1
|
Guo Y, Cheng S, Fang H, Geng J, Li Y, Shi F, Wang H, Chen L, Zhou Y. Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135626. [PMID: 39197279 DOI: 10.1016/j.jhazmat.2024.135626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/27/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024]
Abstract
The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.
Collapse
Affiliation(s)
- Yifan Guo
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulan Cheng
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huajun Fang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; The Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an 343000, China.
| | - Jing Geng
- School of Geospatial Engineering and Science, Sun Yat-sen University, Zhuhai 519082, China
| | - Yuna Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangying Shi
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Chen
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhou
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
2
|
Feng XY, Li Q, Liu Y, Zhang YM, Shao ZQ. Evolutionary and immune-activating character analyses of NLR genes in algae suggest the ancient origin of plant intracellular immune receptors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2316-2330. [PMID: 38972042 DOI: 10.1111/tpj.16919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/24/2024] [Accepted: 06/18/2024] [Indexed: 07/09/2024]
Abstract
Nucleotide-binding leucine-rich repeat (NLR) proteins are crucial intracellular immune receptors in plants, responsible for detecting invading pathogens and initiating defense responses. While previous studies on the evolution and function of NLR genes were mainly limited to land plants, the evolutionary trajectory and immune-activating character of NLR genes in algae remain less explored. In this study, genome-wide NLR gene analysis was conducted on 44 chlorophyte species across seven classes and seven charophyte species across five classes. A few but variable number of NLR genes, ranging from one to 20, were identified in five chlorophytes and three charophytes, whereas no NLR gene was identified from the remaining algal genomes. Compared with land plants, algal genomes possess fewer or usually no NLR genes, implying that the expansion of NLR genes in land plants can be attributed to their adaptation to the more complex terrestrial pathogen environments. Through phylogenetic analysis, domain composition analysis, and conserved motifs profiling of the NBS domain, we detected shared and lineage-specific features between NLR genes in algae and land plants, supporting the common origin and continuous evolution of green plant NLR genes. Immune-activation assays revealed that both TNL and RNL proteins from green algae can elicit hypersensitive responses in Nicotiana benthamiana, indicating the molecular basis for immune activation has emerged in the early evolutionary stage of different types of NLR proteins. In summary, the results from this study suggest that NLR proteins may have taken a role as intracellular immune receptors in the common ancestor of green plants.
Collapse
Affiliation(s)
- Xing-Yu Feng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Qian Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yan-Mei Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| |
Collapse
|
3
|
Liu Y, Delgado-Baquerizo M, Bing H, Wang Y, Wang J, Chen J, Qiu S, Zhu H, Wu Y, Fang L, Chang R. Warming-induced shifts in alpine soil microbiome: An ecosystem-scale study with environmental context-dependent insights. ENVIRONMENTAL RESEARCH 2024; 255:119206. [PMID: 38782346 DOI: 10.1016/j.envres.2024.119206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Climate warming is a pressing global issue with substantial impacts on soil health and function. However, the influence of environmental context on the responses of soil microorganisms to warming remains largely elusive, particularly in alpine ecosystems. This study examined the responses of the soil microbiome to in situ experimental warming across three elevations (3850 m, 4100 m, and 4250 m) in the meadow of Gongga Mountain, eastern Tibetan Plateau. Our findings demonstrate that soil microbial diversity is highly resilient to warming, with significant impacts observed only at specific elevations. Furthermore, the influence of warming on the composition of the soil microbial community is also elevation-dependent, underscoring the importance of local environmental context in shaping microbial evolution in alpine soils under climate warming. Notably, we identified soil moisture at 3850 m and carbon-to-nitrogen ratio at 4250 m as indirect predictors regulating the responses of microbial diversity to warming at specific elevations. These findings underscore the paramount importance of considering pre-existing environmental conditions in predicting the response of alpine soil microbiomes to climate warming. Our study provides novel insights into the intricate interactions between climate warming, soil microbiome, and environmental context in alpine ecosystems, illuminating the complex mechanisms governing soil microbial ecology in these fragile and sensitive environments.
Collapse
Affiliation(s)
- Ye Liu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Institutode Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Haijian Bing
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China.
| | - Yuhan Wang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China; Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, 430070, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, 710061, China
| | - Shaojun Qiu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
| | - He Zhu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
| | - Yanhong Wu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
| | - Linchuan Fang
- Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, 430070, China
| | - Ruiying Chang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
| |
Collapse
|
4
|
Hu Y, Zhang X, Chen H, Jiang Y, Zhang J. Effects of forest age and season on soil microbial communities in Chinese fir plantations. Microbiol Spectr 2024; 12:e0407523. [PMID: 38980023 PMCID: PMC11302042 DOI: 10.1128/spectrum.04075-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
Understanding changes in the distribution patterns and diversity of soil microbial communities from the perspectives of age-related changes, seasonal variations, and the interaction between the two factors can facilitate the management of plantations. In Chinese fir plantations, we collected soils from different depths in over-mature forests, mature forests, near-mature forests, middle-aged forests, and young forests in summer, autumn, and winter in China's subtropical regions. As the forests developed, bacterial and fungal communities' diversity changed, reached a minimum value at near-mature forests, and then increased in mature forests or over-mature forests. Near-mature forests had the lowest topological properties. The Shannon index of microbial communities varied with seasonal changes (P < 0.05). Bacterial and fungal community composition at genus level was more closely related to temperature indicators (including daily average temperature, daily maximum temperature, and daily minimum temperature) (P < 0.01, 0.5554 < R2 <0.8185) than daily average precipitation (P > 0.05, 0.0321 < R2 <0.6773). Bacteria were clustered by season and fungi were clustered by forest age. We suggested that extending the tree cultivation time of plantations could promote microbial community recovery. In addition, we found some species worthy of attention, including Bacteroidetes in autumn in over-mature forests, and Firmicutes in summer in young forests.IMPORTANCEChinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important fast-growing species with the largest artificial forest area in China, with the outstanding problems of low quality in soil. Soil microorganisms play a crucial role in soil fertility by decomposing organic matter, optimizing soil structure, and releasing essential nutrients for plant growth. In order to maintain healthy soil quality and prevent nutrient depletion and land degradation, it is crucial to understand the changes of soil microbial composition and diversity. Our study determined to reveal the change of soil microbial community from stand age, season, and the interaction between the two aspects, which is helpful to understand how interannual changes in different years and seasonal changes in one year affect soil fertility restoration and sustainable forest plantation management. It is a meaningful exploration of soil microbial communities and provides new information for further research.
