Nitrogen(N)deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields.However,relatively little is known how bacterial consortia,especially abundant and rare taxa,respond to N dee...Nitrogen(N)deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields.However,relatively little is known how bacterial consortia,especially abundant and rare taxa,respond to N deep placement,which is critical for understanding the biodiversity and function of agricultural ecosystem.In this study,lllumina sequencing and ecological models were conducted to examine the diversity patterns and underlying assembly mechanisms of abundant and rare taxa in rice rhizosphere soil under different N fertilization regimes at four rice growth stages in paddy fields.The results showed that abundant and rare bacteria had distinct distribution patterns in rhizosphere samples.Abundant bacteria showed ubiquitous distribution;while rare taxa exhibited uneven distribution across all samples.Stochastic processes dominated community assembly of both abundant and rare bacteria,with dispersal limitation playing a more vital role in abundant bacteria,and undominated processes playing a more important role in rare bacteria.The N deep placement was associated with a greater influence of dispersal limitation than the broadcast N fertilizer(BN)and no N fertilizer(NN)treatments in abundant and rare taxa of rhizosphere soil;while greater contributions from homogenizing dispersal were observed for BN and NN in rare taxa.Network analysis indicated that abundant taxa with closer relationships were usually more likely to occupy the central position of the network than rare taxa.Nevertheless,most of the keystone species were rare taxa and might have played essential roles in maintaining the network stability.Overall,these findings highlighted that the ecological mechanisms and co-occurrence patterns of abundant and rare bacteria in rhizosphere soil under N deep placement.展开更多
Background:Diarrhea is a major cause of morbidity and mortality in young calves,resulting in considerable economic loss for dairy farms.To determine if some gut microbes might have resistance to dysbiotic process with...Background:Diarrhea is a major cause of morbidity and mortality in young calves,resulting in considerable economic loss for dairy farms.To determine if some gut microbes might have resistance to dysbiotic process with calf diarrhea by dictating the microbial co-occurrence patterns from birth to post-weaning,we examined the dynamic development of the gut microbiota and diarrhea status using two animal trials,with the first trial having 14 Holstein dairy calves whose fecal samples were collected 18 times over 78 d from birth to 15 d post-weaning and the second trial having 43 Holstein dairy calves whose fecal samples were collected daily from 8 to 18 days of age corresponding to the first diarrhea peak of trial 1.Results:Metataxonomic analysis of the fecal microbiota showed that the development of gut microbiota had three age periods with birth and weaning as the separatrices.Two diarrhea peaks were observed during the transition of the three age periods.Fusobacteriaceae was identified as a diarrhea-associated taxon both in the early stage and during weaning,and Clostridium_sensu_stricto_1 was another increased genus among diarrheic calves in the early stage.In the neonatal calves,Prevotella_2(ASV4 and ASV26),Prevotella_9(ASV43),and Alloprevotella(ASV14)were negatively associated with Clostridium_sensu_stricto_1(ASV48),the keystone taxa of the diarrhea-phase module.During weaning,unclassified Muribaculaceae(ASV28 and ASV44),UBA1819(ASV151),Barnesiella(ASV497),and Ruminococcaceae_UCG-005(ASV254)were identified being associated with non-diarrheic status,and they aggregated in the non-diarrhea module of co-occurrence patterns wherein unclassified Muribaculaceae(ASV28)and Barnesiella(ASV497)had a direct negative relationship with the members of the diarrhea module.Conclusions:Taken together,our results suggest that the dynamic successions of calf gut microbiota and the interactions among some bacteria could influence calf diarrhea,and some species of Prevotella might be the core microbiota in both neonatal and weaning calves,while species of Muribaculaceae might be the core microbiota in weaning calves for preventing calf diarrhea.Some ASVs affiliated with Prevotella_2(ASV4 and ASV26),Prevotella_9(ASV43),Alloprevotella(AVS14),unclassified Muribaculaceae(ASV28 and ASV44),UBA1819(ASV151),Ruminococcaceae_UCG-005(ASV254),and Barnesiella(ASV497)might be proper probiotics for preventing calf diarrhea whereas Clostridium_sensu_stricto_1(ASV48)might be the biomarker for diarrhea risk in specific commercial farms.展开更多
