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Liu Y, Bao L, Sun W, Cui Y, Li X, Ji X, Wei Y, Tan Y. Diversity and composition of active and total bacteria in rhizospheric soil in response to continuous cropping years of Panax notoginseng. Folia Microbiol (Praha) 2024; 69:733-745. [PMID: 38038798 DOI: 10.1007/s12223-023-01109-0] [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: 06/30/2022] [Accepted: 11/12/2023] [Indexed: 12/02/2023]
Abstract
The synchronous research and analysis of total and active soil microbial communities can provide insight into how these communities are impacted by continuous cropping years and pathogen infection. The diversity of total and active bacteria in rhizospheric soil of 2-year-old and 3-year-old healthy and diseased Panax notoginseng can comprehensively reveal the bacterial response characteristics in continuous cropping practice. The results showed that 4916 operational taxonomic units (OTUs) were found in the rhizospheric soil bacterial community of P. notoginseng at the DNA level, but only 2773 OTUs were found at the RNA level. The rhizospheric environment had significant effects on the active and bacterial communities, as indicated by the number of OTUs, Shannon, Chao1, Faith's phylogenetic diversity (Faith's PD), and Simpson's diversity indexes. The DNA level can better show the difference in diversity level before and after infection with root rot. The bacterial Chao1 and Faith's PD diversity indexes of 2-year-old root rot-diseased P. notoginseng rhizospheric soil (D2) were higher than that of healthy plants, while the bacterial Shannon diversity index of 3-year-old root rot-diseased P. notoginseng rhizospheric soil (D3) was the lowest in the total bacteria. Principal coordinate analysis (PCoA) illustrated that the total bacterial species composition changed markedly after root rot disease. There were significant differences in the composition of active bacterial species between the 2-year and 3-year rhizospheres. In conclusion, the total and active edaphic rhizospheric bacterial communities could provide important opportunities to understand the responses of bacteria to continuous cropping of P. notoginseng.
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Affiliation(s)
- Yuyan Liu
- Faculty of Science, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Limei Bao
- Faculty of Science, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Wanwan Sun
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Yinshan Cui
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Xiaoran Li
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Xiuling Ji
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Yunlin Wei
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China.
| | - Yong Tan
- Faculty of Science, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China.
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Manyatsi TS, Lin YH, Jou YT. The isolation and identification of Bacillus velezensis ZN-S10 from vanilla (V. planifolia), and the microbial distribution after the curing process. Sci Rep 2024; 14:16339. [PMID: 39014002 PMCID: PMC11252412 DOI: 10.1038/s41598-024-66753-z] [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: 02/22/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
The market value of vanilla beans (Vanilla planifolia) is constantly increasing due to their natural aroma and flavor properties that improve after a curing process, where bacteria colonization plays a critical role. However, a few publications suggest that bacteria play a role in the curing process. Hence, this study aimed to isolate Bacillus sp. that could be used for fermenting V. planifolia while analyzing their role in the curing process. Bacillus velezensis ZN-S10 identified with 16S rRNA sequencing was isolated from conventionally cured V. planifolia beans. A bacteria culture solution of B. velezensis ZN-S10 (1 mL of 1 × 107 CFU mL-1) was then coated on 1 kg of non-cured vanilla pods that was found to ferment and colonize vanilla. PCA results revealed distinguished bacterial communities of fermented vanilla and the control group, suggesting colonization of vanilla. Phylogenetic analysis showed that ZN-S10 was the dominant Bacillus genus member and narrowly correlated to B. velezensis EM-1 and B. velezensis PMC206-1, with 78% and 73% similarity, respectively. The bacterial taxonomic profiling of cured V. planifolia had a significant relative abundance of Firmicutes, Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes phyla according to the predominance. Firmicutes accounted for 55% of the total bacterial sequences, suggesting their colonization and effective fermentation roles in curing vanilla.
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Affiliation(s)
- Thabani Sydney Manyatsi
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu Shuefu Road 1, 91201, Pingtung, Taiwan
| | - Yu-Hsin Lin
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu Shuefu Road 1, 91201, Pingtung, Taiwan
| | - Ying-Tzy Jou
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu Shuefu Road 1, 91201, Pingtung, Taiwan.
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McCumber AW, Kim YJ, Granek J, Tighe RM, Gunsch CK. Soil exposure modulates the immune response to an influenza challenge in a mouse model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:170865. [PMID: 38340827 DOI: 10.1016/j.scitotenv.2024.170865] [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: 09/25/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
There is increasing evidence that early life microbial exposure aids in immune system maturation, more recently known as the "old friends" hypothesis. To test this hypothesis, 4-week-old mice were exposed to soils of increasing microbial diversity for four weeks followed by an intranasal challenge with either live or heat inactivated influenza A virus and monitored for 7 additional days. Perturbations of the gut and lung microbiomes were explored through 16S rRNA amplicon sequencing. RNA-sequencing was used to examine the host response in the lung tissue through differential gene expression. We determined that compared to the gut microbiome, the lung microbiome is more susceptible to changes in beta diversity following soil exposure with Lachnospiraceae ASVs accounting for most of the differences between groups. While several immune system genes were found to be significantly differentially expressed in lung tissue due to soil exposures, there were no differences in viral load or weight loss. This study shows that exposure to diverse microbial communities through soil exposure alters the gut and lung microbiomes resulting in differential expression of specific immune system related genes within the lung following an influenza challenge.
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Affiliation(s)
- Alexander W McCumber
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Yeon Ji Kim
- Civil and Environmental Engineering Department, Duke University, Durham, NC, USA
| | - Joshua Granek
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Robert M Tighe
- Department of Medicine, Duke University, Durham, NC, USA
| | - Claudia K Gunsch
- Civil and Environmental Engineering Department, Duke University, Durham, NC, USA.
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Qiao J, Chen M, Zhong S, Tong H, Li F. Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2303-2312. [PMID: 38263620 DOI: 10.1021/acs.est.3c07753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Dissimilatory arsenate reduction contributes a large proportion of arsenic flux from flooded paddy soil, which is closely linked to soil organic carbon input and efflux. Humic acid (HA) represents a natural ingredient in soil and is shown to enhance microbial arsenate respiration to promote arsenic mobility. However, the community and function profiles of metabolically active arsenate-respiring bacteria and their interactions with HA in paddy soil remain unclear. To probe this linkage, we performed a genome-centric comparison of potentially active arsenate-respiring bacteria in anaerobic microcosms amended with 13C-lactate and HA by combining stable-isotope probing with genome-resolved metagenomics. Indeed, HA greatly accelerated the microbial reduction of arsenate to arsenite. Enrichment of bacteria that harbor arsenate-respiring reductase genes (arrA) in HA-enriched 13C-DNA was confirmed by metagenomic binning, which are affiliated with Firmicutes (mainly Desulfitobacterium, Bacillus, Brevibacillus, and Clostridia) and Acidobacteria. Characterization of reference extracellular electron transfer (EET)-related genes in these arrA-harboring bacteria supports the presence of EET-like genes, with partial electron-transport chain genes identified. This suggests that Gram-positive Firmicutes- and Acidobacteria-related members may harbor unspecified EET-associated genes involved in metal reduction. Our findings highlight the link between soil HA and potentially active arsenate-respiring bacteria, which can be considered when using HA for arsenic removal.