Collapse
Affiliation(s)
- Yuxin Hu
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xiongqing Zhang
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Hanyue Chen
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yihang Jiang
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianguo Zhang
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
5
|
Boisseaux M, Troispoux V, Bordes A, Cazal J, Cazal SO, Coste S, Stahl C, Schimann H. Are plant traits drivers of endophytic communities in seasonally flooded tropical forests? AMERICAN JOURNAL OF BOTANY 2024:e16366. [PMID: 39010811 DOI: 10.1002/ajb2.16366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 07/17/2024]
Abstract
PREMISE In the Amazon basin, seasonally flooded (SF) forests offer varying water constraints, providing an excellent way to investigate the role of habitat selection on microbial communities within plants. However, variations in the microbial community among host plants cannot solely be attributed to environmental factors, and how plant traits contribute to microbial assemblages remains an open question. METHODS We described leaf- and root-associated microbial communities using ITS2 and 16 S high-throughput sequencing and investigated the stochastic-deterministic balance shaping these community assemblies using two null models. Plant ecophysiological functioning was evaluated by focusing on 10 leaf and root traits in 72 seedlings, belonging to seven tropical SF tree species in French Guiana. We then analyzed how root and leaf traits drove the assembly of endophytic communities. RESULTS While both stochastic and deterministic processes governed the endophyte assembly in the leaves and roots, stochasticity prevailed. Discrepancies were found between fungi and bacteria, highlighting that these microorganisms have distinct ecological strategies within plants. Traits, especially leaf traits, host species and spatial predictors better explained diversity than composition, but they were modest predictors overall. CONCLUSIONS This study widens our knowledge about tree species in SF forests, a habitat sensitive to climate change, through the combined analyses of their associated microbial communities with functional traits. We emphasize the need to investigate other plant traits to better disentangle the drivers of the relationship between seedlings and their associated microbiomes, ultimately enhancing their adaptive capacities to climate change.
Collapse
Affiliation(s)
- Marion Boisseaux
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Valérie Troispoux
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Alice Bordes
- Université Grenoble Alpes, INRAE, URLESSEM, Saint-Martin-d'Hères, France, Grenoble, France
| | - Jocelyn Cazal
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Saint-Omer Cazal
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Sabrina Coste
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Clément Stahl
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Heidy Schimann
- INRAE, Université de Bordeaux, BIOGECO, Cestas, 33610, France
| |
Collapse
|
6
|
Berrios L, Bogar GD, Bogar LM, Venturini AM, Willing CE, Del Rio A, Ansell TB, Zemaitis K, Velickovic M, Velickovic D, Pellitier PT, Yeam J, Hutchinson C, Bloodsworth K, Lipton MS, Peay KG. Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities. mSystems 2024; 9:e0036924. [PMID: 38717159 PMCID: PMC11237468 DOI: 10.1128/msystems.00369-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 06/19/2024] Open
Abstract
Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.
Collapse
Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, California, USA
| | - Glade D. Bogar
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
| | - Laura M. Bogar
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | | | - Claire E. Willing
- Department of Biology, Stanford University, Stanford, California, USA
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Anastacia Del Rio
- Department of Biology, Stanford University, Stanford, California, USA
| | - T. Bertie Ansell
- Department of Biology, Stanford University, Stanford, California, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Kevin Zemaitis
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Marija Velickovic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Dusan Velickovic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Jay Yeam
- Department of Biology, Stanford University, Stanford, California, USA
| | - Chelsea Hutchinson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kent Bloodsworth
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Mary S. Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| |
Collapse
|
7
|
Shang Y, Wang X, Wu X, Dou H, Wei Q, Wang Q, Liu G, Sun G, Wang L, Zhang H. Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors. Microbiol Spectr 2024; 12:e0324523. [PMID: 38602397 PMCID: PMC11064641 DOI: 10.1128/spectrum.03245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.
Collapse
Affiliation(s)
- Yongquan Shang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xibao Wang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xiaoyang Wu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Qinguo Wei
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Gang Liu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Guolei Sun
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Lidong Wang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Honghai Zhang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| |
Collapse
|
8
|
Liu C, Wang Y, Zhou Z, Wang S, Wei Z, Ravanbakhsh M, Shen Q, Xiong W, Kowalchuk GA, Jousset A. Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions. THE ISME JOURNAL 2024; 18:wrae169. [PMID: 39259188 PMCID: PMC11453101 DOI: 10.1093/ismejo/wrae169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/26/2024] [Accepted: 09/03/2024] [Indexed: 09/12/2024]
Abstract
Antibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top-down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.
Collapse
Affiliation(s)
- Chen Liu
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Key Laboratory of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, No. 1 Weigang, Xuanwu district, Nanjing 210095, People’s Republic of China
| | - Yijin Wang
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Key Laboratory of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, No. 1 Weigang, Xuanwu district, Nanjing 210095, People’s Republic of China
| | - Zeyuan Zhou
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Key Laboratory of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, No. 1 Weigang, Xuanwu district, Nanjing 210095, People’s Republic of China
| | - Shimei Wang
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Key Laboratory of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, No. 1 Weigang, Xuanwu district, Nanjing 210095, People’s Republic of China
| | - Zhong Wei
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Key Laboratory of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, No. 1 Weigang, Xuanwu district, Nanjing 210095, People’s Republic of China
| | - Mohammadhossein Ravanbakhsh
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Key Laboratory of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, No. 1 Weigang, Xuanwu district, Nanjing 210095, People’s Republic of China
| | - Wu Xiong
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Key Laboratory of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, No. 1 Weigang, Xuanwu district, Nanjing 210095, People’s Republic of China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre Jousset
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Key Laboratory of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, No. 1 Weigang, Xuanwu district, Nanjing 210095, People’s Republic of China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
9
|
Netherway T, Bengtsson J, Buegger F, Fritscher J, Oja J, Pritsch K, Hildebrand F, Krab EJ, Bahram M. Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe. Nat Commun 2024; 15:159. [PMID: 38167673 PMCID: PMC10761831 DOI: 10.1038/s41467-023-44172-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.
Collapse
Affiliation(s)
- Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden.
| | - Jan Bengtsson
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
| | - Franz Buegger
- Research Unit for Environmental Simulation (EUS), German Research Center for Environmental Health, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Joachim Fritscher
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Digital Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Jane Oja
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Karin Pritsch
- Research Unit for Environmental Simulation (EUS), German Research Center for Environmental Health, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Digital Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Eveline J Krab
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, 750 07, Uppsala, Sweden
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| |
Collapse
|
10
|
Cerk K, Ugalde‐Salas P, Nedjad CG, Lecomte M, Muller C, Sherman DJ, Hildebrand F, Labarthe S, Frioux C. Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing. Microb Biotechnol 2024; 17:e14396. [PMID: 38243750 PMCID: PMC10832553 DOI: 10.1111/1751-7915.14396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 11/27/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024] Open
Abstract
Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.
Collapse
Affiliation(s)
- Klara Cerk
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | | | - Chabname Ghassemi Nedjad
- Inria, University of Bordeaux, INRAETalenceFrance
- University of Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800TalenceFrance
| | - Maxime Lecomte
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE STLO¸University of RennesRennesFrance
| | | | | | - Falk Hildebrand
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Simon Labarthe
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE, University of Bordeaux, BIOGECO, UMR 1202CestasFrance
| | | |
Collapse
|
11
|
Sun Z, Adeleke BS, Shi Y, Li C. The seed microbiomes of staple food crops. Microb Biotechnol 2023; 16:2236-2249. [PMID: 37815330 PMCID: PMC10686132 DOI: 10.1111/1751-7915.14352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
The scientific community increasingly recognized that seed microbiomes are important for plant growth and nutrition. The versatile roles and modulating properties that microbiomes hold in the context of seeds seem to be an inherited approach to avert adverse conditions. These discoveries attracted extensive interest, especially in staple food crops (SFCs) where grain was consumed as food. Along with the rapid expansion of population and industrialization that posed a severe challenge to the yield of SFCs, microbiologists and botanists began to explore and engineer seed microbiomes, for safer and more fruitful grain production. To utilize seed microbiomes, we present an overall review of the most updated scientific literature on three representative SFCs (wheat, rice and maize) using the 5W1H (Which, Where, What, Why, When and How) method that provides a comprehensive understanding of the issue. These include which factors determine the composition of seed microbiomes? Where do seed microbiomes come from? What are these seed microbes? Why do these microbes choose seeds as their destination and when do microbes settle down and become seed communists? In addition, how do seed microbiomes work and can be manipulated effectively? Therefore, answering the aforementioned questions regarding SFCs seed microbiomes remain fundamental in bridging endophytic research gaps and harnessing their ecological services.