Bacteria in desert soil have unique phylogeny and important ecological functions, and theirresponses to changes in precipitation need further attention. However, relevant studies have mainlyfocused on the surface soil...Bacteria in desert soil have unique phylogeny and important ecological functions, and theirresponses to changes in precipitation need further attention. However, relevant studies have mainlyfocused on the surface soil, and studies on the responses of bacteria at different soil depths to variationsin precipitation are rare. Thus, we used 16S rDNA high-throughput sequencing to investigate the changesin soil bacterial distribution along a mean annual precipitation gradient (50–150 mm) in the Alxa Desert,China, and compared the variation characteristics in the surface soil layer (0–10 cm) and subsurface soillayer (10–20 cm). Results showed that soil bacterial communities significantly changed along theprecipitation gradient in both soil layers. However, the subsurface soil layer could support bacterialcommunities with higher diversity and closer internal relationships but more internal competition than thesurface soil layer. Additionally, compared with the surface soil layer, variations in diversity andco-occurrence patterns in the subsurface soil layer were more in line with the changes in the mean annualprecipitation, while bacterial community structure was less variable in the subsurface soil layer. Comparedwith the mean annual precipitation, soil moisture had little influence on the structure and diversity of soilbacterial community but had a high correlation with intercommunity connectivity. Therefore, soilmoisture might play a complex role in mediating environmental conditions and soil bacterial communitycharacteristics. Due to the different responses of surface and subsurface soil bacteria to the changes inprecipitation, it is necessary to distinguish different soil layers when predicting the trends in desert soilbacterial conditions associated with precipitation, and prediction of subsurface soil bacteria may be moreaccurate.展开更多
Ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) play crucial roles in removing nitrogen from sewage in wastewater treatment plants (WWTPs) to protect water resources. However, the differences in ...Ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) play crucial roles in removing nitrogen from sewage in wastewater treatment plants (WWTPs) to protect water resources. However, the differences in ecological properties and putative interactions of AOB and NOB in WWTPs at a large spatial scale remain unclear. Hence, 132 activated sludge (AS) samples collected from 11 cities across China were studied by utilizing 16S rRNA gene sequencing technology. Results indicated that Nitrosomonas and Nitrosospira accounted for similar ratios of the AOB community and might play nearly equal roles in ammonia oxidation in AS. However, Nitrospira greatly outnumbered other NOB genera, with proportions varying from 94.7% to 99.9% of the NOB community in all WWTPs. Similar compositions and, hence, a low distance–decay turnover rate of NOB (0.035) across China were observed. This scenario might have partly resulted from the high proportions of homogenizing dispersal (~13%). Additionally, drift presented dominant roles in AOB and NOB assembling mechanisms (85.2% and 81.6% for AOB and NOB, respectively). The partial Mantel test illustrated that sludge retention time and temperature were the primary environmental factors affecting AOB and NOB communities. Network results showed that NOB played a leading role in maintaining module structures and node connections in AS. Moreover, most links between NOB and other microorganisms were positive, indicating that NOB were involved in complex symbioses with bacteria in AS.展开更多