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Affiliation(s)
- Jiangtao Qiao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Manjia Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Songxiong Zhong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Hui Tong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
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Lu Y, Cheung S, Koh XP, Xia X, Jing H, Lee P, Kao SJ, Gan J, Dai M, Liu H. Active degradation-nitrification microbial assemblages in the hypoxic zone in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166694. [PMID: 37660824 DOI: 10.1016/j.scitotenv.2023.166694] [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: 02/02/2022] [Revised: 08/06/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
In 2017 summer, we observed widespread bottom hypoxia at the lower estuary of the Pearl River estuary (PRE). Our previous study noticed that AOA and bacteria were highly abundant and clustered within the hypoxia zone. Moreover, nitrification and respiration rates were also evidently higher in these hypoxic waters. These observations prompt us to investigate whether these two oxygen-consuming microorganisms have symbiotic relationships and whether specific groups consistently coexist and form ecological-meaningful associations. In this study, we use network analysis to investigate the presence and active communities (DNA-RNA) based on bacterial and AOA communities sequencing (inferred from the 16S rRNA and amoA gene, respectively) to gain more insight into ecological-meaningful associations. We observed a highly diverse and active bacterial community in the hypoxia zone. The RNA networks were more modulized than the corresponding DNA networks, indicating that the active communities were better parsed into functional microbial assemblages. The network topology revealed that Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia, Cyanobacteria (Synechococcales), and AOA sublineages were module hubs and connectors, indicating that they were the keystone taxa of the microbial communities. The hub-subnetwork further showed robust co-occurrence between Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia with AOA sublineages, and Nitrospinae (presumably NOB) reflecting the formation of Degradation-Nitrification (sequential oxidation of Organic matter degradation to ammonia, then nitrate) microbial assemblage in the hypoxia zone. The subnetworks revealed AOA ecotype-specific modularization and niche partitioning of different AOA sublineages. Interestingly, the recurring co-occurrence of nitrifiers assemblage in the RNA subnetworks (SCM1-like-II (AOA) and Nitrospinae OTUs (NOB) suggests an active interaction via nitrite exchange. The Degradation-Nitrification microbial assemblage may contribute substantially to the oxygen consumption in the hypoxia formation in PRE. Our results provide new insight into the functional microbial assemblages, which is worth further investigation on their ecological implication in estuarine waters.
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Affiliation(s)
- Yanhong Lu
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, Guangdong; Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong; Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong; Shenzhen Marine Development and Promotion Center, Shenzhen, Guangdong.
| | - Shunyan Cheung
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Xiu Pei Koh
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan
| | - Puiyin Lee
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian
| | - Jianping Gan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong; Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong.
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Pan L, Cai B. Phosphate-Solubilizing Bacteria: Advances in Their Physiology, Molecular Mechanisms and Microbial Community Effects. Microorganisms 2023; 11:2904. [PMID: 38138048 PMCID: PMC10745930 DOI: 10.3390/microorganisms11122904] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42- and H2PO4-, which are known as usable phosphorus. At present, the total phosphorus content of soils worldwide is 400-1000 mg/kg, of which only 1.00-2.50% is plant-available, which seriously affects the growth of plants and the development of agriculture, resulting in a high level of total phosphorus in soils and a scarcity of available phosphorus. Traditional methods of applying phosphorus fertilizer cannot address phosphorus deficiency problems; they harm the environment and the ore material is a nonrenewable natural resource. Therefore, it is imperative to find alternative environmentally compatible and economically viable strategies to address phosphorus scarcity. Phosphorus-solubilizing bacteria (PSB) can convert insoluble phosphorus in the soil into usable phosphorus that can be directly absorbed by plants, thus improving the uptake and utilization of phosphorus by plants. However, there is no clear and systematic report on the mechanism of action of PSB. Therefore, this paper summarizes the discovery process, species, and distribution of PSB, focusing on the physiological mechanisms outlining the processes of acidolysis, enzymolysis, chelation and complexation reactions of PSB. The related genes regulating PSB acidolysis and enzymatic action as well as genes related to phosphate transport and the molecular direction mechanism of its pathway are examined. The effects of PSB on the structure and abundance of microbial communities in soil are also described, illustrating the mechanism of how PSB interact with microorganisms in soil and indirectly increase the amount of available phosphorus in soil. And three perspectives are considered in further exploring the PSB mechanism in utilizing a synergistic multi-omics approach, exploring PSB-related regulatory genes in different phosphorus levels and investigating the application of PSB as a microbial fungicide. This paper aims to provide theoretical support for improving the utilization of soil insoluble phosphorus and providing optimal management of elemental phosphorus in the future.
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Affiliation(s)
- Lin Pan
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, Key Laboratory of Molecular Biology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China;
| | - Baiyan Cai
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, Key Laboratory of Molecular Biology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China;
- Hebei Key Laboratory of Agroecological Safety, Hebei University of Environmental Engineering, Qinhuangdao 066102, China
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Fu X, Huang Y, Fu Q, Qiu Y, Zhao J, Li J, Wu X, Yang Y, Liu H, Yang X, Chen H. Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects. FRONTIERS IN PLANT SCIENCE 2023; 14:1252821. [PMID: 38023904 PMCID: PMC10676204 DOI: 10.3389/fpls.2023.1252821] [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: 07/04/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xian Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, Guangdong, China
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Qi JQ, Yuan HY, Zhuang QL, Zama EF, Tian XF, Tao BX, Zhang BH. Effect of different types of biochar on soil properties and functional microbial communities in rhizosphere and bulk soils and their relationship with CH 4 and N 2O emissions. Front Microbiol 2023; 14:1292959. [PMID: 38029118 PMCID: PMC10656817 DOI: 10.3389/fmicb.2023.1292959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Biochar as an agricultural soil amendment plays vital roles in mediating methane (CH4) and nitrous oxide (N2O) emissions in soils. The link between different types of biochar, bulk soil, and rhizosphere microbial communities in relation to CH4 and N2O emissions is being investigated in this study. The rice pot experiment was conducted using biochar at two temperatures (300°C and 500°C) in combination with three biochar levels (0, 2, 10% w/w). Soil properties and the abundance of genes associated with CH4 and N2O emissions from both rhizosphere and bulk soils were investigated. The study also aimed to examine the structure of microbial communities (pmoA, nosZ) in rhizosphere and bulk soils whereas CH4 and N2O emissions were monitored while growing rice. Results showed that biochar at 300°C and 10% incorporation significantly increased the CH4 emissions by up to 59% rise compared to the control group. Random Forest analysis revealed that the ratio of mcrA/pmoA along with the abundance of mcrA from both rhizosphere and bulk soils, the abundance of AOA, TN, DOC, and the community composition of pmoA-harboring microorganisms from both bulk and rhizosphere soils were important predictors of CH4 emissions. Therefore, the ratio of mcrA/pmoA in rhizosphere soil and the abundance of AOA in bulk soil were the main factors influencing CH4 emissions. Variation Partitioning Analysis (VPA) results indicated that the effects of these factors on bulk soil were 9% of CH4 emissions variations in different treatments, which contributed more than rhizosphere soils' factors. Moreover, random forest analysis results indicated that the abundance of AOB in bulk soil was the most important predictor influencing N2O emissions. The VPA result revealed that the factors in rhizosphere soil could explain more than 28% of the variations in N2O emissions. Our study highlights that rhizosphere soil has a more significant effect than bulk soil on N2O production. Our findings further the understanding of the link between bulk and rhizosphere attributes, and their impact on CH4 and N2O emissions in paddy soils. In summary, we recommend the application of biochar at 500°C and 2% incorporation rate for agricultural production in the area.