Collapse
Affiliation(s)
- Zhongke Sun
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
- Food Laboratory of ZhongyuanLuoheChina
| | - Bartholomew Saanu Adeleke
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
- Department of Biological Sciences, School of ScienceOlusegun Agagu University of Science and TechnologyOkitipupaNigeria
| | - Yini Shi
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
| | - Chengwei Li
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
| |
Collapse
|
12
|
Simister RL, Iulianella Phillips BP, Wickham AP, Cayer EM, Hart CJR, Winterburn PA, Crowe SA. DNA sequencing, microbial indicators, and the discovery of buried kimberlites. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:387. [PMID: 38665197 PMCID: PMC11041713 DOI: 10.1038/s43247-023-01020-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 09/19/2023] [Indexed: 04/28/2024]
Abstract
Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.
Collapse
Affiliation(s)
- Rachel L. Simister
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Bianca P. Iulianella Phillips
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Andrew P. Wickham
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Erika M. Cayer
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Craig J. R. Hart
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Peter A. Winterburn
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Sean A. Crowe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| |
Collapse
|
13
|
Chauhan BV, Higgins Jones D, Banerjee G, Agrawal S, Sulaiman IM, Jia C, Banerjee P. Indoor Bacterial and Fungal Burden in "Moldy" versus "Non-Moldy" Homes: A Case Study Employing Advanced Sequencing Techniques in a US Metropolitan Area. Pathogens 2023; 12:1006. [PMID: 37623966 PMCID: PMC10457890 DOI: 10.3390/pathogens12081006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
The presence of fungi in the indoor environment is associated with allergies and other respiratory symptoms. The aim of this study was to use sequencing and molecular methods, including next-generation sequencing (NGS) approaches, to explore the bacterial and fungal communities and their abundance in the indoor environment of houses (n = 20) with visible "moldy" (HVM) and nonvisible "non-moldy" (HNM) in Memphis, TN, USA. Dust samples were collected from air vents and ground surfaces, and the total DNA was analyzed for bacteria and fungi by amplifying 16S rRNA and ITS genes on the Illumina Miseq. Results indicated that Leptosphaerulina was the most abundant fungal genus present in the air vent and ground samples from HNM and HVM. At the same time, the most abundant bacterial genera in the air vent and ground samples were Propionibacterium and Streptococcus. The fungi community diversity was significantly different in the air vent samples. The abundance of fungal species known to be associated with respiratory diseases in indoor dust samples was similar, regardless of the visibility of fungi in the houses. The existence of fungi associated with respiratory symptoms was compared with several parameters like dust particulate matter (PM), CO2 level, temperature, and humidity. Most of these parameters are either positively or negatively correlated with the existence of fungi associated with respiratory diseases; however, none of these correlations were significant at p = 0.05. Our results indicate that implementing molecular methods for detecting indoor fungi may strengthen common exposure and risk assessment practices.
Collapse
Affiliation(s)
- Bhavin V. Chauhan
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | | | - Goutam Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Saumya Agrawal
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Irshad M. Sulaiman
- Southeast Regional Laboratory, U.S. Food and Drug Administration, Atlanta, GA 30309, USA
| | - Chunrong Jia
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Pratik Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| |
Collapse
|
14
|
Hao Y, Pan Y, Chen W, Rashid MAR, Li M, Che N, Duan X, Zhao Y. Contribution of Duplicated Nucleotide-Binding Leucine-Rich Repeat (NLR) Genes to Wheat Disease Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:2794. [PMID: 37570947 PMCID: PMC10420896 DOI: 10.3390/plants12152794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
Wheat has a large and diverse repertoire of NLRs involved in disease resistance, with over 1500 NLRs detected in some studies. These NLR genes occur as singletons or clusters containing copies of NLRs from different phylogenetic clades. The number of NLRs and cluster size can differ drastically among ecotypes and cultivars. Primarily, duplication has led to the evolution and diversification of NLR genes. Among the various mechanisms, whole genome duplication (WGD) is the most intense and leading cause, contributing to the complex evolutionary history and abundant gene set of hexaploid wheat. Tandem duplication or recombination is another major mechanism of NLR gene expansion in wheat. The diversity and divergence of duplicate NLR genes are responsible for the broad-spectrum resistance of most plant species with limited R genes. Understanding the mechanisms underlying the rapid evolution and diversification of wheat NLR genes will help improve disease resistance in crops. The present review focuses on the diversity and divergence of duplicate NLR genes and their contribution to wheat disease resistance. Moreover, we provide an overview of disease resistance-associated gene duplication and the underlying strategies in wheat.
Collapse
Affiliation(s)
- Yongchao Hao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Wuying Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Muhammad Abdul Rehman Rashid
- Department of Agricultural Sciences/Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Mengyao Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Naixiu Che
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Xu Duan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| |
Collapse
|
15
|
Wei X, Fu T, He G, Zhong Z, Yang M, Lou F, He T. Types of vegetables shape composition, diversity, and co-occurrence networks of soil bacteria and fungi in karst areas of southwest China. BMC Microbiol 2023; 23:194. [PMID: 37468849 PMCID: PMC10354930 DOI: 10.1186/s12866-023-02929-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Microorganisms are of significant importance in soil. Yet their association with specific vegetable types remains poorly comprehended. This study investigates the composition of bacterial and fungal communities in soil by employing high-throughput sequencing of 16 S rRNA genes and ITS rRNA genes while considering the cultivation of diverse vegetable varieties. RESULTS The findings indicate that the presence of cultivated vegetables influenced the bacterial and fungal communities leading to discernible alterations when compared to uncultivated soil. In particular, the soil of leafy vegetables (such as cabbage and kale) exhibited higher bacterial α-diversity than melon and fruit vegetable (such as cucumber and tomato), while fungal α-diversity showed an inverse pattern. The prevailing bacterial phyla in both leafy vegetable and melon and fruit vegetable soils were Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. In leafy vegetable soil, dominant fungal phyla included Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota whereas in melon and fruit vegetable soil. Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota held prominence. Notably, the relative abundance of Ascomycota was lower in leafy vegetable soil compared to melon and fruit vegetable soil. Moreover, leafy vegetable soil exhibited a more complex and stable co-occurrence network in comparison to melon and fruit vegetable soil. CONCLUSION The findings enhance our understanding of how cultivated soil bacteria and fungi respond to human disturbance, thereby providing a valuable theoretical basis for soil health in degraded karst areas of southwest China.
Collapse
Affiliation(s)
- Xiaoliao Wei
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Tianling Fu
- Institute of New Rural Development, Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, PR China
| | - Guandi He
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Zhuoyan Zhong
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Fei Lou
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Tengbing He
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China.
