylum Planctomycetes, four genera（Planctomyces, Pirellula, Gemmata and Singulisphaera） are included in the top 30 abundant genera, suggesting the key role of ANAMMOX in nitrogen metabolism in the A2O sludge.展开更多
In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an ave...In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an average length of 248 bp. Running the 454 assembly algorithm over our sequences yielded 22 239 significant contigs. After excluding the M. aeruginosa sequences, we obtained 1 322 assembled contigs longer than 1 000 bp. Taxonomic analysis indicated that four kingdoms were represented in the community: Archaea (n = 9; 0.01%), Bacteria (n = 98 921; 99.6%), Eukaryota (n = 373; 3.7%), and Viruses (n = 18; 0.02%). The bacterial sequences were predominantly Alphaproteobacteria (n = 41 805; 83.3%), Betaproteobacteria (n = 5 254; 10.5%) and Gammaproteobacteria (n = 1 180; 2.4%). Gene annotations and assignment of COG (clusters of orthologous groups) functional categories indicate that a large number of the predicted genes are involved in metabolic, genetic, and environmental information processes. Our results demonstrate the extraordinary diversity of a microbial community in an ectosymbiotic system and further establish the tremendous utility of pyrosequencing.展开更多
Lipolytic enzymes, including esterases and lipases, represent a group of hydrolases that catalyze the cleavage and formation of ester bonds. A novel esterase gene, scsEst01, was cloned from a South China Sea sediment ...Lipolytic enzymes, including esterases and lipases, represent a group of hydrolases that catalyze the cleavage and formation of ester bonds. A novel esterase gene, scsEst01, was cloned from a South China Sea sediment metagenome. The scsEst01 gene consisted of 921 bp encoding 307 amino acid residues. The predicted amino acid sequence shared less than 90% identity with other lipolytic enzymes in the NCBI nonredundant protein database. Scs Est01 was successfully co-expressed in E scherichia coli BL21(DE3) with chaperones(dnaK-dna J-grp E) to prevent the formation of inclusion bodies. The recombinant protein was purified on an immobilized metal ion affinity column containing chelating Sepharose charged with Ni2 +. The enzyme was characterized using p-nitrophenol butyrate as a substrate. Scs Est01 had the highest lipolytic activity at 35℃ and p H 8.0, indicative of a meso-thermophilic alkaline esterase. Scs Est01 was thermostable at 20℃. The lipolytic activity of scs Est01 was strongly increased by Fe2 +, Mn 2+ and 1% Tween 80 or Tween 20.展开更多
With the aim of identifying novel thermostable esterases, comprehensive sequence databases and cloned fosmid libraries of metagenomes derived from an offshore oil reservoir on the Norwegian Continental Shelf were scre...With the aim of identifying novel thermostable esterases, comprehensive sequence databases and cloned fosmid libraries of metagenomes derived from an offshore oil reservoir on the Norwegian Continental Shelf were screened for enzyme candidates using both sequence-and function-based screening. From several candidates identified in both approaches, one enzyme discovered by the functional approach was verified as a novel esterase and subjected to a deeper characterization. The enzyme was successfully over-produced in Escherichia coli and was shown to be thermostable up to 90°C, with the highest esterase activity on short-chain ester substrates and with tolerance to solvents and metal ions. The fact that the thermostable enzyme was solely found by functional screening of the oil reservoir metagenomes illustrates the importance of this approach as a complement to purely sequence-based screening, in which the enzyme candidate was not detected. In addition, this example indicates the large potential of deep-sub-surface oil reservoir metagenomes as a source of novel, thermostable enzymes of potential relevance for industrial applications.展开更多
Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect their gut microbiota and resistome. T...Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect their gut microbiota and resistome. To better understand how continuous antimicrobial use in farm animals alters their microbial ecology, we used a metagenomic approach to investigate the effects of pulsed antimicrobial administration on the bacterial community, antibiotic resistance genes(ARGs) and ARG bacterial hosts in the feces of broiler chickens. Chickens received three 5-day courses of individual or combined antimicrobials, including amoxicillin, chlortetracycline and florfenicol. The florfenicol administration significantly increased the abundance of mcr-1 gene accompanied by floR gene, while amoxicillin significantly increased the abundance of genes encoding the AcrAB-tolC multidrug efflux pump(marA, soxS, sdiA, rob, evgS and phoP).These three antimicrobials all led to an increase in Proteobacteria. The increase in ARG host, Escherichia, was mainly attributed to the β-lactam, chloramphenicol and tetracycline resistance genes harbored by Escherichia under the pulsed antimicrobial treatments. These results indicated that pulsed antimicrobial administration with amoxicillin,chlortetracycline, florfenicol or their combinations significantly increased the abundance of Proteobacteria and enhanced the abundance of particular ARGs. The ARG types were occupied by the multidrug resistance genes and had significant correlations with the total ARGs in the antimicrobial-treated groups. The results of this study provide comprehensive insight into pulsed antimicrobial-mediated alteration of chicken fecal microbiota and resistome.展开更多