The efficacy of traditional Chinese medicine(TCM) treatments for Western medicine(WM) diseases relies heavily on the proper classification of patients into TCM syndrome types.The authors developed a data-driven method...The efficacy of traditional Chinese medicine(TCM) treatments for Western medicine(WM) diseases relies heavily on the proper classification of patients into TCM syndrome types.The authors developed a data-driven method for solving the classification problem,where syndrome types were identified and quantified based on statistical patterns detected in unlabeled symptom survey data.The new method is a generalization of latent class analysis(LCA),which has been widely applied in WM research to solve a similar problem,i.e.,to identify subtypes of a patient population in the absence of a gold standard.A well-known weakness of LCA is that it makes an unrealistically strong independence assumption.The authors relaxed the assumption by first detecting symptom co-occurrence patterns from survey data and used those statistical patterns instead of the symptoms as features for LCA.This new method consists of six steps:data collection,symptom co-occurrence pattern discovery,statistical pattern interpretation,syndrome identification,syndrome type identification and syndrome type classification.A software package called Lantern has been developed to support the application of the method.The method was illustrated using a data set on vascular mild cognitive impairment.展开更多
The pollution caused by agricultural production poses a threat to the ecological integrity of river ecosystems,altering the structure and function of river ecosystems.Differences in microbial community structure provi...The pollution caused by agricultural production poses a threat to the ecological integrity of river ecosystems,altering the structure and function of river ecosystems.Differences in microbial community structure provide useful information about the impact of agricultural pollution on the biological integrity of ecosystems,but generally convey little information regarding ecosystem functions.In this study,using Illumina MiSeq sequencing technology based on the 16 S rRNA gene,river sediment samples associated with four different types of agricultural pollution were comprehensively analyzed.The results show that the total organic carbon(TOC)content was highest at the YZS site(animal husbandry sewage)among the assayed sites,but the species richness and uniformity were lowest at this site,which may have been caused by the high nutrient source of the sewage.Furthermore,in the three YZS samples affected by the long-term discharge of aquaculture tail-water,the unique genus Dechloromonas and the genus Candidatus-Competitor were observed,which are strongly correlated with phosphorus conversion.The formation of network modules may correspond to the coexistence of functional bacteria accustomed to multiple niche combinations under different agricultural pollution conditions in river sediments.According to the PICRUSt functional prediction,the bacterial community in the agricultural polluted river sediment primarily harbored 46 subfunctions,exhibiting richness of functions.Overall,our results provide a more comprehensive understanding of the structure and ecological processes associated with the aggregation of bacterial communities,which is beneficial for the management of river environments.展开更多
基金the National Key Research and Development Program of China(2016YFD0200309 and 2018YFD0301104-01).
文摘Nitrogen(N)deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields.However,relatively little is known how bacterial consortia,especially abundant and rare taxa,respond to N deep placement,which is critical for understanding the biodiversity and function of agricultural ecosystem.In this study,lllumina sequencing and ecological models were conducted to examine the diversity patterns and underlying assembly mechanisms of abundant and rare taxa in rice rhizosphere soil under different N fertilization regimes at four rice growth stages in paddy fields.The results showed that abundant and rare bacteria had distinct distribution patterns in rhizosphere samples.Abundant bacteria showed ubiquitous distribution;while rare taxa exhibited uneven distribution across all samples.Stochastic processes dominated community assembly of both abundant and rare bacteria,with dispersal limitation playing a more vital role in abundant bacteria,and undominated processes playing a more important role in rare bacteria.The N deep placement was associated with a greater influence of dispersal limitation than the broadcast N fertilizer(BN)and no N fertilizer(NN)treatments in abundant and rare taxa of rhizosphere soil;while greater contributions from homogenizing dispersal were observed for BN and NN in rare taxa.Network analysis indicated that abundant taxa with closer relationships were usually more likely to occupy the central position of the network than rare taxa.Nevertheless,most of the keystone species were rare taxa and might have played essential roles in maintaining the network stability.Overall,these findings highlighted that the ecological mechanisms and co-occurrence patterns of abundant and rare bacteria in rhizosphere soil under N deep placement.