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Affiliation(s)
- Jian-Qing Qi
- School of Geography and Environment, Liaocheng University, Liaocheng, China
| | - Hai-Yan Yuan
- School of Geography and Environment, Liaocheng University, Liaocheng, China
| | - Qi-Lu Zhuang
- School of Geography and Environment, Liaocheng University, Liaocheng, China
| | - Eric-Fru Zama
- Department of Agricultural and Environmental Engineering, College of Technology, University of Bamenda, Bambili, Cameroon
| | - Xiao-Fei Tian
- School of Geography and Environment, Liaocheng University, Liaocheng, China
| | - Bao-Xian Tao
- School of Geography and Environment, Liaocheng University, Liaocheng, China
| | - Bao-Hua Zhang
- School of Geography and Environment, Liaocheng University, Liaocheng, China
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Zhao J, Duan G, Zhu Y, Zhu D. Gut microbiota and transcriptome response of earthworms (Metaphire guillelmi) to polymyxin B exposure. J Environ Sci (China) 2023; 133:37-47. [PMID: 37451787 DOI: 10.1016/j.jes.2022.07.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 07/18/2023]
Abstract
Polymyxin B (PMB) has received widespread attention for its use as a last-line therapy against multidrug-resistant bacterial infection. However, the consequences of unintended PMB exposure on organisms in the surrounding environment remain inconclusive. Therefore, this study investigated the effects of soil PMB residue on the gut microbiota and transcriptome of earthworms (Metaphire guillelmi). The results indicated that the tested doses of PMB (0.01-100 mg/kg soil) did not significantly affect the richness and Shannon's diversity index of the earthworm gut microbiota, but PMB altered its community structure and taxonomic composition. Moreover, PMB significantly affected Lysobacter, Aeromonas, and Sphingomonas in the soil microbiota, whereas Pseudomonas was significantly impacted the earthworm gut microbiota. Furthermore, active bacteria responded more significantly to PMB than the total microbial community. Bacterial genera such as Acinetobacter and Bacillus were highly correlated with differential expression of some genes, including up-regulated genes associated with folate biosynthesis, sulphur metabolism, and the IL-17 signalling pathway, and downregulated genes involved in vitamin digestion and absorption, salivary secretion, other types of O-glycan biosynthesis, and the NOD-like receptor signalling pathway. These results suggest that adaptation to PMB stress by earthworms involves changes in energy metabolism, their immune and digestive systems, as well as glycan biosynthesis. The study findings help elucidate the relationship between earthworms and their microbiota, while providing a reference for understanding the environmental risks of PMB.
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Affiliation(s)
- Jun Zhao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guilan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongguan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dong Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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10
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Zhu F, Zhang X, Guo X, Yang X, Xue S. Root architectures differentiate the composition of organic carbon in bauxite residue during natural vegetation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163588. [PMID: 37105477 DOI: 10.1016/j.scitotenv.2023.163588] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 04/13/2023] [Accepted: 04/15/2023] [Indexed: 06/03/2023]
Abstract
Understanding plant root architectures induced changes in organic carbon accumulation and conversion is critical to predicting carbon cycling and screening appropriate plant species for ecological restoration on bauxite residue disposal areas. According to the ecological investigation of a weathered bauxite residue disposal area, three plants with different root architectures including Artemisia lavandulaefolia (A. lavandulaefolia), moss, and Zanthoxylum simulans (Z. simulans) were selected to investigate the rhizosphere effects on the composition and structure of organic carbon in bauxite residue. The physic-chemical properties, the contents and structure of different organic carbon fractions, and microbial communities of bauxite residue from rhizosphere and non-rhizosphere were analyzed. Plant growth decreased the saline-alkalinity, increased the contents of total organic carbon, particulate organic carbon and dissolved organic carbon, whilst enhancing the enzymatic activities of bauxite residue. Meanwhile, the rhizosphere effects had significant effects on the accumulation and stabilization of organic carbon in bauxite residue. A. lavandulaefolia had the strongest rhizosphere effects on the composition and structure of total organic carbon and dissolved organic carbon, whilst moss was more effective on the accumulation of particulate organic carbon in bauxite residue. Plant growth and root architecture changed the abundance of specific functional microorganisms and the complexity of microbial co-occurrence networks, thus elevating organic carbon levels in bauxite residue. During natural vegetation encroachment, rhizosphere exciting effects of the salt-tolerated plants could change the composition and structure of organic carbon fractions due to the comprehensive effectiveness of the improvement of physic-chemical properties and microbial communities. The findings improve our understanding of the responses of sequestration and stabilization of organic carbon pools to ecological restoration on bauxite residue disposal areas.
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Affiliation(s)
- Feng Zhu
- School of Metallurgy and Environment, Central South University, Changsha 410083, PR China; Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Central South University, Changsha, PR China
| | - Xianchao Zhang
- School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Xuyao Guo
- School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Xingwang Yang
- School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Shengguo Xue
- School of Metallurgy and Environment, Central South University, Changsha 410083, PR China; Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Central South University, Changsha, PR China.
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11
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Qian C, Wu J, Wang H, Yang D, Cui J. Metabolomic profiles reveals the dose-dependent effects of rice grain yield and nutritional quality upon exposure zero-valent iron nanoparticles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163089. [PMID: 37001268 DOI: 10.1016/j.scitotenv.2023.163089] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023]
Abstract
Zero-valent iron nanoparticles (nZVI) were widely used material in environmental remediation, which has attracted increasing concern for their safety. Previous studies have shown that the addition of nZVI could inhibit rice seedling growth. However, the effect of nZVI on the soil-rice system during the entire life cycle was not reported. Furthermore, the effect of nZVI on the quality of rice grain has also not been studied. Therefore, we investigated the effects of rice grain yield and nutritional quality upon exposure nZVI. The results showed that the soil pH value, redox potential and Fe (II) content in the nZVI-treated group were decreased in a dose-dependent manner. Interestingly, 2500 mg/kg nZVI significantly decreased the relative abundance of several functional microbial communities (10.52-73.53 %) associated with carbon and nitrogen cycles in response to plants compared to the control. Meanwhile, the nZVI treatment clearly reduced grain yield (8.71-18.21 %). Furthermore, the content of protein (51.72-57.79 %) and several essential nutrients (Zn, Cu, Mn and Mo) in the nZVI-treated grains was also decreased in a dose-dependent manner. The results of grain metabolomics indicated that nZVI could interfere with the relative expression of lysine and glutathione by regulating the metabolic pathways of antioxidant and protein synthesis in rice.
