Heavy metal pollution affects soil ecological function.Biochar and compost can effectively remediate heavy metals and increase soil nutrients.The effects and mechanisms of biochar and compost amendments on soil nitrog...Heavy metal pollution affects soil ecological function.Biochar and compost can effectively remediate heavy metals and increase soil nutrients.The effects and mechanisms of biochar and compost amendments on soil nitrogen cycle function in heavy-metal contaminated soils are not fully understood.This study examined how biochar,compost,and their integrated use affected ammonia-oxidizing microorganisms in heavy metal polluted soil.Quantitative PCR was used to determine the abundance of ammonia-oxidizing archaea(AOA)and bacteria(AOB).Ammonia monooxygenase(AMO)activity was evaluated by the enzymelinked immunosorbent assay.Results showed that compost rather than biochar improved nitrogen conversion in soil.Biochar,compost,or their integrated application significantly reduced the effective Zn and Cd speciation.Adding compost obviously increased As and Cu effective speciation,bacterial 16 S rRNA abundance,and AMO activity.AOB,stimulated by compost addition,was significantly more abundant than AOA throughout remediation.Correlation analysis showed that AOB abundance positively correlated with NO_(3)^(-)-N(r=0.830,P<0.01),and that AMO activity had significant correlation with EC(r=-0.908,P<0.01)and water-soluble carbon(r=-0.868,P<0.01).Those seem to be the most vital factors affecting AOB community and their function in heavy metal-polluted soil remediated by biochar and compost.展开更多
In this review,we summarize the recent microbiome studies related to diabetes disease and discuss the key findings that show the early emerging potential causal roles for diabetes.On a global scale,diabetes causes a s...In this review,we summarize the recent microbiome studies related to diabetes disease and discuss the key findings that show the early emerging potential causal roles for diabetes.On a global scale,diabetes causes a significant negative impact to the health status of human populations.This review covers type 1 diabetes and type 2 diabetes.We examine promising studies which lead to a better understanding of the potential mechanism of microbiota in diabetes diseases.It appears that the human oral and gut microbiota are deeply interdigitated with diabetes.It is that simple.Recent studies of the human microbiome are capturing the attention of scientists and healthcare practitioners worldwide by focusing on the interplay of gut microbiome and diabetes.These studies focus on the role and the potential impact of intestinal microflora in diabetes.We paint a clear picture of how strongly microbes are linked and associated,both positively and negatively,with the fundamental and essential parts of diabetes in humans.The microflora seems to have an endless capacity to impact and transform diabetes.We conclude that there is clear and growing evidence of a close relationship between the microbiota and diabetes and this is worthy of future investments and research efforts.展开更多
Dynamic communication between hepatocytes and the environment is critical in hepatocellular carcinoma (HCC) development.Clinical immunotherapy against HCC is currently unsatisfactory and needs more systemic considerat...Dynamic communication between hepatocytes and the environment is critical in hepatocellular carcinoma (HCC) development.Clinical immunotherapy against HCC is currently unsatisfactory and needs more systemic considerations, including theidentification of new biomarkers and immune checkpoints. Transmembrane 4 L six family member 5 (TM4SF5) is known to promoteHCC, but it remains unclear how cancerous hepatocytes avoid immune surveillance and whether avoidance can be blocked. Weinvestigated how TM4SF5-mediated hepatic tumorigenesis avoids surveillance by natural killer (NK) cells, which are prevalent in theliver, and whether the avoidance can be blocked by anti-TM4SF5 agents. We used comprehensive structure activity relationshipanalysis to identify TM4SF5-specific isoxazole (TSI)-based small molecules that inhibit TM4SF5-mediated effects. TM4SF5 expressedby hepatocytes reduced NK cell cytotoxicity by downregulating stimulatory ligands/receptors, including signaling lymphocyticactivation molecule family member 7 (SLAMF7). TM4SF5 bound SLAMF7 depending on N-glycosylation and caused intracellulartrafficking of SLAMF7 from the plasma membrane to lysosomes for degradation. TSI treatments in cell lines and animal models ofHCC blocked this binding, intracellular trafficking, and downregulation, resulting in higher levels of stimulatory NK cell ligands. Inmouse xenograft models, TSI treatment abrogated HCC development by increasing the abundance and dispersion of Slamf7-positive cells in liver tissues, recapitulating the phenotype of Tm4sf5-knockout mice and indicating TSI-mediated restoration of NKcell surveillance. These findings suggest that TSIs can inhibit TM4SF5-mediated liver carcinogenesis by increasing NK cellsurveillance.展开更多
Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycli...Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycling of rhizosphere microbiomes remains unclear.To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres,we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies.Compared with the native mangrove(Kandelia obovata,KO),the introduced mangrove(Sonneratia apetala,SA)rhizosphere microbiome had significantly(p<0.05)higher average genome size(AGS)(5.8 vs.5.5 Mb),average 16S ribosomal RNA gene copy number(3.5 vs.3.1),relative abundances of mobile genetic elements,and functional diversity in terms of the Shannon index(7.88 vs.7.84)but lower functional potentials involved in CH4 cycling(e.g.,mcrABCDG and pmoABC),N2 fixation(nifHDK),and inorganic S cycling(dsrAB,dsrC,dsrMKJOP,soxB,sqr,and fccAB).Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere.Additionally,salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes.This study advances our understanding of microbially mediated biogeochemical cycling of CH_(4),N,and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions,which has important implications for future mangrove reforestation.展开更多
The role of microbiota in health and diseases is being highlighted by numerous studies since its discovery.Depending on the localized regions,microbiota can be classified into gut,oral,respiratory,and skin microbiota....The role of microbiota in health and diseases is being highlighted by numerous studies since its discovery.Depending on the localized regions,microbiota can be classified into gut,oral,respiratory,and skin microbiota.The microbial communities are in symbiosis with the host,contributing to homeostasis and regulating immune function.However,microbiota dysbiosis can lead to dysregulation of bodily functions and diseases including cardiovascular diseases(CVDs),cancers,respiratory diseases.展开更多
Due to the toxicity of bioaccumulative organohalides to human beings and ecosystems,a variety of biotic and abiotic remediation methods have been developed to remove organohalides from contaminated environments.Biorem...Due to the toxicity of bioaccumulative organohalides to human beings and ecosystems,a variety of biotic and abiotic remediation methods have been developed to remove organohalides from contaminated environments.Bioremediation employing organohalide-respiring bacteria(OHRB)-mediated microbial reductive dehalogenation(Bio-RD)represents a cost-effective and environmentally friendly approach to attenuate highly-halogenated organohalides,specifically organohalides in soil,sediment and other anoxic environments.Nonetheless,many factors severely restrict the implications of OHRB-based bioremediation,including incomplete dehalogenation,low abundance of OHRB and consequent low dechlorination activity.Recently,the development of in situ chemical oxidation(ISCO)based on sulfate radicals(SO_(4)^(·−))via the persulfate activation and oxidation(PAO)process has attracted tremendous research interest for the remediation of lowly-halogenated organohalides due to its following advantages,e.g.,complete attenuation,high reactivity and no selectivity to organohalides.Therefore,integration of OHRB-mediated Bio-RD and subsequent PAO(Bio-RD-PAO)may provide a promising solution to the remediation of organohalides.In this review,we first provide an overview of current progress in Bio-RD and PAO and compare their limitations and advantages.We then critically discuss the integration of Bio-RD and PAO(Bio-RD-PAO)for complete attenuation of organohalides and its prospects for future remediation applications.Overall,Bio-RD-PAO opens up opportunities for complete attenuation and consequent effective in situ remediation of persistent organohalide pollution.展开更多
Gut microbiota of four economically important Asian carp species(silver carp, Hypophthalmichthys molitrix; bighead carp,Hypophthalmichthys nobilis; grass carp, Ctenopharyngodon idella; common carp, Cyprinus carpio) we...Gut microbiota of four economically important Asian carp species(silver carp, Hypophthalmichthys molitrix; bighead carp,Hypophthalmichthys nobilis; grass carp, Ctenopharyngodon idella; common carp, Cyprinus carpio) were compared using 16 S rRNA gene pyrosequencing. Analysis of more than 590,000 quality-filtered sequences obtained from the foregut, midgut and hindgut of these four carp species revealed high microbial diversity among the samples. The foregut samples of grass carp exhibited more than 1,600 operational taxonomy units(OTUs) and the highest alpha-diversity index, followed by the silver carp foregut and midgut. Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria were the predominant phyla regardless of fish species or gut type. Pairwise(weighted) UniFrac distance-based permutational multivariate analysis of variance with fish species as a factor produced significant association(P<0.01). The gut microbiotas of all four carp species harbored saccharolytic or proteolytic microbes, likely in response to the differences in their feeding habits. In addition, extensive variations were also observed even within the same fish species. Our results indicate that the gut microbiotas of Asian carp depend on the exact species, even when the different species were cohabiting in the same environment. This study provides some new insights into developing commercial fish feeds and improving existing aquaculture strategies.展开更多