基金the National Key Research and Development Program of China(2017YFD0500502)。
文摘Background:Diarrhea is a major cause of morbidity and mortality in young calves,resulting in considerable economic loss for dairy farms.To determine if some gut microbes might have resistance to dysbiotic process with calf diarrhea by dictating the microbial co-occurrence patterns from birth to post-weaning,we examined the dynamic development of the gut microbiota and diarrhea status using two animal trials,with the first trial having 14 Holstein dairy calves whose fecal samples were collected 18 times over 78 d from birth to 15 d post-weaning and the second trial having 43 Holstein dairy calves whose fecal samples were collected daily from 8 to 18 days of age corresponding to the first diarrhea peak of trial 1.Results:Metataxonomic analysis of the fecal microbiota showed that the development of gut microbiota had three age periods with birth and weaning as the separatrices.Two diarrhea peaks were observed during the transition of the three age periods.Fusobacteriaceae was identified as a diarrhea-associated taxon both in the early stage and during weaning,and Clostridium_sensu_stricto_1 was another increased genus among diarrheic calves in the early stage.In the neonatal calves,Prevotella_2(ASV4 and ASV26),Prevotella_9(ASV43),and Alloprevotella(ASV14)were negatively associated with Clostridium_sensu_stricto_1(ASV48),the keystone taxa of the diarrhea-phase module.During weaning,unclassified Muribaculaceae(ASV28 and ASV44),UBA1819(ASV151),Barnesiella(ASV497),and Ruminococcaceae_UCG-005(ASV254)were identified being associated with non-diarrheic status,and they aggregated in the non-diarrhea module of co-occurrence patterns wherein unclassified Muribaculaceae(ASV28)and Barnesiella(ASV497)had a direct negative relationship with the members of the diarrhea module.Conclusions:Taken together,our results suggest that the dynamic successions of calf gut microbiota and the interactions among some bacteria could influence calf diarrhea,and some species of Prevotella might be the core microbiota in both neonatal and weaning calves,while species of Muribaculaceae might be the core microbiota in weaning calves for preventing calf diarrhea.Some ASVs affiliated with Prevotella_2(ASV4 and ASV26),Prevotella_9(ASV43),Alloprevotella(AVS14),unclassified Muribaculaceae(ASV28 and ASV44),UBA1819(ASV151),Ruminococcaceae_UCG-005(ASV254),and Barnesiella(ASV497)might be proper probiotics for preventing calf diarrhea whereas Clostridium_sensu_stricto_1(ASV48)might be the biomarker for diarrhea risk in specific commercial farms.
基金This work was financially supported by the National Key Research and Development Program of China(2016YFC0501001)the Key Laboratory Cooperative Research Project of Chinese Academy of Sciences.
文摘Bacteria in desert soil have unique phylogeny and important ecological functions, and theirresponses to changes in precipitation need further attention. However, relevant studies have mainlyfocused on the surface soil, and studies on the responses of bacteria at different soil depths to variationsin precipitation are rare. Thus, we used 16S rDNA high-throughput sequencing to investigate the changesin soil bacterial distribution along a mean annual precipitation gradient (50–150 mm) in the Alxa Desert,China, and compared the variation characteristics in the surface soil layer (0–10 cm) and subsurface soillayer (10–20 cm). Results showed that soil bacterial communities significantly changed along theprecipitation gradient in both soil layers. However, the subsurface soil layer could support bacterialcommunities with higher diversity and closer internal relationships but more internal competition than thesurface soil layer. Additionally, compared with the surface soil layer, variations in diversity andco-occurrence patterns in the subsurface soil layer were more in line with the changes in the mean annualprecipitation, while bacterial community structure was less variable in the subsurface soil layer. Comparedwith the mean annual precipitation, soil moisture had little influence on the structure and diversity of soilbacterial community but had a high correlation with intercommunity connectivity. Therefore, soilmoisture might play a complex role in mediating environmental conditions and soil bacterial communitycharacteristics. Due to the different responses of surface and subsurface soil bacteria to the changes inprecipitation, it is necessary to distinguish different soil layers when predicting the trends in desert soilbacterial conditions associated with precipitation, and prediction of subsurface soil bacteria may be moreaccurate.
基金supported by the major project of the National Natural Science Foundation of China(No.52193268013)the Fundamental Research Funds for the Central Universities(No.2022QNPY56).