White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial comm...White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial community, are regarded as a stressful lowpH and/or nutrient environment. We investigated whether the functional soil metagenome also shows a predicted set of indicators of stressful conditions in WS. Based on stress-tolerant strategies exhibited by larger organisms, we hypothesized that genes for stress tolerance, dormancy, sporulation, and nutrient processing are more abundant in the soil microbiota of WS. We also hypothesized that there is less evidence of biotic interaction in white sand soils, with lower connectivity and fewer genes related to organismic interactions. In Brunei, we sampled soils from a WS and a normal primary dipterocarp forest, together with an inland heath, an intermediate forest type. Soil DNA was extracted, and shotgun sequencing was performed using Illumina HiSeq platform, with classification by the Metagenomics Rapid Annotation using Subsystem Technology(MG-RAST). The results, on one hand, supported our hypothesis(on greater abundance of dormancy, virulence, and sporulation-related genes). However, some aspects of our results showed no significant difference(specifically in stress tolerance, antibiotic resistance, viruses, and clustered regularly interspaced short palindrome repeats(CRISPRs)). It appears that in certain respects, the extreme white sand environment produces the predicted strategy of less biotic interaction, but exhibits high soil microbiota connectivity and functional diversity.展开更多
Probiotics are considered to exert beneficial effects in humans and animals by modulating the structure and metabolic functions of the gut microbiota.Therefore,the identification of functional probiotics and in-depth ...Probiotics are considered to exert beneficial effects in humans and animals by modulating the structure and metabolic functions of the gut microbiota.Therefore,the identification of functional probiotics and in-depth exploration of the characteristics and applicability of probiotics are of paramount significance for the development of more effective probiotic products and the formulation of personalized probiotic treatment strategies in the fields of human health and livestock farming.However,due to current limitations in sequencing technologies and considering that microbial communities may encompass closely related lineages,rendering metagenome assembly complex,the generation of complete metagenomeassembled genomes(c MAGs)is hindered.This limitation constrains our comprehensive resolution at the probiotic strain level.In this review,we summarized the effects of probiotics on gut microbiota balance and host health from a functional perspective.The technical methods of functional probiotics identification were summarized from the technical point of view.Furthermore,we introduced methods for microbial metagenome assembly to elucidate the associated progress and advantages and disadvantages of these approaches.Finally,we highlight more advanced metagenomic assembly techniques that may help us assemble high-fidelity intestinal metagenomes,providing powerful tools for the identification of functional probiotics.展开更多
The consumption of fermented soybean products is linked to health advantages often rooted in traditional practices and beliefs.Bemerthu is one such traditionally made,spontaneously fermented soybean food,yet its compl...The consumption of fermented soybean products is linked to health advantages often rooted in traditional practices and beliefs.Bemerthu is one such traditionally made,spontaneously fermented soybean food,yet its complex microbial community remains largely unexplored.This study employed a shotgun metagenomic approach to investigate the functional significance of the existing microbial community.The metataxonomic analysis identified the microbial community as belonging to 34 phyla,103 orders,209 families,639 genera,and 1273 species across six bemerthu metagenomes.Metagenome-assembled genomes(MAGs)were constructed and functionally annotated to clarify the characteristics of the retrieved genomes.Four MAGs were taxonomically classified from the shotgun metagenomic data:Bacillus subtilis,B.thermoamylovorans,Paenibacillus amylolyticus,and Lysinibacillus boronitolerans.Additionally,gene annotation for these classified MAGs indicated the presence of genes associated with various bio-functionalities,including vitamin synthesis,secondary metabolite production,bioactive peptide formation,and immunomodulatory effects,among others.Functional microbial characterization was performed using the eggNOG database for clusters of orthologous groups/non-supervised orthologous groups(COGs/NOGs)and the Kyoto Encyclopedia of Genes and Genomes(KEGG)for KEGG ID annotation,underscoring the vital role of the core microbial community in the fermentation process.In conclusion,our findings emphasize the significance of native microbial communities in providing health advantages to consumers and underscore their traditional knowledge of food fermentation.展开更多
Wild bees are ecologically vital but increasingly threatened by anthropogenic activities,leading to uncertain survival and health outcomes in urban environments.The gut microbiome contains features indicating host hea...Wild bees are ecologically vital but increasingly threatened by anthropogenic activities,leading to uncertain survival and health outcomes in urban environments.The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors.Moving beyond bacteria,we propose a comprehensive analysis integrating diet,bacteriome,virome,resistome,and their association to understand the survival status of urban lives better.We conducted a study on mason bees(Osmia excavata)across 10 urban agricultural sites in Suzhou,China,using shotgun gut metagenome sequencing for data derived from total gut DNA.Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus,indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity.Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance.The gut bacterial community,dominated by Gammaproteobacteria,showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites.Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes,highlighting environmental threats to both bees and humans.The virome analysis identified honeybee pathogens,suggesting potential virus spillover.Many unknown bacteriophages were detected,some of which targeted the core gut bacteria,underscoring their role in maintaining gut homeostasis.These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats,thereby guiding probiotic development and city management for effective bee conservation.展开更多
The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number...The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.展开更多
Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysi...Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysis on seven samples of metagenomic data from different depth seawater in Hawaii. The results of gene prediction and function annotation indicate that there are large amounts of potential novel genes of which functions remain unknown at present. Based on the gene annotation, codon usage bias is studied on ribosomal protein-related genes and shows an evident influence by the marine extreme environment. Furthermore, focusing on the marine environmental differences such as light intensity, dissolved oxygen, temperature and pressure among various depths, comparative analysis is carried out on related genes and metabolic pathways. Thus, the understanding as well as new insights into the correlation between marine environment and microbes are proposed at molecular level. Therefore, the studies herein afford a clue to reveal the special living strategies of microbial community from sea surface to deep sea.展开更多
Dietary fat content can reduce the methane production of dairy cows;however,the relevance fatty acid(FA)composition has towards this inhibitory effect is debatable.Furthermore,in-depth studies elucidating the effects ...Dietary fat content can reduce the methane production of dairy cows;however,the relevance fatty acid(FA)composition has towards this inhibitory effect is debatable.Furthermore,in-depth studies elucidating the effects of unsaturated fatty acids(UFA)on rumen function and the mechanism of reducing methane(CH_(4))production are lacking.This study exposed 10 Holstein cows with the same parity,similar milk yield to two total mixed rations:low unsaturated FA(LUFA)and high unsaturated FA(HUFA)with similar fat content.The LUFA group mainly added fat powder(C16:0>90%),and the HUFA group mainly replaced fat powder with extruded flaxseed.The experiment lasted 26 d,the last 5 d of which,gas exchange in respiratory chambers was conducted to measure gas emissions.We found that an increase in the UFA in diet did not affect milk production(P>0.05)and could align the profile of milk FAs more closely with modern human nutritional requirements.Furthermore,we found that increasing the UFA content in the diet lead to a decrease in the abundance of Methanobrevibacter in the rumen(|linear discriminant analysis[LDA]score|>2 and P 2 and P<0.05),which ultimately decreased CH4 production(P<0.05).Our results illustrated the mechanism involving decreased CH4 production when fed a UFA diet in dairy cows.We believe that our study provides new evidence to explore CH4 emission reduction measures for dairy cows.展开更多
Estimating taxonomic content constitutes a key problem in metagenomic sequencing data analysis.However,extracting such content from high-throughput data of next-generation sequencing is very time-consuming with the cu...Estimating taxonomic content constitutes a key problem in metagenomic sequencing data analysis.However,extracting such content from high-throughput data of next-generation sequencing is very time-consuming with the currently available software.Here,we present CloudLCA,a parallel LCA algorithm that significantly improves the efficiency of determining taxonomic composition in metagenomic data analysis.Results show that CloudLCA(1)has a running time nearly linear with the increase of dataset magnitude,(2)displays linear speedup as the number of processors grows,especially for large datasets,and(3)reaches a speed of nearly 215 million reads each minute on a cluster with ten thin nodes.In comparison with MEGAN,a well-known metagenome analyzer,the speed of CloudLCA is up to 5 more times faster,and its peak memory usage is approximately 18.5%that of MEGAN,running on a fat node.CloudLCA can be run on one multiprocessor node or a cluster.It is expected to be part of MEGAN to accelerate analyzing reads,with the same output generated as MEGAN,which can be import into MEGAN in a direct way to finish the following analysis.Moreover,CloudLCA is a universal solution for finding the lowest common ancestor,and it can be applied in other fields requiring an LCA algorithm.展开更多
In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from me...In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi.The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure,namely amino acid usages,codon usages,and codon contexts of 3-codon DNA 9-mers.SeSaMe PS Function searches a query sequence against reference sequence database,identifies 3-codon DNA 9-mers with structural roles,and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera.The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset.3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions.The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications.SeSaMe PS Function is freely accessible at www.fungalsesame.org.展开更多
Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be...Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be grouped within a mechanism of antibiotic resistance. Different protocols have been designed for detection and confirmation that a functional gene was found. In this study, we present a sequence-based screening of candidate genes encoding beta-lactamases in 14 metagenomes of Antarctic microbial mats. The samples were obtained from different sites, representing diverse biogeographic regions of maritime and continental Antarctica. A protocol was designed based on generation of Hidden Markov Models from the four beta-lactamase classes by Ambler classification, using sequences from the Comprehensive Antibiotic Resistance Database (CARD). The models were used as queries for metagenome analysis and recovered contigs were subsequently annotated using RAST. According to our analysis, 14 metagenomes analyzed contain A, B and C beta-lactamase genes. Class D genes, however, were identified in 11 metagenomes. The most abundant was class C (46.8%), followed by classes B (35.5%), A (14.2%) and D (3.5%). A considerable number of sequences formed clusters which included, in some cases, contigs from different metagenomes. These assemblies are clearly separated from reference clusters, previously identified using CARD beta-lactamase sequences. While bacterial antibiotic resistance is a major challenge of public health worldwide, our results suggest that environmental diversity of beta-lactamase genes is higher than that currently reported, although this should be complemented with gene function analysis.展开更多
Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalle...Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalleled reservoir of microbial genetic diversity.Here,by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types,we present a comprehensive Cold Seep Microbiomic Database(CSMD)to archive the genomic and functional diversity of cold seep microbiomes.The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes,which represent 1895 species spanning 105 phyla.In addition,beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition.Heterotrophic and anaerobic metabolisms are prevalent in microbial communities,accompanied by considerable mixotrophs and facultative anaerobes,highlighting the versatile metabolic potential in cold seeps.Furthermore,secondary metabolic gene cluster analysis indicates that at least 98.81%of the sequences potentially encode novel natural products,with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria.Overall,the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.展开更多
Melioidosis is a zoonotic infectious disease caused by Burkholderia(B.)pseudomallei.It is predominantly endemic in Southeast Asia[1-3].Clinical manifestations are often non-specific,commonly presenting as pneumonia or...Melioidosis is a zoonotic infectious disease caused by Burkholderia(B.)pseudomallei.It is predominantly endemic in Southeast Asia[1-3].Clinical manifestations are often non-specific,commonly presenting as pneumonia or skin abscesses[4],and may progress to severe sepsis with a high case-fatality rate of 10%-50%[5].Due to its early flu-like symptoms,melioidosis is frequently misdiagnosed by clinicians in non-endemic regions.Beijing,located in the North Temperate Zone,rarely reports melioidosis cases;the lack of awareness among healthcare professionals may lead to misdiagnosis and fatal outcomes.展开更多
Ecological floating bed is an important biological remediation method for water pollution control.During the removal of excess nutrients and pollutants,changes in environmental factors affect the characteristics of mi...Ecological floating bed is an important biological remediation method for water pollution control.During the removal of excess nutrients and pollutants,changes in environmental factors affect the characteristics of microorganisms in aquatic ecosystems.To understand the influences of ecological floating beds on size-fractionated microorganisms,we investigated the community assembly and nitrogen metabolic characteristics of three size-fractionated microorganism groups in the ecological floating bed area,using 18S rDNA,16S rDNA metabarcoding,and metagenomic sequencing techniques.Firstly,we discovered substantial differences between size-fractionated groups in the diversity and compositions of both microeukaryotic and bacterial communities,as well as the influences of floating beds on specific groups.The floating beds appeared to provide more habitats for heterotrophs and symbiotes while potentially inhibiting the growth of certain phytoplankton(cyanobacteria).Secondly,we observed that microeukaryotic and bacterial communities were predominantly influenced by stochastic and deterministic processes,respectively,and they both exhibited distinct patterns across different size-fractionated groups.Notably,microeukaryotic community assembly demonstrated a greater sensitivity to ecological floating beds,as indicated by an increase in dispersal limitation processes.Finally,the nitrogen metabolism functional genes revealed that microbes associated with large-sized particles played a crucial role in dissimilatory nitrate reduction to ammonium(DNRA)and denitrification processes within the floating bed area,thereby facilitating the removal of excess nitrogen nutrients from the water.In contrast,freeliving microorganisms from small-sized groups were linked mainly to the genes involved in nitrogen assimilation and assimilatory nitrate reduction to ammonium(ANRA)processes.These findings help understand the impact of ecological floating beds on the diversity and functional characteristics of microorganism communities in different size-fractionated groups.展开更多
基金supported by the National Key R&D Program of China,No.2022YFE0210100(to XY)the Shanghai Rising-Star Program,No.22QA1405700(to XY)the National Natural Science Foundation of China,Nos.82301418(to YZ),82171246(to QX),and 82371251(to QX).
文摘Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.However,there is an urgent need to study the function of the gut microbiome at the genome level using metagenome-assembled genomes.Here,we conducted single-sample metagenomic binning analysis using shotgun metagenomic sequencing data and retrieved 2837 metagenome-assembled genomes to explore the gut microbiota profile at the genome level.Reconstructing microbial genomes from metagenomic sequences greatly enriched the diversity and number of microbial genomes,especially those of uncultivable strains.By integrating the analysis of metagenome-assembled genomes with clinical parameters,we observed higherα-diversity indexes and a very different composition of microbial communities in patients with Parkinson’s disease.We also identified microbial species and metagenome-assembled genomes that were significantly associated with clinical characteristics,including disease severity,medication,motor complications,and non-motor symptoms.The genes of Parkinson’s disease severity-associated metagenome-assembled genomes were distributed across multiple pathways,such as carbon metabolism,phosphonate metabolism,carbohydrate metabolism,amino acid metabolism,fatty acid metabolism,bile acid metabolism,metabolism of cofactors and vitamins,neuroprotective molecules,immunogenic components,toxic metabolites,translation,and bacterial secretion.Our work provides a comprehensive resource for investigating the gut microbiota-Parkinson’s disease relationship at the genome level,which may enhance our comprehension of the underlying mechanisms of this disease.