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Affiliation(s)
- Cancan Qian
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Shihezi University, Shihezi, Xinjiang 832003, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Jian Wu
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Shihezi University, Shihezi, Xinjiang 832003, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Haodong Wang
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Shihezi University, Shihezi, Xinjiang 832003, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Desong Yang
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Jianghu Cui
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
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12
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González-Reguero D, Robas-Mora M, Fernández-Pastrana VM, Probanza-Lobo A, Jiménez-Gómez PA. Reduced Antibiotic Resistance in the Rhizosphere of Lupinus albus in Mercury-Contaminated Soil Mediated by the Addition of PGPB. BIOLOGY 2023; 12:801. [PMID: 37372086 DOI: 10.3390/biology12060801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
The emergence of antibiotic resistance (AR) poses a threat to the "One Health" approach. Likewise, mercury (Hg) pollution is a serious environmental and public health problem. Its ability to biomagnify through trophic levels induces numerous pathologies in humans. As well, it is known that Hg-resistance genes and AR genes are co-selected. The use of plant-growth-promoting bacteria (PGPB) can improve plant adaptation, decontamination of toxic compounds and control of AR dispersal. The cenoantibiogram, a technique that allows estimating the minimum inhibitory concentration (MIC) of a microbial community, has been postulated as a tool to effectively evaluate the evolution of a soil. The present study uses the metagenomics of 16S rRNA gene amplicons to understand the distribution of the microbial soil community prior to bacterial inoculation, and the cenoantibiogram technique to evaluate the ability of four PGPB and their consortia to minimize antibiotic resistance in the rhizosphere of Lupinus albus var. Orden Dorado grown in Hg-contaminated soils. Results showed that the addition of A1 strain (Brevibacterium frigoritolerans) and its consortia with A2, B1 and B2 strains reduced the edaphic community´s MIC against cephalosporins, ertapenem and tigecycline. The metagenomic study revealed that the high MIC of non-inoculated soils could be explained by the bacteria which belong to the detected taxa,. showing a high prevalence of Proteobacteria, Cyanobacteria and Actinobacteria.
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Affiliation(s)
- Daniel González-Reguero
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Marina Robas-Mora
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Vanesa M Fernández-Pastrana
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Agustín Probanza-Lobo
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Pedro Antonio Jiménez-Gómez
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
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13
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Ma C, Hua J, Li H, Zhang J, Luo S. Inoculation with carbofuran-degrading rhizobacteria promotes maize growth through production of IAA and regulation of the release of plant-specialized metabolites. CHEMOSPHERE 2022; 307:136027. [PMID: 35973507 DOI: 10.1016/j.chemosphere.2022.136027] [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: 05/03/2022] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Toxic residues of the insecticide carbofuran in farmland is an urgent problem, and high concentrations of carbofuran have been found in the rhizoshperic soil of maize treated with seed coating agents 120-180 days after planting. Using an enrichment co-culture method, we identify a bacterial strain obtained from these carbofuran-contaminated rhizosphere soils as Leclercia adecarboxylata MCH-1. This strain exhibited a significant ability to degrade both carbofuran and 3-keto carbofuran, with total degradation of 55.6 ± 4.6% and 75.7 ± 3.4%, respectively, 24 h following start of co-culture. Further activity screening revealed that the inoculation of maize roots with L. adecarboxylata MCH-1 promoted maize seedling growth. Quantitative analysis demonstrated that this bacterial strain had the ability to synthesize the phytohormone IAA. Simultaneously, the concentration of IAA in the rhizospheric soil increased following inoculation of maize roots with L. adecarboxylata MCH-1. Moreover, the concentrations of plant specialized metabolites, including phenolics, terpenoids, and alkaloids, decreased in maize seedlings and were elevated in the rhizospheric soil after maize roots had been inoculated with the MCH-1 strain. Interestingly, the growth of the strain MCH-1 was improved by co-culture with root exudates obtained from the rhizospheric soil, specifically 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, and zealexin A1 (ZA1). Taken together, our results suggest that the carbofuran-degrading rhizobacterium L. adecarboxylata MCH-1 is able to interact with maize plants through the regulation of maize root exudates. Moreover, inoculation with L. adecarboxylata MCH-1 promotes maize growth through the production of IAA and regulation of the release of plant specialized metabolites. Our results provide a new model organism for the remediation of farmland soils from pollution with carbofuran residues.
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Affiliation(s)
- Caihong Ma
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning Province, China
| | - Juan Hua
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning Province, China
| | - Hongdi Li
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning Province, China
| | - Jiaming Zhang
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning Province, China
| | - Shihong Luo
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning Province, China.
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14
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Luo X, Ye X, Wang W, Chen Y, Li Z, Wang Y, Huang Y, Ran W, Cao H, Cui Z. Temporal dynamics of total and active root-associated diazotrophic communities in field-grown rice. Front Microbiol 2022; 13:1016547. [PMID: 36312965 PMCID: PMC9606772 DOI: 10.3389/fmicb.2022.1016547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022] Open
Abstract
Plant-associated nitrogen-fixing microorganisms (diazotrophs) are essential to host nutrient acquisition, productivity and health, but how host growth affects the succession characteristics of crop diazotrophic communities is still poorly understood. Here, Illumina sequencing of DNA- and RNA-derived nifH genes was employed to investigate the dynamics of total and active diazotrophic communities across rhizosphere soil and rice roots under four fertilization regimes during three growth periods (tillering, heading and mature stages) of rice in 2015 and 2016. Our results indicated that 71.9–77.2% of the operational taxonomic units (OTUs) were both detected at the DNA and RNA levels. According to the nonmetric multidimensional scaling ordinations of Bray–Curtis distances, the variations in community composition of active rhizosphere diazotrophs were greater than those of total rhizosphere diazotrophs. The community composition (β-diversity) of total and active root-associated diazotrophs was shaped predominantly by microhabitat (niche; R2 ≥ 0.959, p < 0.001), followed by growth period (R2 ≥ 0.15, p < 0.001). The growth period had a stronger effect on endophytic diazotrophs than on rhizosphere diazotrophs. From the tillering stage to the heading stage, the α-diversity indices (Chao1, Shannon and phylogenetic diversity) and network topological parameters (edge numbers, average clustering coefficient and average degree values) of total endophytic diazotrophic communities increased. The proportions of OTUs shared by the total rhizosphere and endophytic diazotrophs in rhizosphere diazotrophs gradually increased during rice growth. Moreover, total diazotrophic α-diversity and network complexity decreased from rhizosphere soil to roots. Collectively, compared with total diazotrophic communities, active diazotrophic communities were better indicators of biological response to environmental changes. The host microhabitat profoundly drove the temporal dynamics of total and active root-associated diazotrophic communities, followed by the plant growth period.
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Affiliation(s)
- Xue Luo
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Zhongli Cui, , ; Xianfeng Ye,
| | - Wenhui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yang Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Wei Ran
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Zhongli Cui, , ; Xianfeng Ye,
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15
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Effects of three regeneration methods on the growth and bacterial community diversity of Populus × euramericana. PLoS One 2022; 17:e0273306. [PMID: 36018851 PMCID: PMC9416986 DOI: 10.1371/journal.pone.0273306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/06/2022] [Indexed: 11/19/2022] Open
Abstract
To study the effects of different regeneration methods on the growth and bacterial community diversity of Populus × euramericana cv. ‘74/76’ (poplar 107), we investigated the growth of poplar 107 trees under three regeneration methods in 2017 and 2020, and sequenced the 16S rDNA V5–V7 regions in stem endophytic, root endophytic, and rhizosphere soil bacteria present in samples from the three regeneration methods using the Illumina high-throughput sequencing platform. The growth analysis showed that stump grafting regeneration (ST) and stump sprouting regeneration (SP) presented similar tree height and diameter at breast height (DBH), which were significantly lower by planted seedling regeneration (CK). The high-throughput sequencing results showed that the rhizosphere soil bacteria appeared to be significantly more diverse and rich than the root and stem endophytic bacteria. Cluster analysis showed that the similarity of bacterial community structure among the rhizosphere soil, root, and stem was small. Thus, the three sample types showed significant differences in bacteria. While comparing the two years, 2020 was significantly more diverse and rich than 2017. With the increase in stand age, the abundance of Proteobacteria increased and the abundance of Acidobacteria decreased. Among the three regeneration methods, ST significantly increased the diversity of stem endophytic bacteria. Chthoniobacter was enriched in SP, which promoted the decomposition of organic matter, and more plant growth promoting rhizobacteria (PGPR) were accumulated in the rhizosphere of SP and ST. The composition of the bacterial community was similar in the three regeneration methods, but the community composition was different. Regeneration and transformation of poplar plantations can be better carried out by stump grafting and stump sprouting.