The goal of achieving carbon neutrality in the next 30-40 years is approaching worldwide consensus and requires coordinated efforts to combat the increasing threat of climate change.Two main sets of actions have been ...The goal of achieving carbon neutrality in the next 30-40 years is approaching worldwide consensus and requires coordinated efforts to combat the increasing threat of climate change.Two main sets of actions have been proposed to address this grand goal.One is to reduce anthropogenic CO2emissions to the atmosphere,and the other is to increase carbon sinks or negative emissions,i.e.,removing CO2from the atmosphere.Here we advocate eco-engineering approaches for ocean negative carbon emission(ONCE),aiming to enhance carbon sinks in the marine environment.An international program is being established to promote coordinated efforts in developing ONCE-relevant strategies and methodologies,taking into consideration ecological/biogeochemical processes and mechanisms related to different forms of carbon(inorganic/organic,biotic/abiotic,particulate/dissolved) for sequestration.We focus on marine ecosystem-based approaches and pay special attention to mechanisms that require transformative research,including those elucidating interactions between the biological pump(BP),the microbial carbon pump(MCP),and microbially induced carbonate precipitation(MICP).Eutrophic estuaries,hypoxic and anoxic waters,coral reef ecosystems,as well as aquaculture areas are particularly considered in the context of efforts to increase their capacity as carbon sinks.ONCE approaches are thus expected to be beneficial for both carbon sequestration and alleviation of environmental stresses.展开更多
Submerged plants in wetlands play important roles as ecosystem engineers to improve self-purification and promote elemental cycling.However,their effects on the functional capacity of microbial communities in wetland ...Submerged plants in wetlands play important roles as ecosystem engineers to improve self-purification and promote elemental cycling.However,their effects on the functional capacity of microbial communities in wetland sediments remain poorly understood.Here,we provide detailed metagenomic insights into the biogeochemical potential of microbial communities in wetland sediments with and without submerged plants(i.e.,Vallisneria natans).A large number of functional genes involved in carbon(C),nitrogen(N)and sulfur(S)cycling were detected in the wetland sediments.However,most functional genes showed higher abundance in sediments with submerged plants than in those without plants.Based on the comparison of annotated functional genes in the N and S cycling databases(i.e.,NCycDB and SCycDB),we found that genes involved in nitrogen fixation(e.g.,nifD/H/K/W),assimilatory nitrate reduction(e.g.,nasA and nirA),denitrification(e.g.,nirK/S and nosZ),assimilatory sulfate reduction(e.g.,cysD/H/J/N/Q and sir),and sulfur oxidation(e.g.,glpE,soeA,sqr and sseA)were significantly higher(correctedp<0.05)in vegetated vs.unvegetated sediments.This could be mainly driven by environmental factors including total phosphorus,total nitrogen,and C:N ratio.The binning of metagenomes further revealed that some archaeal taxa could have the potential of methane metabolism including hydrogenotrophic,acetoclastic,and methylotrophic methanogenesis,which are crucial to the wetland methane budget and carbon cycling.This study opens a new avenue for linking submerged plants with microbial functions,and has further implications for understanding global carbon,nitrogen and sulfur cycling in wetland ecosystems.展开更多
Sulfur(S)is an essential biological element,and S cycling is mainly driven by metabolically versatile microorganisms.The river–wetland–ocean(RWO)continuum here is defined as the dynamically connected region with est...Sulfur(S)is an essential biological element,and S cycling is mainly driven by metabolically versatile microorganisms.The river–wetland–ocean(RWO)continuum here is defined as the dynamically connected region with estuary,wetland,and near-marine ecosystems,and it is considered a hotspot of biogeochemical cycling,especially a major biotope for S cycling.Various forms and oxidation states of S compounds are considered ideal electron donors or acceptors and are widely utilized by microorganisms via inorganic or organic S-cycling processes.The S-cycling pathways are intimately linked to the carbon(C),nitrogen,phosphorus,and metal cycles,playing crucial roles in biogeochemical cycling,C sequestration,and greenhouse gas emissions through various mechanisms in the RWO continuum.This review provides a comprehensive understanding of microbially driven S cycling in the RWO continuum.We first illustrate the importance of S cycling in this continuum,including key microorganisms and functional processes(e.g.,dissimilatory sulfate reduction,S oxidation,dimethylsulfoniopropionate production,and catabolism)as well as their corresponding S flux characteristics.In particular,we emphasize recent advances in the coupling mechanisms of the S cycle with other major element cycles.We further propose important perspectives for developing microbiome engineering of S-cycling microbial communities via integration of current knowledge about the multidimensional diversity,cultivation,evolution,and interaction of S-cycling microorganisms and their coupling mechanisms in the RWO continuum,providing a new window on applying microbiome-based biotechnologies to overcome global climate challenges.展开更多