- Institute of New Rural Development, Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, PR China.
| |
Collapse
|
16
|
Ma X, Ren B, Yu J, Wang J, Bai L, Li J, Li D, Meng M. Changes in grassland soil types lead to different characteristics of bacterial and fungal communities in Northwest Liaoning, China. Front Microbiol 2023; 14:1205574. [PMID: 37448571 PMCID: PMC10336218 DOI: 10.3389/fmicb.2023.1205574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Soil microbial communities are critical in regulating grassland biogeochemical cycles and ecosystem functions, but the mechanisms of how environmental factors affect changes in the structural composition and diversity of soil microbial communities in different grassland soil types is not fully understood in northwest Liaoning, China. Methods We investigated the characteristics and drivers of bacterial and fungal communities in 4 grassland soil types with 11 sites across this region using high-throughput Illumina sequencing. Results and Discussion Actinobacteria and Ascomycota were the dominant phyla of bacterial and fungal communities, respectively, but their relative abundances were not significantly different among different grassland soil types. The abundance, number of OTUs, number of species and diversity of both bacterial and fungal communities in warm and temperate ecotone soil were the highest, while the warm-temperate shrub soil had the lowest microbial diversity. Besides, environmental factors were not significantly correlated with soil bacterial Alpha diversity index. However, there was a highly significant negative correlation between soil pH and Shannon index of fungal communities, and a highly significant positive correlation between plant cover and Chao1 index as well as Observed species of fungal communities. Analysis of similarities showed that the structural composition of microbial communities differed significantly among different grassland soil types. Meanwhile, the microbial community structure of temperate steppe-sandy soil was significantly different from that of other grassland soil types. Redundancy analysis revealed that soil total nitrogen content, pH and conductivity were important influencing factors causing changes in soil bacterial communities, while soil organic carbon, total nitrogen content and conductivity mainly drove the differentiation of soil fungal communities. In addition, the degree of connection in the soil bacterial network of grassland was much higher than that in the fungal network and soil bacterial and fungal communities were inconsistently limited by environmental factors. Our results showed that the microbial community structure, composition and diversity of different grassland soil types in northwest Liaoning differed significantly and were significantly influenced by environmental factors. Microbial community structure and the observation of soil total nitrogen and organic carbon content can predict the health changes of grassland ecosystems to a certain extent.
Collapse
|
17
|
Wang J, Chen Y, Du W, Yang S, He Y, Zhao X, Sun W, Chen Q. Insights into the responses of fungal taxonomy and function to different metal(loid) contamination levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162931. [PMID: 36934934 DOI: 10.1016/j.scitotenv.2023.162931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
Fungi possess prominent tolerance and detoxification capacities in highly metal(loid)-polluted systems, yet little is known about their responding behaviors under different contamination conditions. Here, we systematically investigated the structure and function profiles of fungal communities in an abandoned reservoir mainly contaminated by multiple metal(loid)s such as Al, Be, Cd, Co, Cr, and Cu. This abandoned reservoir consisted of three distinct zones, i.e., Zone I with the shortest deprecation time and the highest metal(loid) contamination; Zone II with the medium deprecation time and medium metal(loid) contamination; and Zone III with the longest abandonment time and the lowest metal(loid)contamination. The lowest pH and the highest contents of OM, TN, and TP were also observed for the high-contamination Zone I, followed by the moderate-contamination Zone II and the low-contamination Zone III. Fungal biodiversity was found to be robust and dominated by many endurable genera in Zone I, and notable cooperative relationships among fungal species facilitated their viability and prosperity under severe metal(loid) contaminations. Differently, the lowest biodiversity and fragile co-occurrence network were identified in Zone II. As metal(loid) contaminations reduced from Zone I to Zone III, dominant fungal functions gradually changed from undefined saprotroph guild to parasites or pathogens of plant-animal (i.e. animal pathogen, endophyte, and plant pathogen). Moreover, metal(loid)s combined with physicochemical properties jointly mediated the fungal taxonomic and functional responses to different metal(loid) contamination levels. Overall, this study not only broadens the understanding of taxonomic and functional repertoires of fungal communities under different metal(loid) contaminated conditions, but also highlights the crucial contributions of specific fungi to bioremediation and management in varying metal(loid)-polluted environments.
Collapse
Affiliation(s)
- Jiawen Wang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
| | - Ying Chen
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Wenran Du
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Yifan He
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; School of Water Resources and Hydropower Engineering, Xi'an University of Technology, Xi'an 710048, China
| | - Xiaohui Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; School of Water Resources and Hydropower Engineering, Xi'an University of Technology, Xi'an 710048, China
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
| |
Collapse
|
18
|
Hu X, Gu H, Sun X, Wang Y, Liu J, Yu Z, Li Y, Jin J, Wang G. Distinct influence of conventional and biodegradable microplastics on microbe-driving nitrogen cycling processes in soils and plastispheres as evaluated by metagenomic analysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131097. [PMID: 36898310 DOI: 10.1016/j.jhazmat.2023.131097] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Plastic mulching is one of the large contributors to microplastic (MP) accumulation in agricultural landscapes. However, the effects of conventional (PE-MPs) and biodegradable MPs (BMPs) on microbial functional and genomic information encoding nitrogen (N) cycling have yet to be addressed. Here, a soil microcosmic experiment was conducted by adding PE-MPs and BMPs to a Mollisol at dosage of 5% (w/w) followed by incubation for 90 days. The soils and MPs were examined by metagenomics and genome binning methods. The results revealed that BMPs harbored rougher surfaces and induced stronger alterations in microbial functional and taxonomic profiles in the soil and plastisphere than PE-MPs. In comparison to their respective soils, the plastispheres of PE-MPs and BMPs stimulated the processes of N fixation, N degradation and assimilatory nitrate reduction (ANRA) and reduced the gene abundances encoding nitrification and denitrification, in which BMPs induced stronger influences than PE-MPs. Ramlibacter mainly drove the differences in N cycling processes between the soils containing two types of MPs and was further enriched in the BMP plastisphere. Three high-quality genomes were identified as Ramlibacter stains with higher abundances in the plastisphere of BMP than that of PE-MP. These Ramlibacter strains had the metabolic capacities of N fixation, N degradation, ANRA and ammonium transport, which were potentially attributed to their biosynthesis and the accumulation of soil NH4+-N. Taken together, our results highlight the genetic mechanisms of soil N bioavailability in the presence of biodegradable MPs, which have important implications for maintaining sustainable agriculture and controlling microplastic risk.