文摘Ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) play crucial roles in removing nitrogen from sewage in wastewater treatment plants (WWTPs) to protect water resources. However, the differences in ecological properties and putative interactions of AOB and NOB in WWTPs at a large spatial scale remain unclear. Hence, 132 activated sludge (AS) samples collected from 11 cities across China were studied by utilizing 16S rRNA gene sequencing technology. Results indicated that Nitrosomonas and Nitrosospira accounted for similar ratios of the AOB community and might play nearly equal roles in ammonia oxidation in AS. However, Nitrospira greatly outnumbered other NOB genera, with proportions varying from 94.7% to 99.9% of the NOB community in all WWTPs. Similar compositions and, hence, a low distance–decay turnover rate of NOB (0.035) across China were observed. This scenario might have partly resulted from the high proportions of homogenizing dispersal (~13%). Additionally, drift presented dominant roles in AOB and NOB assembling mechanisms (85.2% and 81.6% for AOB and NOB, respectively). The partial Mantel test illustrated that sludge retention time and temperature were the primary environmental factors affecting AOB and NOB communities. Network results showed that NOB played a leading role in maintaining module structures and node connections in AS. Moreover, most links between NOB and other microorganisms were positive, indicating that NOB were involved in complex symbioses with bacteria in AS.
基金supported by Hong Kong Research Grants Council under grants No.16202515 and16212516Guangzhou HKUST Fok Ying Tung Research Institute,China Ministry of Science and Technology TCM Special Research Projects Program under grants No.200807011,No.201007002 and No.201407001-8+2 种基金Beijing Science and Technology Program under grant No.Z111107056811040Beijing New Medical Discipline Development Program under grant No.XK100270569Beijing University of Chinese Medicine under grant No.2011-CXTD-23
文摘The efficacy of traditional Chinese medicine(TCM) treatments for Western medicine(WM) diseases relies heavily on the proper classification of patients into TCM syndrome types.The authors developed a data-driven method for solving the classification problem,where syndrome types were identified and quantified based on statistical patterns detected in unlabeled symptom survey data.The new method is a generalization of latent class analysis(LCA),which has been widely applied in WM research to solve a similar problem,i.e.,to identify subtypes of a patient population in the absence of a gold standard.A well-known weakness of LCA is that it makes an unrealistically strong independence assumption.The authors relaxed the assumption by first detecting symptom co-occurrence patterns from survey data and used those statistical patterns instead of the symptoms as features for LCA.This new method consists of six steps:data collection,symptom co-occurrence pattern discovery,statistical pattern interpretation,syndrome identification,syndrome type identification and syndrome type classification.A software package called Lantern has been developed to support the application of the method.The method was illustrated using a data set on vascular mild cognitive impairment.
基金the Key University Science Research Project of Anhui Province(No.KJ2019A0641)the Key Research and development program of Anhui Province(No.202004i07020010)+1 种基金the Resistance in Winter Wheat Region in the Middle and Lower Reaches of the Yangtze River(No.2017YFD0100800)the Anhui Academy of Agricultural Sciences Research and Application Innovation Team Project of Aquaculture Water Environment(No.2020YL043)。
文摘The pollution caused by agricultural production poses a threat to the ecological integrity of river ecosystems,altering the structure and function of river ecosystems.Differences in microbial community structure provide useful information about the impact of agricultural pollution on the biological integrity of ecosystems,but generally convey little information regarding ecosystem functions.In this study,using Illumina MiSeq sequencing technology based on the 16 S rRNA gene,river sediment samples associated with four different types of agricultural pollution were comprehensively analyzed.The results show that the total organic carbon(TOC)content was highest at the YZS site(animal husbandry sewage)among the assayed sites,but the species richness and uniformity were lowest at this site,which may have been caused by the high nutrient source of the sewage.Furthermore,in the three YZS samples affected by the long-term discharge of aquaculture tail-water,the unique genus Dechloromonas and the genus Candidatus-Competitor were observed,which are strongly correlated with phosphorus conversion.The formation of network modules may correspond to the coexistence of functional bacteria accustomed to multiple niche combinations under different agricultural pollution conditions in river sediments.According to the PICRUSt functional prediction,the bacterial community in the agricultural polluted river sediment primarily harbored 46 subfunctions,exhibiting richness of functions.Overall,our results provide a more comprehensive understanding of the structure and ecological processes associated with the aggregation of bacterial communities,which is beneficial for the management of river environments.