Amoeboid protists,an assemblage of organisms belonging to different phylogenetic lineages,have drawn increasing attention due to their crucial ecological roles in various environments and their potential health risks....Amoeboid protists,an assemblage of organisms belonging to different phylogenetic lineages,have drawn increasing attention due to their crucial ecological roles in various environments and their potential health risks.Currently,18S rRNA gene sequencing is widely applied for the detection of amoebae.However,it is not clear which is the best primer pair for 18S rRNA gene amplification in amoebae.This study compared the four most commonly used primer pairs for revealing the diversity,composition,core species,and community assembly processes of amoebae in water and sediments.We found that the choice of primers artificially influences the detection of community composition of amoebae.We also found that short-read fragments may lead to mismatches in taxonomy and were not suitable for phylogenetic analyses.In contrast,full-length primers could detect the highest number of amoeba lineages and annotate 80%of reads belonging to amoebae to known species.However,full-length primers did not detect as many amoeba species as V4 primers.Moreover,we showed that beta diversity and community assembly determination were largely unaffected by primer choice,but different primers could influence our interpretations of the ecological process underlying stochasticity and determinism.This study indicates that full-length read sequencing and V4 region Illumina sequencing are suitable for profiling amoeba diversity in the environment.展开更多
Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems.Although their diversity and composition have been widely investigated in aquaculture systems,the co-...Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems.Although their diversity and composition have been widely investigated in aquaculture systems,the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood.This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds.Chlorophyta and fungi were dominant phyla in the microeukaryotic–bacterial bipartite networks in water and sediment,respectively.Chlorophyta also had overrepresented links with bacteria in water.Most microeukaryotes and bacteria were classified as generalists,and tended to have symmetric positive and negative links with bacteria in both water and sediment.However,some microeukaryotes with high density of links showed asymmetric links with bacteria in water.Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections.Moreover,the microeukaryotic–bacterial bipartite network in sediment harbored significantly more nestedness than that in water.The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment.This study unveils the topology,dominant taxa,keystone species,and robustness in the microeukaryotic–bacterial bipartite networks in coastal aquaculture ecosystems.These species herein can be applied for further management of ecological services,and such knowledge may also be very useful for the regulation of other eutrophic ecosystems.展开更多
基金supported by the Hunan Provincial Key Research and Development Project(Nos.2019WK2031 and 2017SK2351)the National Natural Science Foundation of China(No.51408219)+1 种基金the Natural Science Foundation of Hu-nan Province(No.2020JJ5259)the Outstanding Youth Fund Project of the Hunan Education Department(No.18B094)。
文摘Heavy metal pollution affects soil ecological function.Biochar and compost can effectively remediate heavy metals and increase soil nutrients.The effects and mechanisms of biochar and compost amendments on soil nitrogen cycle function in heavy-metal contaminated soils are not fully understood.This study examined how biochar,compost,and their integrated use affected ammonia-oxidizing microorganisms in heavy metal polluted soil.Quantitative PCR was used to determine the abundance of ammonia-oxidizing archaea(AOA)and bacteria(AOB).Ammonia monooxygenase(AMO)activity was evaluated by the enzymelinked immunosorbent assay.Results showed that compost rather than biochar improved nitrogen conversion in soil.Biochar,compost,or their integrated application significantly reduced the effective Zn and Cd speciation.Adding compost obviously increased As and Cu effective speciation,bacterial 16 S rRNA abundance,and AMO activity.AOB,stimulated by compost addition,was significantly more abundant than AOA throughout remediation.Correlation analysis showed that AOB abundance positively correlated with NO_(3)^(-)-N(r=0.830,P<0.01),and that AMO activity had significant correlation with EC(r=-0.908,P<0.01)and water-soluble carbon(r=-0.868,P<0.01).Those seem to be the most vital factors affecting AOB community and their function in heavy metal-polluted soil remediated by biochar and compost.