Collapse
Affiliation(s)
- Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xiangxin Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongbin Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
| |
Collapse
|
19
|
Liu Y, Zhang YM, Tang Y, Chen JQ, Shao ZQ. The evolution of plant NLR immune receptors and downstream signal components. CURRENT OPINION IN PLANT BIOLOGY 2023; 73:102363. [PMID: 37094492 DOI: 10.1016/j.pbi.2023.102363] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/09/2023] [Accepted: 03/12/2023] [Indexed: 05/03/2023]
Abstract
Along with the emergence of green plants on this planet one billion years ago, the nucleotide binding site leucine-rich repeat (NLR) gene family originated and diverged into at least three subclasses. Two of them, with either characterized N-terminal toll/interleukin-1 receptor (TIR) or coiled-coil (CC) domain, serve as major types of immune receptor of effector-triggered immunity (ETI) in plants, whereas the one having a N-terminal Resistance to powdery mildew8 (RPW8) domain, functions as signal transfer component to them. In this review, we briefly summarized the history of identification of diverse NLR subclasses across Viridiplantae lineages during the establishment of NLR category, and highlighted recent advances on the evolution of NLR genes and several key downstream signal components under the background of ecological adaption.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yan-Mei Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Yao Tang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| |
Collapse
|
20
|
Moreira C, Figueiredo C, Ferreira RM. The Role of the Microbiota in Esophageal Cancer. Cancers (Basel) 2023; 15:cancers15092576. [PMID: 37174041 PMCID: PMC10177416 DOI: 10.3390/cancers15092576] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
Esophageal cancer is a major health problem, being the seventh most incidence cancer worldwide. Due to the often-late diagnosis and lack of efficient treatments, the overall 5-year survival is as low as 10%. Therefore, understanding the etiology and the mechanisms that drive the development of this type of cancer could improve the management of patients, increasing the chance of achieving a better clinical outcome. Recently, the microbiome has been studied as a putative etiological factor for esophageal cancer. Nevertheless, the number of studies tackling this issue is low, and the heterogeneity in the study design and data analysis has hindered consistent findings. In this work, we reviewed the current literature on the evaluation of the role of microbiota in the development of esophageal cancer. We analyzed the composition of the normal microbiota and the alterations found in precursor lesions, namely Barrett's esophagus and dysplasia, as well as in esophageal cancer. Additionally, we explored how other environmental factors can modify microbiota and contribute to the development of this neoplasia. Finally, we identify critical aspects to be improved in future studies, with the aim of refining the interpretation of the relationship between the microbiome and esophageal cancer.
Collapse
Affiliation(s)
- Clara Moreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine of the University of Porto, 4200-319 Porto, Portugal
| | - Ceu Figueiredo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine of the University of Porto, 4200-319 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Rui Manuel Ferreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| |
Collapse
|
21
|
Jiang C, Sun X, Liu Y, Zhu S, Wu K, Li H, Shui W. Karst tiankeng shapes the differential composition and structure of bacterial and fungal communities in karst land. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:32573-32584. [PMID: 36469271 DOI: 10.1007/s11356-022-24229-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Karst tiankeng are important biodiversity conservation reservoirs. However, the unique habitats of karst tiankeng affect microbial community structure remained poorly understood. In this study, we collected soil samples from karst tiankeng (TK) and karst land (KL) and subjected to high-throughput sequencing. Based on the classification of the total, abundance, and rare taxa for bacteria and fungi, a multivariate statistical analysis was carried out. The results revealed that bacterial community Shannon diversity and Pielou's evenness were highest in TK. The rare taxa were ubiquitous in all soil samples, while the higher Shannon diversity of the abundant taxa of TK may be related to the habitat preferences of species and niche differentiation. The community composition of bacterial and fungal sub-communities exhibited significant dissimilarity between TK and KL. The redundancy analysis further demonstrated that abundant taxa were environmentally more constrained than rare taxa. The bacterial and fungal networks of KL were more complex than TK. The keystones of the network transforms may suggest their significant role in the ecological function of the karst tiankeng ecosystem. This study represents the first reports of the characteristics of bacterial and fungal communities in karst tiankeng.
Collapse
Affiliation(s)
- Cong Jiang
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Xiang Sun
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China
| | - Yuanmeng Liu
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China
| | - Sufeng Zhu
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100871, People's Republic of China
| | - Kexing Wu
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China
| | - Hui Li
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China
| | - Wei Shui
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China.
| |
Collapse
|
22
|
Lv QB, Meng JX, Ma H, Liu R, Qin Y, Qin YF, Geng HL, Ni HB, Zhang XX. Description of Gut Mycobiota Composition and Diversity of Caprinae Animals. Microbiol Spectr 2023; 11:e0242422. [PMID: 36625628 PMCID: PMC9927506 DOI: 10.1128/spectrum.02424-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
The fungal community, also known as mycobiota, plays pivotal roles in host nutrition and metabolism and has potential to cause disease. However, knowledge of the gut fungal structure in Caprinae is quite limited. In this study, the composition and diversity of the gut mycobiota of Caprinae animals from different geographical locations (Anhui, Jilin, Guangxi, Shandong, Shanxi, and Tibet) were comprehensively characterized by analyzing the internal transcribed spacer 2 (ITS-2) sequences of the fungal community. The results showed that Ascomycota and Basidiomycota were the dominant phyla, which, respectively, accounted for 90.86 to 95.27% and 2.58 to 7.62% of sequences in samples from each region. Nonetheless, the structure of the gut mycobiota was largely different in Caprinae animals in the different provinces. Therein, Sporormiaceae and Thelebolaceae were the dominant fungal families in the samples from Tibet, whereas their abundance was generally low in other regions. The intestinal diversity of individuals from Guangxi was higher than that in other regions. In addition, there were 114 differential genera among all regions. Finally, the co-occurrence network revealed 285 significant correlations in cross-family pairs in the guts of Caprinae animals, which contained 149 positive and 136 negative relationships, with 96 bacterial and 86 fungal participants at the family level. This study has improved the understanding of the mycobiota of ruminants and provided support for the improvement in animal health and productivity. IMPORTANCE In this study, we elucidated and analyzed the structure of the gut mycobiota of Caprinae animals from different regions. This study revealed differences in the structure of the gut mycobiota among Caprinae animals from different geographical environments. Based on previous findings, correlations between fungal and bacterial communities were analyzed. This study adds to previous research that has expanded the present understanding of the gut microbiome of Caprinae animals.
Collapse
Affiliation(s)
- Qing-Bo Lv
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jin-Xin Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - He Ma
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Rui Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Ya Qin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Yi-Feng Qin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Hong-Li Geng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
| |
Collapse
|
23
|
Shang Y, Wu X, Wang X, Dou H, Wei Q, Ma S, Sun G, Wang L, Sha W, Zhang H. Environmental factors and stochasticity affect the fungal community structures in the water and sediments of Hulun Lake, China. Ecol Evol 2022; 12:e9510. [PMID: 36415879 PMCID: PMC9674472 DOI: 10.1002/ece3.9510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/06/2022] [Accepted: 10/27/2022] [Indexed: 08/26/2023] Open
Abstract
Aquatic fungi form both morphologically and ecologically diverse communities. However, lake ecosystems are frequently overlooked as fungal habitats, despite the potentially important role of fungi in matter cycling and energy flow. Hulun Lake is a typical example of a seasonal glacial lake; however, previous studies have only focused on bacteria in this ecosystem. Therefore, in the current study, internal transcribed spacer ribosomal RNA (ITS rRNA) gene high-throughput sequencing was used to investigate the fungal communities in paired water and sediment samples from the Hulun Lake Basin in China. A significant difference was found between the fungal communities of the two sample types. Across all samples, we identified nine phyla, 30 classes, 78 orders, 177 families, and 307 genera. The dominant phyla in the lake were Ascomycota, Basidiomycota and Chytridiomycota. Our results show that both water and sediments have very high connectivity, are dominated by positive interactions, and have similar interaction patterns. The fungal community structures were found to be significantly affected by environmental factors (temperature, chemical oxygen demand, electrical conductivity, total phosphorus, and pH). In addition, the dispersal limitations of the fungi affected the structure of the fungal communities, and it was revealed that stochasticity is more important than deterministic mechanisms in influencing the structure and function of fungal communities. This study provides unique theoretical support for the study of seasonally frozen lake fungal communities and a scientific basis for the future management and protection of Hulun Lake.