基金supported by the National Natural Science Foundation of China (No. 41430643)
文摘The anaerobic/anoxic/oxic（A2O） process is globally one of the widely used biological sewage treatment processes. This is the first report of a metagenomic analysis using Illumina sequencing of full-scale A2O sludge from a municipal sewage treatment plant.With more than 530,000 clean reads from different taxa and metabolic categories, the metagenome results allow us to gain insight into the functioning of the biological community of the A2O sludge. There are 51 phyla and nearly 900 genera identified from the A2O activated sludge ecosystem. Proteobacteria, Bacteroidetes, Nitrospirae and Chloroflexi are predominant phyla in the activated sludge, suggesting that these organisms play key roles in the biodegradation processes in the A2O sewage treatment system.Nitrospira, Thauera, Dechloromonas and Ignavibacterium, which have abilities to metabolize nitrogen and aromatic compounds, are most prevalent genera. The percent of nitrogen and phosphorus metabolism in the A2O sludge is 2.72% and 1.48%, respectively. In the current A2O sludge, the proportion of Candidatus Accumulibacter is 1.37%, which is several times more than that reported in a recent study of A2O sludge. Among the four processes of nitrogen metabolism, denitrification related genes had the highest number of sequences（76.74%）, followed by ammonification（15.77%）, nitrogen fixation（3.88%） and nitrification（3.61%）. In phylum Planctomycetes, four genera（Planctomyces, Pirellula, Gemmata and Singulisphaera） are included in the top 30 abundant genera, suggesting the key role of ANAMMOX in nitrogen metabolism in the A2O sludge.
基金Supported by the Knowledge Innovation Program of Chinese Academy of Sciences (No. KSCX2-YW-G-073)
文摘In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an average length of 248 bp. Running the 454 assembly algorithm over our sequences yielded 22 239 significant contigs. After excluding the M. aeruginosa sequences, we obtained 1 322 assembled contigs longer than 1 000 bp. Taxonomic analysis indicated that four kingdoms were represented in the community: Archaea (n = 9; 0.01%), Bacteria (n = 98 921; 99.6%), Eukaryota (n = 373; 3.7%), and Viruses (n = 18; 0.02%). The bacterial sequences were predominantly Alphaproteobacteria (n = 41 805; 83.3%), Betaproteobacteria (n = 5 254; 10.5%) and Gammaproteobacteria (n = 1 180; 2.4%). Gene annotations and assignment of COG (clusters of orthologous groups) functional categories indicate that a large number of the predicted genes are involved in metabolic, genetic, and environmental information processes. Our results demonstrate the extraordinary diversity of a microbial community in an ectosymbiotic system and further establish the tremendous utility of pyrosequencing.
基金Supported by the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDA11030404)the National High Technology Research and Development Program of China(863 Program)(Nos.2012AA092103,2014AA093501,2014AA093505)+1 种基金the Knowledge Innovation Program of Chinese Academy of Sciences(No.KZCX2-YW-JC201)the Open Project Program of Key Laboratory of Marine Bio-Resources Sustainable Utilization,South China Sea Institute of Oceanology,Chinese Academy of Sciences(No.LMB121006)
文摘Lipolytic enzymes, including esterases and lipases, represent a group of hydrolases that catalyze the cleavage and formation of ester bonds. A novel esterase gene, scsEst01, was cloned from a South China Sea sediment metagenome. The scsEst01 gene consisted of 921 bp encoding 307 amino acid residues. The predicted amino acid sequence shared less than 90% identity with other lipolytic enzymes in the NCBI nonredundant protein database. Scs Est01 was successfully co-expressed in E scherichia coli BL21(DE3) with chaperones(dnaK-dna J-grp E) to prevent the formation of inclusion bodies. The recombinant protein was purified on an immobilized metal ion affinity column containing chelating Sepharose charged with Ni2 +. The enzyme was characterized using p-nitrophenol butyrate as a substrate. Scs Est01 had the highest lipolytic activity at 35℃ and p H 8.0, indicative of a meso-thermophilic alkaline esterase. Scs Est01 was thermostable at 20℃. The lipolytic activity of scs Est01 was strongly increased by Fe2 +, Mn 2+ and 1% Tween 80 or Tween 20.
文摘With the aim of identifying novel thermostable esterases, comprehensive sequence databases and cloned fosmid libraries of metagenomes derived from an offshore oil reservoir on the Norwegian Continental Shelf were screened for enzyme candidates using both sequence-and function-based screening. From several candidates identified in both approaches, one enzyme discovered by the functional approach was verified as a novel esterase and subjected to a deeper characterization. The enzyme was successfully over-produced in Escherichia coli and was shown to be thermostable up to 90°C, with the highest esterase activity on short-chain ester substrates and with tolerance to solvents and metal ions. The fact that the thermostable enzyme was solely found by functional screening of the oil reservoir metagenomes illustrates the importance of this approach as a complement to purely sequence-based screening, in which the enzyme candidate was not detected. In addition, this example indicates the large potential of deep-sub-surface oil reservoir metagenomes as a source of novel, thermostable enzymes of potential relevance for industrial applications.