基金Supported by Shandong Provincial Key Research and Development Program,No.2018CXGC1219City of Weihai Technique Extension Project,No.2016GNS023+1 种基金TaiShan Scholars Program of Shandong Province,No.tshw20120206TaiShan Industrial Experts Program,No.tscy20190612.
文摘In this review,we summarize the recent microbiome studies related to diabetes disease and discuss the key findings that show the early emerging potential causal roles for diabetes.On a global scale,diabetes causes a significant negative impact to the health status of human populations.This review covers type 1 diabetes and type 2 diabetes.We examine promising studies which lead to a better understanding of the potential mechanism of microbiota in diabetes diseases.It appears that the human oral and gut microbiota are deeply interdigitated with diabetes.It is that simple.Recent studies of the human microbiome are capturing the attention of scientists and healthcare practitioners worldwide by focusing on the interplay of gut microbiome and diabetes.These studies focus on the role and the potential impact of intestinal microflora in diabetes.We paint a clear picture of how strongly microbes are linked and associated,both positively and negatively,with the fundamental and essential parts of diabetes in humans.The microflora seems to have an endless capacity to impact and transform diabetes.We conclude that there is clear and growing evidence of a close relationship between the microbiota and diabetes and this is worthy of future investments and research efforts.
基金supported by the National Research Foundation of Korea(NRF)funded by the Korea government(MSIT)(NRF-2022R1C1C2003502)to HSKby Basic Science Research Program through the National Research Foundation of Korea(NRF)funded by the Ministry of Science,ICT&Future Planning(NRF-2020R1A2C3008993 and NRF-2021M3A9D3024752)to J.W.L.Graphical elements used in the figures of this manuscript were created with BioRender.com.
文摘Dynamic communication between hepatocytes and the environment is critical in hepatocellular carcinoma (HCC) development.Clinical immunotherapy against HCC is currently unsatisfactory and needs more systemic considerations, including theidentification of new biomarkers and immune checkpoints. Transmembrane 4 L six family member 5 (TM4SF5) is known to promoteHCC, but it remains unclear how cancerous hepatocytes avoid immune surveillance and whether avoidance can be blocked. Weinvestigated how TM4SF5-mediated hepatic tumorigenesis avoids surveillance by natural killer (NK) cells, which are prevalent in theliver, and whether the avoidance can be blocked by anti-TM4SF5 agents. We used comprehensive structure activity relationshipanalysis to identify TM4SF5-specific isoxazole (TSI)-based small molecules that inhibit TM4SF5-mediated effects. TM4SF5 expressedby hepatocytes reduced NK cell cytotoxicity by downregulating stimulatory ligands/receptors, including signaling lymphocyticactivation molecule family member 7 (SLAMF7). TM4SF5 bound SLAMF7 depending on N-glycosylation and caused intracellulartrafficking of SLAMF7 from the plasma membrane to lysosomes for degradation. TSI treatments in cell lines and animal models ofHCC blocked this binding, intracellular trafficking, and downregulation, resulting in higher levels of stimulatory NK cell ligands. Inmouse xenograft models, TSI treatment abrogated HCC development by increasing the abundance and dispersion of Slamf7-positive cells in liver tissues, recapitulating the phenotype of Tm4sf5-knockout mice and indicating TSI-mediated restoration of NKcell surveillance. These findings suggest that TSIs can inhibit TM4SF5-mediated liver carcinogenesis by increasing NK cellsurveillance.
基金supported by the Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(SML2020SP004)the National Natural Science Foundation of China(91951207,32100077,31770539,31870469,42177011,41676105,41771095,62170346)the China Postdoctoral Science Foundation(2021M703751).