Collapse
Affiliation(s)
| | - Xiaoyang Wu
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Xibao Wang
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid AreasHulunbuirChina
| | - Qinguo Wei
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Shengchao Ma
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Guolei Sun
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Lidong Wang
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Weilai Sha
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Honghai Zhang
- College of Life SciencesQufu Normal UniversityQufuChina
| |
Collapse
|
24
|
Li X, Wang T, Fu B, Mu X. Improvement of aquaculture water quality by mixed Bacillus and its effects on microbial community structure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:69731-69742. [PMID: 35576039 DOI: 10.1007/s11356-022-20608-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Microbial remediation, especially the application of probiotics, has recently gained popularity in improving water quality and maintaining aquatic animal health. The efficacy and mechanism of mixed Bacillus for improvement of water quality and its effects on aquatic microbial community structure remain unknown. To elucidate these issues, we applied two groups of mixed Bacillus (Bacillus megaterium and Bacillus subtilis (A0 + BS) and Bacillus megaterium and Bacillus coagulans (A0 + BC)) to the aquaculture system of Crucian carp. Our results showed that the improvement effect of mixed Bacillus A0 + BS on water quality was better than that of A0 + BC, and the NH4+-N, NO2--N, NO3--N, and total phosphorus (TP) concentrations were reduced by 46.3%, 76.3%, 35.6%, and 80.3%, respectively. In addition, both groups of mixed Bacillus increased the diversity of the bacterial community and decreased the diversity of the fungal community. Microbial community analysis showed that mixed Bacillus A0 + BS increased the relative abundance of bacteria related with nitrogen and phosphorus removal, such as Proteobacteria, Actinobacteria, Comamonas, and Stenotrophomonas, but decreased the relative abundance of pathogenic bacteria (Acinetobacter and Pseudomonas) and fungi (Epicoccum and Fusarium). Redundancy analysis showed that NH4+-N, NO2--N, and TP were the primary environmental factors affecting the microbial community in aquaculture water. PICRUST analysis indicated that all functional pathways in the A0 + BS group were richer than those in other groups. These results indicated that mixed Bacillus A0 + BS addition produced good results in reducing nitrogenous and phosphorus compounds and shaped a favorable microbial community structure to further improve water quality.
Collapse
Affiliation(s)
- Xue Li
- School of Environmental Science, Liaoning University, Shenyang, 110036, People's Republic of China
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, 100141, People's Republic of China
| | - Tianjie Wang
- School of Environmental Science, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Baorong Fu
- School of Environmental Science, Liaoning University, Shenyang, 110036, People's Republic of China.
| | - Xiyan Mu
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, 100141, People's Republic of China
| |
Collapse
|
25
|
Rani J, Pandey KP, Kushwaha J, Priyadarsini M, Dhoble AS. Antibiotics in anaerobic digestion: Investigative studies on digester performance and microbial diversity. BIORESOURCE TECHNOLOGY 2022; 361:127662. [PMID: 35872275 DOI: 10.1016/j.biortech.2022.127662] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/15/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
The ever-increasing consumption of antibiotics in both humans and animals has increased their load in municipal and pharmaceutical industry waste and may cause serious damage to the environment. Impact of antibiotics on the performance of commercially used anaerobic digesters in terms of bioenergy output, antibiotics' removal and COD removal have been compared critically with a few studies indicating >90% removal of antibiotics. AnMBR performed the best in terms of antibiotic removal, COD removal and methane yield. Most of the antibiotics investigated have adverse effects on microbiome associated with different stages and methane generation pathways of AD which has been assessed using high throughput technologies like metatranscriptomics, metaproteomics and flow cytometry. Perspectives have been given for understanding the fate and elimination of antibiotics from AD. The challenge of optimization and process improvement needs to be addressed to increase efficiency of the anaerobic digesters.
Collapse
Affiliation(s)
- Jyoti Rani
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Kailash Pati Pandey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Jeetesh Kushwaha
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Madhumita Priyadarsini
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Abhishek S Dhoble
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India.
| |
Collapse
|
26
|
Le N, Zhang M, Kim K. Quantum Dots and Their Interaction with Biological Systems. Int J Mol Sci 2022; 23:ijms231810763. [PMID: 36142693 PMCID: PMC9501347 DOI: 10.3390/ijms231810763] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Quantum dots are nanocrystals with bright and tunable fluorescence. Due to their unique property, quantum dots are sought after for their potential in several applications in biomedical sciences as well as industrial use. However, concerns regarding QDs’ toxicity toward the environment and other biological systems have been rising rapidly in the past decade. In this mini-review, we summarize the most up-to-date details regarding quantum dots’ impacts, as well as QDs’ interaction with mammalian organisms, fungal organisms, and plants at the cellular, tissue, and organismal level. We also provide details about QDs’ cellular uptake and trafficking, and QDs’ general interactions with biological structures. In this mini-review, we aim to provide a better understanding of our current standing in the research of quantum dots, point out some knowledge gaps in the field, and provide hints for potential future research.
Collapse
Affiliation(s)
- Nhi Le
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA
| | - Min Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA
- Correspondence: ; Tel.: +1-417-836-5440; Fax: +1-417-836-5126
| |
Collapse
|
27
|
Okrasińska A, Decewicz P, Majchrowska M, Dziewit L, Muszewska A, Dolatabadi S, Kruszewski Ł, Błocka Z, Pawłowska J. Marginal lands and fungi - linking the type of soil contamination with fungal community composition. Environ Microbiol 2022; 24:3809-3825. [PMID: 35415861 PMCID: PMC9544152 DOI: 10.1111/1462-2920.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
Fungi can be found in almost all ecosystems. Some of them can even survive in harsh, anthropogenically transformed environments, such as post-industrial soils. In order to verify how the soil fungal diversity may be changed by pollution, two soil samples from each of the 28 post-industrial sites were collected. Each soil sample was characterized in terms of concentration of heavy metals and petroleum derivatives. To identify soil fungal communities, fungal internal transcribed spacer 2 (ITS2) amplicon was sequenced for each sample using Illumina MiSeq platform. There were significant differences in the community structure and taxonomic diversity among the analysed samples. The highest taxon richness and evenness were observed in the non-polluted sites, and lower numbers of taxa were identified in multi-polluted soils. The presence of monocyclic aromatic hydrocarbons, gasoline and mineral oil was determined as the factors driving the differences in the mycobiome. Furthermore, in the culture-based selection experiment, two main groups of fungi growing on polluted media were identified - generalists able to live in the presence of pollution, and specialists adapted to the usage of BTEX as a sole source of energy. Our selection experiment proved that it is long-term soil contamination that shapes the community, rather than temporary addition of pollutant.