基金supported by the Laboratory of Lingnan Modern Agriculture Project, China (NT2021006)the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (32121004)the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program, China (2019BT02N054)。
文摘Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect their gut microbiota and resistome. To better understand how continuous antimicrobial use in farm animals alters their microbial ecology, we used a metagenomic approach to investigate the effects of pulsed antimicrobial administration on the bacterial community, antibiotic resistance genes(ARGs) and ARG bacterial hosts in the feces of broiler chickens. Chickens received three 5-day courses of individual or combined antimicrobials, including amoxicillin, chlortetracycline and florfenicol. The florfenicol administration significantly increased the abundance of mcr-1 gene accompanied by floR gene, while amoxicillin significantly increased the abundance of genes encoding the AcrAB-tolC multidrug efflux pump(marA, soxS, sdiA, rob, evgS and phoP).These three antimicrobials all led to an increase in Proteobacteria. The increase in ARG host, Escherichia, was mainly attributed to the β-lactam, chloramphenicol and tetracycline resistance genes harbored by Escherichia under the pulsed antimicrobial treatments. These results indicated that pulsed antimicrobial administration with amoxicillin,chlortetracycline, florfenicol or their combinations significantly increased the abundance of Proteobacteria and enhanced the abundance of particular ARGs. The ARG types were occupied by the multidrug resistance genes and had significant correlations with the total ARGs in the antimicrobial-treated groups. The results of this study provide comprehensive insight into pulsed antimicrobial-mediated alteration of chicken fecal microbiota and resistome.
基金supported by the National Research Foundation (NRF) of Korea (No. NRF-040920150076)
文摘White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial community, are regarded as a stressful lowpH and/or nutrient environment. We investigated whether the functional soil metagenome also shows a predicted set of indicators of stressful conditions in WS. Based on stress-tolerant strategies exhibited by larger organisms, we hypothesized that genes for stress tolerance, dormancy, sporulation, and nutrient processing are more abundant in the soil microbiota of WS. We also hypothesized that there is less evidence of biotic interaction in white sand soils, with lower connectivity and fewer genes related to organismic interactions. In Brunei, we sampled soils from a WS and a normal primary dipterocarp forest, together with an inland heath, an intermediate forest type. Soil DNA was extracted, and shotgun sequencing was performed using Illumina HiSeq platform, with classification by the Metagenomics Rapid Annotation using Subsystem Technology(MG-RAST). The results, on one hand, supported our hypothesis(on greater abundance of dormancy, virulence, and sporulation-related genes). However, some aspects of our results showed no significant difference(specifically in stress tolerance, antibiotic resistance, viruses, and clustered regularly interspaced short palindrome repeats(CRISPRs)). It appears that in certain respects, the extreme white sand environment produces the predicted strategy of less biotic interaction, but exhibits high soil microbiota connectivity and functional diversity.
基金supported by the Guangdong Basic and Applied Basic Research Foundation,China(2022A1515010766)the Shenzhen Science and Technology Program,China(RCBS20210609104512021 and KCXFZ20201221173205015)+1 种基金the National Natural Science Foundation of China(32202653)the Project Funded by the China Postdoctoral Science Foundation(BX2021367 and 2021M703543)。
文摘Probiotics are considered to exert beneficial effects in humans and animals by modulating the structure and metabolic functions of the gut microbiota.Therefore,the identification of functional probiotics and in-depth exploration of the characteristics and applicability of probiotics are of paramount significance for the development of more effective probiotic products and the formulation of personalized probiotic treatment strategies in the fields of human health and livestock farming.However,due to current limitations in sequencing technologies and considering that microbial communities may encompass closely related lineages,rendering metagenome assembly complex,the generation of complete metagenomeassembled genomes(c MAGs)is hindered.This limitation constrains our comprehensive resolution at the probiotic strain level.In this review,we summarized the effects of probiotics on gut microbiota balance and host health from a functional perspective.The technical methods of functional probiotics identification were summarized from the technical point of view.Furthermore,we introduced methods for microbial metagenome assembly to elucidate the associated progress and advantages and disadvantages of these approaches.Finally,we highlight more advanced metagenomic assembly techniques that may help us assemble high-fidelity intestinal metagenomes,providing powerful tools for the identification of functional probiotics.
基金the Department of Biotechnology(DBT),Ministry of Science and Technology,Government of India for financial support through DBT project,sanction number:BT/NER/95/SP47965/2022CSIR for Junior Research Fellowship.
文摘The consumption of fermented soybean products is linked to health advantages often rooted in traditional practices and beliefs.Bemerthu is one such traditionally made,spontaneously fermented soybean food,yet its complex microbial community remains largely unexplored.This study employed a shotgun metagenomic approach to investigate the functional significance of the existing microbial community.The metataxonomic analysis identified the microbial community as belonging to 34 phyla,103 orders,209 families,639 genera,and 1273 species across six bemerthu metagenomes.Metagenome-assembled genomes(MAGs)were constructed and functionally annotated to clarify the characteristics of the retrieved genomes.Four MAGs were taxonomically classified from the shotgun metagenomic data:Bacillus subtilis,B.thermoamylovorans,Paenibacillus amylolyticus,and Lysinibacillus boronitolerans.Additionally,gene annotation for these classified MAGs indicated the presence of genes associated with various bio-functionalities,including vitamin synthesis,secondary metabolite production,bioactive peptide formation,and immunomodulatory effects,among others.Functional microbial characterization was performed using the eggNOG database for clusters of orthologous groups/non-supervised orthologous groups(COGs/NOGs)and the Kyoto Encyclopedia of Genes and Genomes(KEGG)for KEGG ID annotation,underscoring the vital role of the core microbial community in the fermentation process.In conclusion,our findings emphasize the significance of native microbial communities in providing health advantages to consumers and underscore their traditional knowledge of food fermentation.