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16
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Zhao YH, Wang N, Yu MK, Yu JG, Xue LH. Rhizosphere and Straw Return Interactively Shape Rhizosphere Bacterial Community Composition and Nitrogen Cycling in Paddy Soil. Front Microbiol 2022; 13:945927. [PMID: 35875526 PMCID: PMC9301285 DOI: 10.3389/fmicb.2022.945927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Currently, how rice roots interact with straw return in structuring rhizosphere communities and nitrogen (N) cycling functions is relatively unexplored. In this study, paddy soil was amended with wheat straw at 1 and 2% w/w and used for rice growth. The effects of the rhizosphere, straw, and their interaction on soil bacterial community composition and N-cycling gene abundances were assessed at the rice maturity stage. For the soil without straw addition, rice growth, i.e., the rhizosphere effect, significantly altered the bacterial community composition and abundances of N-cycling genes, such as archaeal and bacterial amoA (AOA and AOB), nirK, and nosZ. The comparison of bulk soils between control and straw treatments showed a shift in bacterial community composition and decreased abundance of AOA, AOB, nirS, and nosZ, which were attributed to sole straw effects. The comparison of rhizosphere soils between control and straw treatments showed an increase in the nifH gene and a decrease in the nirK gene, which were attributed to the interaction of straw and the rhizosphere. The number of differentially abundant genera in bulk soils between control and straw treatments was 13-23, similar to the number of 16-22 genera in rhizosphere soil between control and straw treatment. However, the number of genera affected by the rhizosphere effect was much lower in soil amended with straw (3-4) than in soil without straw addition (9). Results suggest possibly more pronounced impacts of straw amendments in shaping soil bacterial community composition.
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Affiliation(s)
- Ya-Hui Zhao
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ning Wang
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Meng-Kang Yu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Henan Institute of Science and Technology, Xinxiang, China
| | - Jian-Guang Yu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Li-Hong Xue
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
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17
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Speciation Distribution and Influencing Factors of Heavy Metals in Rhizosphere Soil of Miscanthus Floridulus in the Tailing Reservoir Area of Dabaoshan Iron Polymetallic Mine in Northern Guangdong. Processes (Basel) 2022. [DOI: 10.3390/pr10061217] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Through field investigation and experimental analysis, the forms, contents and distribution of heavy metals (Zn, Pb, Cu, Cd, Ni, Cr) in rhizosphere and non-rhizosphere soils of Miscanthus floridulus growing everywhere in Tielongwei mine pond (sample plot 1), Caoduikeng tailings pond (sample plot 2), Donghua tailings pond (sample plot 3) and Small tailings pond (sample plot 4) in Dabaoshan, Guangdong Province were studied. The results showed that the main forms and distributions of heavy metals in rhizosphere and non-rhizosphere soils are basically the same, which shows that the mineral content accounts for most of the total amount of heavy metals, while the exchange content is low. Compared with non-rhizosphere soil, the proportion of exchangeable and organic heavy metals in rhizosphere soil increased significantly, in which the proportion of organic-bound Cu increased by 53.25%, the proportion of organic-bound Cd and Pb increased by more than 17%, and the proportion of Zn increased by 5.67%. At the same time, the contents of carbonate-bound and iron manganese oxide-bound decreased. Statistical analyses showed that the morphological distribution of Zn, Pb, Cu, Cd, Ni and Cr in rhizosphere soil was closely related to soil pH value, organic matter content, plant growth and other factors. The results of this study provided a basis for the restoration of heavy metal-contaminated sites by Miscanthus.
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18
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Cao W, Gong J, Zeng G, Qin M, Qin L, Zhang Y, Fang S, Li J, Tang S, Chen Z. Impacts of typical engineering nanomaterials on the response of rhizobacteria communities and rice (Oryza sativa L.) growths in waterlogged antimony-contaminated soils. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128385. [PMID: 35152103 DOI: 10.1016/j.jhazmat.2022.128385] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The combined eco-risks of Sb (widely presented in soils, especially nearing mining areas) and the engineering nanomaterials (ENMs) (applied in agriculture and soil remediation) still remain uncovered. The current study investigated the impacts of single and combined exposure of CuO, CeO2 nanoparticles (NPs) and multi-walled carbon nanotube (MWCNTs) with Sb on rice growths and rhizosphere bacterial communities. The results showed that co-exposure of CuO NPs (0.075 wt%) with Sb (III) posed the most adverse impacts on root biomass and branches (up to 66.59% and 70.00% compared to other treatments, respectively). Treatments containing MWCNTs showed insignificant dose-dependent effects, while CeO2 NPs combined with Sb (III) showed significant synergistic stimulating effects on the fresh weights of root and shoot, by 68.30% and 73.48% (p < 0.05) compared to single Sb exposure, respectively. The rice planting increased the percentage of non-specifically sorbed Sb in soils by 1.50-14.49 than the no-planting stage. Analysis on microbial communities revealed that co-exposure of CuO NPs with Sb (III) induced the greatest adverse impacts on rhizobacteria abundances and community structures at both phylum and genus levels. Therein, significant decrease of Bacteroidetes, Acidobacteria and increase of Firmicutes abundance at the phylum level were observed. This study provided information about the risks of different ENMs released to Sb-contaminated soils under flooded condition on both crops and bacterial communities.
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Affiliation(s)
- Weicheng Cao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Jilai Gong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China; State Environmental Protection Key Laboratory of Monitoring for Heavy Metal Pollutants, Changsha 410082, PR China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Meng Qin
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Lei Qin
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Yiqiu Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Siyuan Fang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Juan Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Siqun Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Zengping Chen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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19
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Zhou Q, He R, Zhao D, Zeng J, Yu Z, Wu QL. Contrasting Patterns of the Resident and Active Rhizosphere Bacterial Communities of Phragmites Australis. MICROBIAL ECOLOGY 2022; 83:314-327. [PMID: 33956174 DOI: 10.1007/s00248-021-01767-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Rhizosphere microbes play a key role in maintaining plant health and regulating biogeochemical cycles. The active bacterial community (ABC) in rhizosphere, as a small fraction of the rhizosphere resident bacterial community (RBC), has the potential to actively participate in nutrient cycling processes at the root-sediment interface. Here, we investigated the ABC and RBC within the rhizosphere of Phragmites australis (P. australis) subjected to different environmental conditions (i.e., seasons and flooding conditions) in Lake Taihu, China. Our results indicated that RBC exhibited significantly higher alpha diversity as well as lower beta diversity than ABC. The active ratios of 16S rRNA to 16S rDNA (also RNA/DNA) of the bacterial communities in summer and winter suggested a lower proportion of potential active taxa in the rhizosphere bacterial community during summer. Network analysis showed that negative correlations in each network were observed to dominate the species correlations between the rhizosphere and bulk sediment bacterial communities. Our results revealed that niche differentiation and seasonal variation played crucial roles in driving the assembly of ABC and RBC associated with the rhizospheres of P. australis. These findings broaden our knowledge about how rhizosphere bacterial communities respond to environmental variations through changing their diversity and composition.