文摘Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycling of rhizosphere microbiomes remains unclear.To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres,we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies.Compared with the native mangrove(Kandelia obovata,KO),the introduced mangrove(Sonneratia apetala,SA)rhizosphere microbiome had significantly(p<0.05)higher average genome size(AGS)(5.8 vs.5.5 Mb),average 16S ribosomal RNA gene copy number(3.5 vs.3.1),relative abundances of mobile genetic elements,and functional diversity in terms of the Shannon index(7.88 vs.7.84)but lower functional potentials involved in CH4 cycling(e.g.,mcrABCDG and pmoABC),N2 fixation(nifHDK),and inorganic S cycling(dsrAB,dsrC,dsrMKJOP,soxB,sqr,and fccAB).Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere.Additionally,salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes.This study advances our understanding of microbially mediated biogeochemical cycling of CH_(4),N,and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions,which has important implications for future mangrove reforestation.
文摘The role of microbiota in health and diseases is being highlighted by numerous studies since its discovery.Depending on the localized regions,microbiota can be classified into gut,oral,respiratory,and skin microbiota.The microbial communities are in symbiosis with the host,contributing to homeostasis and regulating immune function.However,microbiota dysbiosis can lead to dysregulation of bodily functions and diseases including cardiovascular diseases(CVDs),cancers,respiratory diseases.
基金This study was supported by the National Natural Science Foundation of China(Grant Nos.41922049 and 41877111)the Fundamental Research Funds for the Central Universities(No.19lgzd30)the Guangzhou Science and Technology Program general project(No.201804010141).
文摘Due to the toxicity of bioaccumulative organohalides to human beings and ecosystems,a variety of biotic and abiotic remediation methods have been developed to remove organohalides from contaminated environments.Bioremediation employing organohalide-respiring bacteria(OHRB)-mediated microbial reductive dehalogenation(Bio-RD)represents a cost-effective and environmentally friendly approach to attenuate highly-halogenated organohalides,specifically organohalides in soil,sediment and other anoxic environments.Nonetheless,many factors severely restrict the implications of OHRB-based bioremediation,including incomplete dehalogenation,low abundance of OHRB and consequent low dechlorination activity.Recently,the development of in situ chemical oxidation(ISCO)based on sulfate radicals(SO_(4)^(·−))via the persulfate activation and oxidation(PAO)process has attracted tremendous research interest for the remediation of lowly-halogenated organohalides due to its following advantages,e.g.,complete attenuation,high reactivity and no selectivity to organohalides.Therefore,integration of OHRB-mediated Bio-RD and subsequent PAO(Bio-RD-PAO)may provide a promising solution to the remediation of organohalides.In this review,we first provide an overview of current progress in Bio-RD and PAO and compare their limitations and advantages.We then critically discuss the integration of Bio-RD and PAO(Bio-RD-PAO)for complete attenuation of organohalides and its prospects for future remediation applications.Overall,Bio-RD-PAO opens up opportunities for complete attenuation and consequent effective in situ remediation of persistent organohalide pollution.
基金supported by the National Natural Science Foundation of China(31400109,31372202)the Youth Innovation Promotion Association,Chinese Academy of Sciences(Y22Z07)
文摘Gut microbiota of four economically important Asian carp species(silver carp, Hypophthalmichthys molitrix; bighead carp,Hypophthalmichthys nobilis; grass carp, Ctenopharyngodon idella; common carp, Cyprinus carpio) were compared using 16 S rRNA gene pyrosequencing. Analysis of more than 590,000 quality-filtered sequences obtained from the foregut, midgut and hindgut of these four carp species revealed high microbial diversity among the samples. The foregut samples of grass carp exhibited more than 1,600 operational taxonomy units(OTUs) and the highest alpha-diversity index, followed by the silver carp foregut and midgut. Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria were the predominant phyla regardless of fish species or gut type. Pairwise(weighted) UniFrac distance-based permutational multivariate analysis of variance with fish species as a factor produced significant association(P<0.01). The gut microbiotas of all four carp species harbored saccharolytic or proteolytic microbes, likely in response to the differences in their feeding habits. In addition, extensive variations were also observed even within the same fish species. Our results indicate that the gut microbiotas of Asian carp depend on the exact species, even when the different species were cohabiting in the same environment. This study provides some new insights into developing commercial fish feeds and improving existing aquaculture strategies.