基金supported by the Research Development Fund(RDF-23-01-067)the Summer Undergraduate Research Fellowship(SURF)Program(SURF-2023-0079)from Xi'an Jiaotong-Liverpool University to M.T.
文摘Wild bees are ecologically vital but increasingly threatened by anthropogenic activities,leading to uncertain survival and health outcomes in urban environments.The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors.Moving beyond bacteria,we propose a comprehensive analysis integrating diet,bacteriome,virome,resistome,and their association to understand the survival status of urban lives better.We conducted a study on mason bees(Osmia excavata)across 10 urban agricultural sites in Suzhou,China,using shotgun gut metagenome sequencing for data derived from total gut DNA.Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus,indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity.Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance.The gut bacterial community,dominated by Gammaproteobacteria,showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites.Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes,highlighting environmental threats to both bees and humans.The virome analysis identified honeybee pathogens,suggesting potential virus spillover.Many unknown bacteriophages were detected,some of which targeted the core gut bacteria,underscoring their role in maintaining gut homeostasis.These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats,thereby guiding probiotic development and city management for effective bee conservation.
基金supported by the National Natural Science Foundation of China (Grant No. 30770298)
文摘The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.
基金supported by the National ‘‘Twelfth Five-Year’’ Plan for Science and Technology of China(2012BAI06B02)the National Natural Science Foundation of China(91231119, 30970667 and 11021463)the National Basic Research Program of China (2011CB707500)
文摘Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysis on seven samples of metagenomic data from different depth seawater in Hawaii. The results of gene prediction and function annotation indicate that there are large amounts of potential novel genes of which functions remain unknown at present. Based on the gene annotation, codon usage bias is studied on ribosomal protein-related genes and shows an evident influence by the marine extreme environment. Furthermore, focusing on the marine environmental differences such as light intensity, dissolved oxygen, temperature and pressure among various depths, comparative analysis is carried out on related genes and metabolic pathways. Thus, the understanding as well as new insights into the correlation between marine environment and microbes are proposed at molecular level. Therefore, the studies herein afford a clue to reveal the special living strategies of microbial community from sea surface to deep sea.
基金supported by the National Key R&D Program of China (No.2022YFD1301001).
文摘Dietary fat content can reduce the methane production of dairy cows;however,the relevance fatty acid(FA)composition has towards this inhibitory effect is debatable.Furthermore,in-depth studies elucidating the effects of unsaturated fatty acids(UFA)on rumen function and the mechanism of reducing methane(CH_(4))production are lacking.This study exposed 10 Holstein cows with the same parity,similar milk yield to two total mixed rations:low unsaturated FA(LUFA)and high unsaturated FA(HUFA)with similar fat content.The LUFA group mainly added fat powder(C16:0>90%),and the HUFA group mainly replaced fat powder with extruded flaxseed.The experiment lasted 26 d,the last 5 d of which,gas exchange in respiratory chambers was conducted to measure gas emissions.We found that an increase in the UFA in diet did not affect milk production(P>0.05)and could align the profile of milk FAs more closely with modern human nutritional requirements.Furthermore,we found that increasing the UFA content in the diet lead to a decrease in the abundance of Methanobrevibacter in the rumen(|linear discriminant analysis[LDA]score|>2 and P 2 and P<0.05),which ultimately decreased CH4 production(P<0.05).Our results illustrated the mechanism involving decreased CH4 production when fed a UFA diet in dairy cows.We believe that our study provides new evidence to explore CH4 emission reduction measures for dairy cows.
文摘Estimating taxonomic content constitutes a key problem in metagenomic sequencing data analysis.However,extracting such content from high-throughput data of next-generation sequencing is very time-consuming with the currently available software.Here,we present CloudLCA,a parallel LCA algorithm that significantly improves the efficiency of determining taxonomic composition in metagenomic data analysis.Results show that CloudLCA(1)has a running time nearly linear with the increase of dataset magnitude,(2)displays linear speedup as the number of processors grows,especially for large datasets,and(3)reaches a speed of nearly 215 million reads each minute on a cluster with ten thin nodes.In comparison with MEGAN,a well-known metagenome analyzer,the speed of CloudLCA is up to 5 more times faster,and its peak memory usage is approximately 18.5%that of MEGAN,running on a fat node.CloudLCA can be run on one multiprocessor node or a cluster.It is expected to be part of MEGAN to accelerate analyzing reads,with the same output generated as MEGAN,which can be import into MEGAN in a direct way to finish the following analysis.Moreover,CloudLCA is a universal solution for finding the lowest common ancestor,and it can be applied in other fields requiring an LCA algorithm.