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Affiliation(s)
- Qi Zhou
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Rujia He
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China
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Wang Q, Huang Q, Wang J, Khan MA, Guo G, Liu Y, Hu S, Jin F, Wang J, Yu Y. Dissolved organic carbon drives nutrient cycling via microbial community in paddy soil. CHEMOSPHERE 2021; 285:131472. [PMID: 34265723 DOI: 10.1016/j.chemosphere.2021.131472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Microbial mediated iron cycling drives the biogeochemical cycling of carbon, nitrogen, sulfur, and phosphorus. However, the fate of the microbial community and the relative metabolic pathways in paddy soil after the addition of biogas slurry are poorly understood. In this study, the response of functional genes was investigated by growing one-season rice in paddy soils in a pot experiment. Seven treatments were prepared: 1) control (CK); 2) organic carbon (OC); 3) fertilizer (F); 4) 5% of biogas slurry (B05); 5) 10% of biogas slurry (B10); 6) 15% of biogas slurry (B15); 7) 20% of biogas slurry (B20). In the biogas slurry treatments, Geobacter increased more than in the other treatments during rice growth, which were structured by TOC. Particularly, in the B10 treatment, the relative abundance of Geobacter was 1.6 and 14.8 times higher than that of CK at the heading and mature stages, respectively. At the heading stage, the addition of biogas slurry and OC shifted the microbial phosphorus-transformation communities differently. There were no significant differences in the carbon, nitrogen, and sulfur metabolic pathways between the two treatments. At the mature stage, the carbon: nitrogen: phosphorus balance was significantly influenced by the regulation of functional gene expression and metabolic activities. These findings provide insight into the key factors affecting carbon, nitrogen, sulfur, phosphorus, and iron during rice growth after carbon inputs.
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Affiliation(s)
- Qingqing Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Qing Huang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Jiaxin Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Muhammad Amjad Khan
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Genmao Guo
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Yin Liu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Shan Hu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Fangming Jin
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Junfeng Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China; College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, Guangdong, 518061, China
| | - Yunbo Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 10085, China
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Leichty SI, Kasanke CP, Bell SL, Hofmockel KS. Site and Bioenergy Cropping System Similarly Affect Distinct Live and Total Soil Microbial Communities. Front Microbiol 2021; 12:725756. [PMID: 34721322 PMCID: PMC8551758 DOI: 10.3389/fmicb.2021.725756] [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] [Received: 06/15/2021] [Accepted: 09/22/2021] [Indexed: 11/21/2022] Open
Abstract
Bioenergy crops are a promising energy alternative to fossil fuels. During bioenergy feedstock production, crop inputs shape the composition of soil microbial communities, which in turn influences nutrient cycling and plant productivity. In addition to cropping inputs, site characteristics (e.g., soil texture, climate) influence bacterial and fungal communities. We explored the response of soil microorganisms to bioenergy cropping system (switchgrass vs. maize) and site (sandy loam vs. silty loam) within two long-term experimental research stations. The live and total microbial community membership was investigated using 16S and ITS amplicon sequencing of soil RNA and DNA. For both nucleic acid types, we expected fungi and prokaryotes to be differentially impacted by crop and site due their dissimilar life strategies. We also expected live communities to be more strongly affected by site and crop than the total communities due to a sensitivity to recent stimuli. Instead, we found that prokaryotic and fungal community composition was primarily driven by site with a secondary crop effect, highlighting the importance of soil texture and fertility in shaping both communities. Specific highly abundant prokaryotic and fungal taxa within live communities were indicative of site and cropping systems, providing insight into treatment-specific, agriculturally relevant microbial taxa that were obscured within total community profiles. Within live prokaryote communities, predatory Myxobacteria spp. were largely indicative of silty and switchgrass communities. Within live fungal communities, Glomeromycota spp. were solely indicative of switchgrass soils, while a few very abundant Mortierellomycota spp. were indicative of silty soils. Site and cropping system had distinct effects on the live and total communities reflecting selection forces of plant inputs and environmental conditions over time. Comparisons between RNA and DNA communities uncovered live members obscured within the total community as well as members of the relic DNA pool. The associations between live communities and relic DNA are a product of the intimate relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter, and in turn shapes soil microbial dynamics.
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Affiliation(s)
- Sarah I Leichty
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Christopher P Kasanke
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sheryl L Bell
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States.,Department of Agronomy, Iowa State University, Ames, IA, United States
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22
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Qiao F, Tan F, Li LY, Lv HB, Chen L, Du ZY, Zhang ML. Alteration and the Function of Intestinal Microbiota in High-Fat-Diet- or Genetics-Induced Lipid Accumulation. Front Microbiol 2021; 12:741616. [PMID: 34603270 PMCID: PMC8484964 DOI: 10.3389/fmicb.2021.741616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
Diet and host genetics influence the composition of intestinal microbiota, yet few studies have compared the function of intestinal microbiota in the diet- or genotype-induced lipid deposition, which limits our understanding of the role of intestinal bacteria in metabolic disorders. The lipid accumulation in wild-type zebrafish fed with control (CON) or high-fat (HF) diet and two gene-knockout zebrafish lines (cpt1b–/– or pparab–/–) fed with control diet was measured after a 4-week feeding experiment. The intestinal microbiota composition of these groups was investigated using 16S ribosomal RNA (rRNA) gene sequencing (DNA-based) and 16S rRNA sequencing (RNA-based). The HF diet or deficiency of two genes induced more weight gain and higher triglyceride content in the liver compared with their control group. 16S rRNA gene sequencing (DNA-based) indicated the decreased abundance of Proteobacteria in the HF group compared with CON, but there was no significant difference in bacterial α diversity among treatments. 16S rRNA sequencing (RNA-based) confirmed the decreased abundance of Proteobacteria and the bacterial α diversity in the HF group compared with CON. Deficiency of cpt1b or pparab showed less change in microbiota composition compared with their wild-type group. Intestinal microbiota of each group was transferred to germ-free zebrafish, and the quantification of Nile red staining indicated that the intestinal microbiota of the HF group induced more lipid accumulation compared with CON, whereas intestinal microbiota of cpt1b–/– and pparab–/– zebrafish did not. The results showed that RNA-based bacterial sequencing revealed more bacterial alteration than DNA-based bacterial sequencing. HF diet had a more dominant role in shaping gut microbiota composition to induce lipid accumulation compared with the gene-knockout of cpt1b or pparab in zebrafish, and the transplant of intestinal microbiota from HF-fed fish induced more lipid deposition in germ-free zebrafish. Together, these data suggested that a high-fat diet exerted a more dominant role over the deletion of cpt1b or pparab on the intestinal bacterial composition, which corresponded to lipid accumulation.