基金support from the National Natural Science Foundation of China (42141003, 91851210, 41876119, 42188102, 91751207, and 91951207)the National Key Research and Development Program of China (2018YFA06055800 and 2020YFA0607600)+9 种基金support by the Korean Ministry of Oceans and Fisheries (20220558)the National Research Foundation of Korea (NRF-2018R1A2B2006340)support by the German Academic Exchange service (Deutscher Akademischer Austauschdienst, Make Our Planet Great Again-German Research Initiative, 57429828)the German Federal Ministry of Education and Researchsupport by the joint National Natural Science Foundation of China-Israel Science Foundation (NSFC-ISF) Research Program (42161144006 and 3511/21, respectively)support by the Russian Foundation for Basic Research (20-05-00381-a)the Russian Fundamental Programs of Pacific Oceanological Institute (01201363041 and 01201353055)supported by the following provincial and municipal authorities of China: Southern Marine Science and Engineering Guangdong Laboratory (K19313901) (Guangzhou)Southern Marine Science and Engineering Guangdong Laboratory (SML2020SP004) (Zhuhai)Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology (ZDSYS201802081843490)。
文摘The goal of achieving carbon neutrality in the next 30-40 years is approaching worldwide consensus and requires coordinated efforts to combat the increasing threat of climate change.Two main sets of actions have been proposed to address this grand goal.One is to reduce anthropogenic CO2emissions to the atmosphere,and the other is to increase carbon sinks or negative emissions,i.e.,removing CO2from the atmosphere.Here we advocate eco-engineering approaches for ocean negative carbon emission(ONCE),aiming to enhance carbon sinks in the marine environment.An international program is being established to promote coordinated efforts in developing ONCE-relevant strategies and methodologies,taking into consideration ecological/biogeochemical processes and mechanisms related to different forms of carbon(inorganic/organic,biotic/abiotic,particulate/dissolved) for sequestration.We focus on marine ecosystem-based approaches and pay special attention to mechanisms that require transformative research,including those elucidating interactions between the biological pump(BP),the microbial carbon pump(MCP),and microbially induced carbonate precipitation(MICP).Eutrophic estuaries,hypoxic and anoxic waters,coral reef ecosystems,as well as aquaculture areas are particularly considered in the context of efforts to increase their capacity as carbon sinks.ONCE approaches are thus expected to be beneficial for both carbon sequestration and alleviation of environmental stresses.
基金This work was supported by the National Natural Science Foundation of China(92051120)the Science&Technology Basic Resources Investigation Program of China(2017FY100300)+1 种基金the Fundamental Research Funds for the Central Universities(191gzd28)the Sun Yat-sen University(project no.18821107).
文摘Submerged plants in wetlands play important roles as ecosystem engineers to improve self-purification and promote elemental cycling.However,their effects on the functional capacity of microbial communities in wetland sediments remain poorly understood.Here,we provide detailed metagenomic insights into the biogeochemical potential of microbial communities in wetland sediments with and without submerged plants(i.e.,Vallisneria natans).A large number of functional genes involved in carbon(C),nitrogen(N)and sulfur(S)cycling were detected in the wetland sediments.However,most functional genes showed higher abundance in sediments with submerged plants than in those without plants.Based on the comparison of annotated functional genes in the N and S cycling databases(i.e.,NCycDB and SCycDB),we found that genes involved in nitrogen fixation(e.g.,nifD/H/K/W),assimilatory nitrate reduction(e.g.,nasA and nirA),denitrification(e.g.,nirK/S and nosZ),assimilatory sulfate reduction(e.g.,cysD/H/J/N/Q and sir),and sulfur oxidation(e.g.,glpE,soeA,sqr and sseA)were significantly higher(correctedp<0.05)in vegetated vs.unvegetated sediments.This could be mainly driven by environmental factors including total phosphorus,total nitrogen,and C:N ratio.The binning of metagenomes further revealed that some archaeal taxa could have the potential of methane metabolism including hydrogenotrophic,acetoclastic,and methylotrophic methanogenesis,which are crucial to the wetland methane budget and carbon cycling.This study opens a new avenue for linking submerged plants with microbial functions,and has further implications for understanding global carbon,nitrogen and sulfur cycling in wetland ecosystems.
基金supported by the National Natural Science Foundation of China(92251306,91951207,and 321000-77)the Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(SML2020SP004,SML2021SP203,and 311022011)the China Postdoctoral Science Foundation(2021M703751).