Collapse
Affiliation(s)
- Alicja Okrasińska
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of BiologyUniversity of WarsawWarsawPoland
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of BiologyUniversity of WarsawWarsawPoland
| | - Maria Majchrowska
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of BiologyUniversity of WarsawWarsawPoland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of BiologyUniversity of WarsawWarsawPoland
| | - Anna Muszewska
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | | | - Łukasz Kruszewski
- Institute of Geological SciencesPolish Academy of SciencesWarsawPoland
| | - Zuzanna Błocka
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of BiologyUniversity of WarsawWarsawPoland
| | - Julia Pawłowska
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of BiologyUniversity of WarsawWarsawPoland
| |
Collapse
|
28
|
Soil Microbial Community Varied with Vegetation Types on a Small Regional Scale of the Qilian Mountains. SUSTAINABILITY 2022. [DOI: 10.3390/su14137910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Clarifying the response of soil microbial communities to the change of different vegetation types on a small regional scale is of great significance for understanding the sustainability of grassland development. However, the distribution patterns and driving factors of the microbial community are not well understood in the Qilian Mountains. Therefore, we characterized and compared the soil microbial communities underlying the four vegetation types in a national natural reserve (reseeded grassland, swamp meadow, steppe meadow, and cultivated grassland) using high-throughput sequencing of the 16S rRNA and ITS. Meanwhile, the plant community and soil physicochemical characteristics were also determined. The results showed that bacterial and fungal communities in all vegetation types had the same dominant species, but the relative abundance differed substantially, which caused significant spatial heterogeneities on the small regional scale. Specifically, bacteria showed higher variability among different vegetation types than fungi, among which the bacterial and fungal communities were more sensitive to the changes in soil than to plant characteristics. Furthermore, soil organic carbon affected the widest portion of the microbial community, nitrate-nitrogen was the main factor affecting bacteria, and aboveground plant biomass was the main factor affecting fungi. Collectively, these results demonstrate the value of considering multiple small regional spatial scales when studying the relationship between the soil microbial community and environmental characteristics. Our study may have important implications for grassland management following natural disturbances or human alterations.
Collapse
|
29
|
Tao R, Zhu P, Zhou Y, Li Q, Wan Z, Li R, Wang R. Altered skin fungal and bacterial community compositions in tinea capitis. Mycoses 2022; 65:834-840. [PMID: 35689543 DOI: 10.1111/myc.13480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Tinea capitis is an infection of the scalp and hair shaft caused by dermatophytes that predominantly occurs in children. Skin fungal infections have been found to be associated with alterations in the overall bacterial and fungal communities. However, the scalp microbiome in tinea capitis have not been fully investigated. OBJECTIVES To investigate and compare the scalp bacterial and fungal microbiomes between children with tinea capitis and healthy children and between children and adults. METHODS Skin samples were collected from the scalp. Bacterial and fungal community compositions were analysed by amplification sequencing of the V3-V4 of 16S rDNA and ITS1-5F, respectively. RESULTS The predominant fungi detected using amplicon sequencing were consistent with the culture- or real-time PCR-positive pathogens in most samples. Children with tinea capitis had lower fungal and higher bacterial Shannon diversity than healthy children. A higher relative abundance of pathogenic fungi and significant alterations in the bacterial community in the lesional sites of tinea capitis than healthy scalps. Compared with adults, healthy children were characterised by higher Shannon diversities with significantly lower relative abundances of Malassezia and Cutibacterium and higher relative abundances of Candida and Streptococcus. CONCLUSIONS We demonstrated that tinea capitis was characterised by significant alterations in both fungal and bacterial communities and amplicon sequencing could be a complementary method for pathogen identification.
Collapse
Affiliation(s)
- Rong Tao
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Peiqiu Zhu
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Yabin Zhou
- Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Qian Li
- Children's Hospital Capital Institute of Pediatrics, Beijing, China
| | - Zhe Wan
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Ruoyu Li
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Ruojun Wang
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| |
Collapse
|
30
|
Mathieu A, Leclercq M, Sanabria M, Perin O, Droit A. Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation. Front Microbiol 2022; 13:811495. [PMID: 35359727 PMCID: PMC8964132 DOI: 10.3389/fmicb.2022.811495] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022] Open
Abstract
Shotgun sequencing of environmental DNA (i.e., metagenomics) has revolutionized the field of environmental microbiology, allowing the characterization of all microorganisms in a sequencing experiment. To identify the microbes in terms of taxonomy and biological activity, the sequenced reads must necessarily be aligned on known microbial genomes/genes. However, current alignment methods are limited in terms of speed and can produce a significant number of false positives when detecting bacterial species or false negatives in specific cases (virus, plasmids, and gene detection). Moreover, recent advances in metagenomics have enabled the reconstruction of new genomes using de novo binning strategies, but these genomes, not yet fully characterized, are not used in classic approaches, whereas machine and deep learning methods can use them as models. In this article, we attempted to review the different methods and their efficiency to improve the annotation of metagenomic sequences. Deep learning models have reached the performance of the widely used k-mer alignment-based tools, with better accuracy in certain cases; however, they still must demonstrate their robustness across the variety of environmental samples and across the rapid expansion of accessible genomes in databases.
Collapse
Affiliation(s)
- Alban Mathieu
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, QC, Canada
| | - Mickael Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, QC, Canada
| | | | - Olivier Perin
- Digital Sciences Department, L'Oréal Advanced Research, Aulnay-sous-Bois, France
| | - Arnaud Droit
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, QC, Canada
| |
Collapse
|
31
|
Gohar D, Põldmaa K, Tedersoo L, Aslani F, Furneaux B, Henkel TW, Saar I, Smith ME, Bahram M. Global diversity and distribution of mushroom-inhabiting bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:254-264. [PMID: 35102713 DOI: 10.1111/1758-2229.13045] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.
Collapse
Affiliation(s)
- Daniyal Gohar
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
- Natural History Museum and Botanical Garden, University of Tartu, Vanemuise 46, Tartu, 51003, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Farzad Aslani
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
- School of Environmental and Rural Sciences, University of New England, Armidale, NSW, Australia
| | - Brendan Furneaux
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, Uppsala, 756 51, Sweden
| |
Collapse
|
32
|
Bizic M, Ionescu D, Karnatak R, Musseau CL, Onandia G, Berger SA, Nejstgaard JC, Lischeid G, Gessner MO, Wollrab S, Grossart HP. Land-use type temporarily affects active pond community structure but not gene expression patterns. Mol Ecol 2022; 31:1716-1734. [PMID: 35028982 DOI: 10.1111/mec.16348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/30/2021] [Accepted: 01/04/2022] [Indexed: 11/30/2022]
Abstract
Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics, to understand the responses of active bacterial, archaeal, and eukaryotic communities, to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel eDNA study which revealed the homogenization of biodiversity across KH conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced in eukaryotes than in bacteria. In contrast, gene expression patterns did not differ between months or across land-use type, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results show that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.