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Affiliation(s)
- Fang Qiao
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Fang Tan
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Ling-Yu Li
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Hong-Bo Lv
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Liqiao Chen
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhen-Yu Du
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Mei-Ling Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
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23
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Li HQ, Li H, Zhou XY, Shen YJ, Su JQ. Distinct patterns of abundant and rare subcommunities in paddy soil during wetting-drying cycles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147298. [PMID: 33940401 DOI: 10.1016/j.scitotenv.2021.147298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 06/12/2023]
Abstract
Wetting-drying cycles typically result in a wide range of soil moistures and redox potentials (Eh) that significantly affect the soil microbial community. Although numerous studies have addressed the effects of soil moisture on soil microbial community structure and composition, the response of active microbes to the fluctuation in soil Eh is still largely unknown; this is especially true for the ecological roles of abundant and rare taxa. To explore the dynamics of active and total microbial communities in response to wetting-drying cycles, we conducted a microcosm experiment based on three wetting-drying cycles and 16S rRNA transcript (active) and 16S rRNA gene (total) amplicon sequencing. We found that both active and total microbial communities during three wetting-drying cycles were clustered according to the number of wetting-drying cycles (temporal factor) rather than soil moisture or Eh. Dynamics of the active microbial community, however, were redox dependent during the first wetting-drying cycle. In addition, rare taxa in the active microbial community exhibited more obvious differences than abundant ones during three wetting-drying cycles. Species turnover of abundant and rare taxa of total and active microbes, rather than species richness, explained the highest percentage of community variation. Rare taxa exhibited the most marked temporal turnover during three wetting-drying cycles. Members of Rhodospirillaceae were the major contributor to the resilience of abundant taxa of active microbes during the first wetting-drying cycle. Overall, these findings expand our current understanding of underlying assembly mechanisms of soil microbial communities responding to wetting-drying cycles.
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Affiliation(s)
- Huan-Qin Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, Fujian 361021, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, Fujian 361021, China
| | - Xin-Yuan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, Fujian 361021, China
| | - Ying-Jia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, Fujian 361021, China.
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24
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Light exposure mediates circadian rhythms of rhizosphere microbial communities. THE ISME JOURNAL 2021; 15:2655-2664. [PMID: 33746202 PMCID: PMC8397761 DOI: 10.1038/s41396-021-00957-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 02/01/2023]
Abstract
Microbial community circadian rhythms have a broad influence on host health and even though light-induced environmental fluctuations could regulate microbial communities, the contribution of light to the circadian rhythms of rhizosphere microbial communities has received little attention. To address this gap, we monitored diel changes in the microbial communities in rice (Oryza sativa L.) rhizosphere soil under light-dark and constant dark regimes, identifying microbes with circadian rhythms caused by light exposure and microbial circadian clocks, respectively. While rhizosphere microbial communities displayed circadian rhythms under light-dark and constant dark regimes, taxa possessing circadian rhythms under the two conditions were dissimilar. Light exposure concealed microbial circadian clocks as a regulatory driver, leading to fewer ecological niches in light versus dark communities. These findings disentangle regulation mechanisms for circadian rhythms in the rice rhizosphere microbial communities and highlight the role of light-induced regulation of rhizosphere microbial communities.
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Wu AL, Jiao XY, Wang JS, Dong EW, Guo J, Wang LG, Sun AQ, Hu HW. Sorghum rhizosphere effects reduced soil bacterial diversity by recruiting specific bacterial species under low nitrogen stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:144742. [PMID: 33736399 DOI: 10.1016/j.scitotenv.2020.144742] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/25/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
Rhizosphere microbiota play a pivotal role in promoting plant growth and defending against pathogens, but their responses to abiotic environmental stress remain largely elusive. Here, we investigated the influences of low-N stress on rhizosphere bacteria of six sorghum cultivars in a glasshouse experiment. The alpha diversity of bacteria (as revealed by Shannon diversity and Chao1 richness indices) was remarkably lower in rhizosphere soils than in bulk soils, and was significantly higher under low-N stress than under N addition. Principal coordinates analysis revealed that the bacterial community compositions in rhizosphere soils were clearly separated from bulk soils, and the rhizosphere soils under low-N stress or with N fertilization were clearly separated, indicating that both rhizosphere effects and N fertilization impacted the rhizosphere bacterial community. Notably, the relative abundances of beneficial bacteria such as Bacillaceae and Streptomycetaceae significantly increased in rhizosphere soils under low-N stress, which had significantly positive correlations with the sorghum N uptake. The relative abundance of Nitrosomonadaceae in rhizosphere soils was significantly lower than that in bulk soils, while the relative abundance of Rhizobiaceae showed an opposite pattern. Taken together, our results suggested that sorghum rhizosphere effects can reduce soil bacterial diversity possibly through recruiting specific bacterial species under low N stress.
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Affiliation(s)
- Ai-Lian Wu
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Xiao-Yan Jiao
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China.
| | - Jin-Song Wang
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Er-Wei Dong
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Jun Guo
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Li-Ge Wang
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - An-Qi Sun
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
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26
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Chen Y, Li S, Liu N, He H, Cao X, Lv C, Zhang K, Dai J. Effects of different types of microbial inoculants on available nitrogen and phosphorus, soil microbial community, and wheat growth in high-P soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:23036-23047. [PMID: 33438124 DOI: 10.1007/s11356-020-12203-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/22/2020] [Indexed: 05/03/2023]
Abstract
Irrational application of chemical fertilizers causes soil nutrient imbalance, reduced microbial diversity, soil diseases, and other soil quality problems and is one of the main sources of non-point pollution. The application of microbial inoculant (MI) can improve the soil environment and crop growth to reduce problems caused by irrational application of chemical fertilizers. Field experiments were carried out in high-phosphorus soils to study the effects of the addition of various MIs combined with chemical fertilizers on soil properties, wheat growth, and soil microbial composition and structure. The MIs consisted of one fungal agent: Trichoderma compound agent (TC) and five bacterial agents, namely soil remediation agent (SR), anti-repeat microbial agent (AM), microbial agent (MA), plant growth-promoting rhizobacteria (PG), and biological fertilizer agent (BF). The wheat yield increased by 15.2-33.4% with the addition of MIs, and PG with Bacillus subtilis as the core microorganism had the most obvious effect on increasing the production (p < 0.05). For the entire growth period of wheat, all MIs applied significantly increased the available nitrogen (AN) (p < 0.05) but did not significantly affect the available phosphorus (AP). BF has the best effect on increasing AN in the soil. The 16S rRNA sequencing results indicated that the dominant phyla of soil bacteria were Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The addition of MIs increased the relative abundance of Acidobacteria, Actinobacteria, Chloroflexi and decreased Proteobacteria and Bacteroidetes. The diversity of soil bacterial community (Chao1) was significantly higher in the soil added with TC than that added with BF (p < 0.05). All bacterial agents significantly enriched various genera (p < 0.05), while the fungal agent (TC) did not enrich the genera significantly. pH and AN, but not TP, were closely related to the dominant bacteria phylum in high-P soil. The application of MIs improved AN in soil, increased the wheat yield, and changed the relative abundance of the soil dominant phylum, and these changes were closely related to the type of MIs. The results provide a scientific basis for rational use of different types of MIs in high-P soil.