文摘Sulfur(S)is an essential biological element,and S cycling is mainly driven by metabolically versatile microorganisms.The river–wetland–ocean(RWO)continuum here is defined as the dynamically connected region with estuary,wetland,and near-marine ecosystems,and it is considered a hotspot of biogeochemical cycling,especially a major biotope for S cycling.Various forms and oxidation states of S compounds are considered ideal electron donors or acceptors and are widely utilized by microorganisms via inorganic or organic S-cycling processes.The S-cycling pathways are intimately linked to the carbon(C),nitrogen,phosphorus,and metal cycles,playing crucial roles in biogeochemical cycling,C sequestration,and greenhouse gas emissions through various mechanisms in the RWO continuum.This review provides a comprehensive understanding of microbially driven S cycling in the RWO continuum.We first illustrate the importance of S cycling in this continuum,including key microorganisms and functional processes(e.g.,dissimilatory sulfate reduction,S oxidation,dimethylsulfoniopropionate production,and catabolism)as well as their corresponding S flux characteristics.In particular,we emphasize recent advances in the coupling mechanisms of the S cycle with other major element cycles.We further propose important perspectives for developing microbiome engineering of S-cycling microbial communities via integration of current knowledge about the multidimensional diversity,cultivation,evolution,and interaction of S-cycling microorganisms and their coupling mechanisms in the RWO continuum,providing a new window on applying microbiome-based biotechnologies to overcome global climate challenges.
基金supported by the National Natural Science Foundation of China(31970384,41907021,21806044,92051120,31802350)the Fundamental Research Funds for the Central Universities Sun Yat-sen University(22lgqb22,19lgzd28)+3 种基金the Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(311021006)the Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(SML2021SP203)the Guangdong Natural Resources Department Contract(GDNRC[2021]62)Guangzhou Basic and Applied Basic Research Foundation(202102020257)。
文摘Amoeboid protists,an assemblage of organisms belonging to different phylogenetic lineages,have drawn increasing attention due to their crucial ecological roles in various environments and their potential health risks.Currently,18S rRNA gene sequencing is widely applied for the detection of amoebae.However,it is not clear which is the best primer pair for 18S rRNA gene amplification in amoebae.This study compared the four most commonly used primer pairs for revealing the diversity,composition,core species,and community assembly processes of amoebae in water and sediments.We found that the choice of primers artificially influences the detection of community composition of amoebae.We also found that short-read fragments may lead to mismatches in taxonomy and were not suitable for phylogenetic analyses.In contrast,full-length primers could detect the highest number of amoeba lineages and annotate 80%of reads belonging to amoebae to known species.However,full-length primers did not detect as many amoeba species as V4 primers.Moreover,we showed that beta diversity and community assembly determination were largely unaffected by primer choice,but different primers could influence our interpretations of the ecological process underlying stochasticity and determinism.This study indicates that full-length read sequencing and V4 region Illumina sequencing are suitable for profiling amoeba diversity in the environment.
基金This study was supported by the Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(SML2021SP203,313022004)the National Natural Science Foundation of China(32102821,92051120)+4 种基金the Yongjiang Talent Introduction Programme,the Natural Science Foundation of Ningbo(2022J050)the Zhejiang Major Program of Science and Technology(2021C02069-5-4)the Key Research and Development Program of Zhejiang Province(2019C02054)the Key Research and Development Program of Ningbo(2022Z172)China Agriculture Research System of MOF and MARA.
文摘Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems.Although their diversity and composition have been widely investigated in aquaculture systems,the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood.This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds.Chlorophyta and fungi were dominant phyla in the microeukaryotic–bacterial bipartite networks in water and sediment,respectively.Chlorophyta also had overrepresented links with bacteria in water.Most microeukaryotes and bacteria were classified as generalists,and tended to have symmetric positive and negative links with bacteria in both water and sediment.However,some microeukaryotes with high density of links showed asymmetric links with bacteria in water.Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections.Moreover,the microeukaryotic–bacterial bipartite network in sediment harbored significantly more nestedness than that in water.The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment.This study unveils the topology,dominant taxa,keystone species,and robustness in the microeukaryotic–bacterial bipartite networks in coastal aquaculture ecosystems.These species herein can be applied for further management of ecological services,and such knowledge may also be very useful for the regulation of other eutrophic ecosystems.