文摘In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi.The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure,namely amino acid usages,codon usages,and codon contexts of 3-codon DNA 9-mers.SeSaMe PS Function searches a query sequence against reference sequence database,identifies 3-codon DNA 9-mers with structural roles,and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera.The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset.3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions.The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications.SeSaMe PS Function is freely accessible at www.fungalsesame.org.
文摘Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be grouped within a mechanism of antibiotic resistance. Different protocols have been designed for detection and confirmation that a functional gene was found. In this study, we present a sequence-based screening of candidate genes encoding beta-lactamases in 14 metagenomes of Antarctic microbial mats. The samples were obtained from different sites, representing diverse biogeographic regions of maritime and continental Antarctica. A protocol was designed based on generation of Hidden Markov Models from the four beta-lactamase classes by Ambler classification, using sequences from the Comprehensive Antibiotic Resistance Database (CARD). The models were used as queries for metagenome analysis and recovered contigs were subsequently annotated using RAST. According to our analysis, 14 metagenomes analyzed contain A, B and C beta-lactamase genes. Class D genes, however, were identified in 11 metagenomes. The most abundant was class C (46.8%), followed by classes B (35.5%), A (14.2%) and D (3.5%). A considerable number of sequences formed clusters which included, in some cases, contigs from different metagenomes. These assemblies are clearly separated from reference clusters, previously identified using CARD beta-lactamase sequences. While bacterial antibiotic resistance is a major challenge of public health worldwide, our results suggest that environmental diversity of beta-lactamase genes is higher than that currently reported, although this should be complemented with gene function analysis.
基金support from the Senior User Project of RV KEXUE(Grant No.KEXUE2019GZ05)the Center for Ocean Mega-Science,Chinese Academy of Sciences+2 种基金funding support from the Second Tibetan Plateau Scientific Expedition and Research Program(Grant No.2021QZKK0100)the National Key R&D Program of China(Grant No.2022YFF1002801)the National Natural Science Foundation of China(Grant No.92251302).
文摘Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalleled reservoir of microbial genetic diversity.Here,by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types,we present a comprehensive Cold Seep Microbiomic Database(CSMD)to archive the genomic and functional diversity of cold seep microbiomes.The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes,which represent 1895 species spanning 105 phyla.In addition,beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition.Heterotrophic and anaerobic metabolisms are prevalent in microbial communities,accompanied by considerable mixotrophs and facultative anaerobes,highlighting the versatile metabolic potential in cold seeps.Furthermore,secondary metabolic gene cluster analysis indicates that at least 98.81%of the sequences potentially encode novel natural products,with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria.Overall,the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.
基金supported by the Capital’s Funds for Health Improvement and Research(2024-1G-4362)the National Key Program for Infectious Disease of China(2018ZX10714002-003-002).
文摘Melioidosis is a zoonotic infectious disease caused by Burkholderia(B.)pseudomallei.It is predominantly endemic in Southeast Asia[1-3].Clinical manifestations are often non-specific,commonly presenting as pneumonia or skin abscesses[4],and may progress to severe sepsis with a high case-fatality rate of 10%-50%[5].Due to its early flu-like symptoms,melioidosis is frequently misdiagnosed by clinicians in non-endemic regions.Beijing,located in the North Temperate Zone,rarely reports melioidosis cases;the lack of awareness among healthcare professionals may lead to misdiagnosis and fatal outcomes.
基金Supported by the National Natural Science Foundation of China(Nos.42141003,42176147)the National Key Research and Development Program of China(No.2022YFF0802204)the Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration(USER)(Nos.USER2021-1,USER2021-5)。
文摘Ecological floating bed is an important biological remediation method for water pollution control.During the removal of excess nutrients and pollutants,changes in environmental factors affect the characteristics of microorganisms in aquatic ecosystems.To understand the influences of ecological floating beds on size-fractionated microorganisms,we investigated the community assembly and nitrogen metabolic characteristics of three size-fractionated microorganism groups in the ecological floating bed area,using 18S rDNA,16S rDNA metabarcoding,and metagenomic sequencing techniques.Firstly,we discovered substantial differences between size-fractionated groups in the diversity and compositions of both microeukaryotic and bacterial communities,as well as the influences of floating beds on specific groups.The floating beds appeared to provide more habitats for heterotrophs and symbiotes while potentially inhibiting the growth of certain phytoplankton(cyanobacteria).Secondly,we observed that microeukaryotic and bacterial communities were predominantly influenced by stochastic and deterministic processes,respectively,and they both exhibited distinct patterns across different size-fractionated groups.Notably,microeukaryotic community assembly demonstrated a greater sensitivity to ecological floating beds,as indicated by an increase in dispersal limitation processes.Finally,the nitrogen metabolism functional genes revealed that microbes associated with large-sized particles played a crucial role in dissimilatory nitrate reduction to ammonium(DNRA)and denitrification processes within the floating bed area,thereby facilitating the removal of excess nitrogen nutrients from the water.In contrast,freeliving microorganisms from small-sized groups were linked mainly to the genes involved in nitrogen assimilation and assimilatory nitrate reduction to ammonium(ANRA)processes.These findings help understand the impact of ecological floating beds on the diversity and functional characteristics of microorganism communities in different size-fractionated groups.