Collapse
Affiliation(s)
- M Bizic
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - D Ionescu
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - R Karnatak
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - C L Musseau
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Institute of Biology, Free University of Berlin, Berlin, Germany
| | - G Onandia
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Research Platform Data Analysis and Simulation, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - S A Berger
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - J C Nejstgaard
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - G Lischeid
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Research Platform Data Analysis and Simulation, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Institute for Environmental Sciences and Geography, Potsdam University, Potsdam, Germany
| | - M O Gessner
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Department of Ecology, Berlin Institute of Technology (TU Berlin), Berlin, Germany
| | - S Wollrab
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - H-P Grossart
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| |
Collapse
|
33
|
Functional and Taxonomic Effects of Organic Amendments on the Restoration of Semiarid Quarry Soils. mSystems 2021; 6:e0075221. [PMID: 34812648 PMCID: PMC8609970 DOI: 10.1128/msystems.00752-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The application of organic amendments to mining soils has been shown to be a successful method of restoration, improving key physicochemical soil properties. However, there is a lack of a clear understanding of the soil bacterial community taxonomic and functional changes that are brought about by these treatments. We present further metagenomic sequencing (MGS) profiling of the effects of different restoration treatments applied to degraded, arid quarry soils in southern Spain which had previously been profiled only with 16S rRNA gene (16S) and physicochemical analyses. Both taxonomic and functional MGS profiles showed clear separation of organic treatment amendments from control samples, and although taxonomic differences were quite clear, functional redundancy was higher than expected and the majority of the latter signal came from the aggregation of minor (<0.1%) community differences. Significant taxonomic differences were seen with the presumably less-biased MGS-for example, the phylum Actinobacteria and the two genera Chloracidobacterium (Acidobacteria) and Paenibacillus (Firmicutes) were determined to be major players by the MGS and this was consistent with their potential functional roles. The former phylum was much less present, and the latter two genera were either minor components or not detected in the 16S data. Mapping of reads to MetaCyc/BioCyc categories showed overall slightly higher biosynthesis and degradation capabilities in all treatments versus control soils, with sewage amendments showing highest values and vegetable-based amendments being at intermediate levels, matching higher nutrient levels, respiration rates, enzyme activities, and bacterial biomass previously observed in the treated soils. IMPORTANCE The restoration of soils impacted by human activities poses specific challenges regarding the reestablishment of functional microbial communities which will further support the reintroduction of plant species. Organic fertilizers, originating from either treated sewage or vegetable wastes, have shown promise in restoration experiments; however, we still do not have a clear understanding of the functional and taxonomic changes that occur during these treatments. We used metagenomics to profile restoration treatments applied to degraded, arid quarry soils in southern Spain. We found that the assortments of individual functions and taxa within each soil could clearly identify treatments, while at the same time they demonstrated high functional redundancy. Functions grouped into higher pathways tended to match physicochemical measurements made on the same soils. In contrast, significant taxonomic differences were seen when the treatments were previously studied with a single marker gene, highlighting the advantage of metagenomic analysis for complex soil communities.
Collapse
|
34
|
Bahram M, Netherway T. Fungi as mediators linking organisms and ecosystems. FEMS Microbiol Rev 2021; 46:6468741. [PMID: 34919672 PMCID: PMC8892540 DOI: 10.1093/femsre/fuab058] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
Fungi form a major and diverse component of most ecosystems on Earth. They are both micro and macroorganisms with high and varying functional diversity as well as great variation in dispersal modes. With our growing knowledge of microbial biogeography, it has become increasingly clear that fungal assembly patterns and processes differ from other microorganisms such as bacteria, but also from macroorganisms such as plants. The success of fungi as organisms and their influence on the environment lies in their ability to span multiple dimensions of time, space, and biological interactions, that is not rivalled by other organism groups. There is also growing evidence that fungi mediate links between different organisms and ecosystems, with the potential to affect the macroecology and evolution of those organisms. This suggests that fungal interactions are an ecological driving force, interconnecting different levels of biological and ecological organisation of their hosts, competitors, and antagonists with the environment and ecosystem functioning. Here we review these emerging lines of evidence by focusing on the dynamics of fungal interactions with other organism groups across various ecosystems. We conclude that the mediating role of fungi through their complex and dynamic ecological interactions underlie their importance and ubiquity across Earth's ecosystems.
Collapse
Affiliation(s)
- Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 40 Lai St. Estonia
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden
| |
Collapse
|
35
|
Geisen S, Thakur MP. Special Issue–Causes and consequences of microbiome changes. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2021.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
36
|
Abstract
Microbes dominate the planet's biodiversity in terms of species number and by driving essential Earth system functions such as the carbon cycle. Soils contain most of this microbial biodiversity. Only recently, we have started to better understand the diversity of bacteria and fungi at the global scale. Here, I list my views on some shortcomings of contemporary soil microbiome studies and potential solutions to overcome them. In particular, I highlight that (soil) microbiome studies should become more holistic in terms of (i) taxa and resolution targeted, (ii) by adding functional to taxonomic information, and (iii) by integrating temporal analysis into spatial analyses. Considering those elements with the methodology that is now available will advance our understanding on (soil) microbiomes to reliably address major ecological hypotheses and to advance insights into the importance for life on Earth.
Collapse
Affiliation(s)
- Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
37
|
Chen QL, Hu HW, Yan ZZ, Li CY, Nguyen BAT, Zhu YG, He JZ. Precipitation increases the abundance of fungal plant pathogens in Eucalyptus phyllosphere. Environ Microbiol 2021; 23:7688-7700. [PMID: 34407308 DOI: 10.1111/1462-2920.15728] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/31/2021] [Accepted: 08/15/2021] [Indexed: 11/27/2022]
Abstract
Understanding the current and future distributions of plant pathogens is critical to predict the plant performance and related economic benefits in the changing environment. Yet, little is known about the roles of environmental drivers in shaping the profiles of fungal plant pathogens in phyllosphere, an important habitat of microbiomes on Earth. Here, using a large-scale investigation of Eucalyptus phyllospheric microbiomes in Australia and the multiple linear regression model, we show that precipitation is the most important predictor of fungal taxonomic diversity and abundance. The abundance of fungal plant pathogens in phyllosphere exhibited a positive linear relationship with precipitation. With this empirical dataset, we constructed current and future atlases of phyllosphere plant pathogens to estimate their spatial distributions under different climate change scenarios. Our atlases indicate that the abundance of fungal plant pathogens would increase especially in the coastal regions with up to 100-fold increase compared with the current abundance. These findings advance our understanding of the distributions of fungal plant pathogens in phyllospheric microbiomes under the climate change, which can improve our ability to predict and mitigate their impacts on plant productivity and economic losses.
Collapse
Affiliation(s)
- Qing-Lin Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Zhen-Zhen Yan
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Chao-Yu Li
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Bao-Anh Thi Nguyen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| |
Collapse
|
38
|
Qin S, Kou D, Mao C, Chen Y, Chen L, Yang Y. Temperature sensitivity of permafrost carbon release mediated by mineral and microbial properties. SCIENCE ADVANCES 2021; 7:eabe3596. [PMID: 34362729 PMCID: PMC8346221 DOI: 10.1126/sciadv.abe3596] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 06/22/2021] [Indexed: 05/04/2023]
Abstract
Temperature sensitivity (Q 10) of permafrost carbon (C) release upon thaw is a vital parameter for projecting permafrost C dynamics under climate warming. However, it remains unclear how mineral protection interacts with microbial properties and intrinsic recalcitrance to affect permafrost C fate. Here, we sampled permafrost soils across a 1000-km transect on the Tibetan Plateau and conducted two laboratory incubations over 400- and 28-day durations to explore patterns and drivers of permafrost C release and its temperature response after thaw. We find that mineral protection and microbial properties are two types of crucial predictors of permafrost C dynamics upon thaw. Both high C release and Q 10 are associated with weak organo-mineral associations but high microbial abundances and activities, whereas high microbial diversity corresponds to low Q 10 The attenuating effects of mineral protection and the dual roles of microbial properties would make the permafrost C-climate feedback more complex than previously thought.
Collapse
Affiliation(s)
- Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Kou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Biogeochemistry Research Group, Department of Biological and Environmental Sciences, University of Eastern Finland, Kuopio 70210, Finland
| | - Chao Mao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongliang Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Leiyi Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|