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Affiliation(s)
- Yihui Chen
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Shuangshuang Li
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Na Liu
- College of Resource and Environment, Shanxi Agricultural University, Taigu, 030801, China
| | - Huan He
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Xiaoyu Cao
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Cheng Lv
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Ke Zhang
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Jiulan Dai
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China.
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Rosatto S, Mariotti M, Romeo S, Roccotiello E. Root and Shoot Response to Nickel in Hyperaccumulator and Non-Hyperaccumulator Species. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10030508. [PMID: 33803420 PMCID: PMC7998499 DOI: 10.3390/plants10030508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/06/2021] [Accepted: 03/06/2021] [Indexed: 05/04/2023]
Abstract
The soil-root interface is the micro-ecosystem where roots uptake metals. However, less than 10% of hyperaccumulators' rhizosphere has been examined. The present study evaluated the root and shoot response to nickel in hyperaccumulator and non-hyperaccumulator species, through the analysis of root surface and biomass and the ecophysiological response of the related aboveground biomass. Ni-hyperaccumulators Alyssoides utriculata (L.) Medik. and Noccaea caerulescens (J. Presl and C. Presl) F.K. Mey. and non-hyperaccumulators Alyssum montanum L. and Thlaspi arvense L. were grown in pot on Ni-spiked soil (0-1000 mg Ni kg-1, total). Development of root surfaces was analysed with ImageJ; fresh and dry root biomass was determined. Photosynthetic efficiency was performed by analysing the fluorescence of chlorophyll a to estimate the plants' physiological conditions at the end of the treatment. Hyperaccumulators did not show a Ni-dependent decrease in root surfaces and biomass (except Ni 1000 mg kg-1 for N. caerulescens). The non-hyperaccumulator A. montanum suffers metal stress which threatens plant development, while the excluder T. arvense exhibits a positive ecophysiological response to Ni. The analysis of the root system, as a component of the rhizosphere, help to clarify the response to soil nickel and plant development under metal stress for bioremediation purposes.
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28
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Wahdan SFM, Heintz-Buschart A, Sansupa C, Tanunchai B, Wu YT, Schädler M, Noll M, Purahong W, Buscot F. Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link. Front Microbiol 2021; 12:629169. [PMID: 33597941 PMCID: PMC7882529 DOI: 10.3389/fmicb.2021.629169] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.
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Affiliation(s)
- Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,Department of Biology, Leipzig University, Leipzig, Germany.,Department of Botany, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Anna Heintz-Buschart
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Chakriya Sansupa
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Benjawan Tanunchai
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Community Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Serbent MP, Dos Anjos Borges LG, Quadros A, Marconatto L, Tavares LBB, Giongo A. Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:2328-2341. [PMID: 32880839 DOI: 10.1007/s11356-020-10614-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Conventional agricultural practices, such as rice plantations, often contaminate the soil and water with xenobiotics. Here we evaluated the microbiota composition in experimental rice planting with a record of prolonged pesticide use, using 16S and 18S rRNA amplicon sequencing. We investigated four components of a complete agricultural system: affluent water (A), rice rhizosphere soil (R), sediment from a storage pond (S), and effluent (E) water (drained from the storage pond). Despite the short spatial distance between our sites, the beta diversity analysis of bacterial communities showed two well-defined clusters, separating the water and sediment/rhizosphere samples; rhizosphere and sediment were richer while the effluent was less diverse. Overall, the site with the highest evenness was the rhizosphere. Unlike the bacterial communities, Shannon diversity of microeukaryotes was significantly different between A and E. The effluent presented the lowest values for all ecological indexes tested and differed significantly from all sampled sites, except on evenness. When mapped the metabolic pathways, genes corresponding to the degradation of aromatic compounds, including genes related to pesticide degradation, were identified. The most abundant genes were related to the degradation of benzoate. Our results indicate that the effluent is a selective environment for fungi. Interestingly, the overall fungal diversity was higher in the affluent, the water that reached the system before pesticide application, and where the prokaryotic diversity was the lowest. The affluent and effluent seem to have the lowest environmental quality, given the presence of bacteria genera previously recorded in environments with high concentrations of pesticide residues. The microbiota, environmental characteristics, and pesticide residues should be further studied and try to elucidate the potential for pesticide degradation by natural consortia. Thus, extensive comparative studies are needed to clarify the microbial composition, diversity, and functioning of rice cultivation environments, and how pesticide use changes may reflect differences in microbial structure.
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Affiliation(s)
- Maria Pilar Serbent
- Santa Catarina State University - UDESC, Ibirama, Brazil.
- Environmental Engineering Graduate Program, PPGEA, Regional University of Blumenau - FURB, Blumenau, Brazil.
| | - Luiz Gustavo Dos Anjos Borges
- Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Aline Quadros
- Pumpkin Science Communication, Porto Alegre, RS, Brazil
| | - Letícia Marconatto
- Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | | | - Adriana Giongo
- Environmental Engineering Graduate Program, PPGEA, Regional University of Blumenau - FURB, Blumenau, Brazil
- Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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30
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Li M, Mi T, He H, Chen Y, Zhen Y, Yu Z. Active bacterial and archaeal communities in coastal sediments: Biogeography pattern, assembly process and co-occurrence relationship. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:142252. [PMID: 33182220 DOI: 10.1016/j.scitotenv.2020.142252] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/12/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
The biogeography of active microbial communities and the underlying mechanisms in marine sediments are important in microbial ecology but remain unclear. Here, using qPCR and high-throughput sequencing, we investigated bacterial and archaeal community abundances and activities by quantifying the abundance and expression of the 16S rRNA gene respectively, RNA-derived bacterial and archaeal community biogeography, assembly mechanisms and co-occurrence relationships in surface sediment samples from the Bohai Sea (BS), South Yellow Sea (SYS) and the north East China Sea (NECS) of the eastern Chinese marginal seas. The results revealed a higher heterogeneity of bacterial and archaeal community activities than of abundances and heterogeneous ecological functions among areas reflected by community compositions. Furthermore, clear geographic groups (i.e., the BS, SYS and NECS groups) were observed for all, abundant and rare active bacterial and archaeal communities, accompanied by significant distance-decay patterns. However, the abundant and rare taxa showed inconsistent geographic patterns. More importantly, deterministic processes played a greater role than stochastic processes in active bacterial and archaeal community assembly. The rare taxa had weaker abilities to disperse and/or adapt and more complex ecological processes than the abundant taxa. In addition, this study also showed that intertaxa competition was the dominant interaction between active bacterial and archaeal members, which could greatly contribute to dispersal limitation. Moreover, active bacterial and archaeal co-occurrence patterns showed significant distance-decay patterns, which were consistent with the community compositions.
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Affiliation(s)
- Mingyue Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Tiezhu Mi
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Hui He
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Ye Chen
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China.
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266100, China
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Liu K, Ding X, Wang J. Soil metabolome correlates with bacterial diversity and co-occurrence patterns in root-associated soils on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 735:139572. [PMID: 32480142 DOI: 10.1016/j.scitotenv.2020.139572] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Metabolites in root-zone soils mediate microbe-to-microbe interactions and govern the overall microbial community. However, how chemicals relate to diversity and co-occurrence patterns of bacterial communities in root-associated soils is still poorly understood. Here, we studied the relationships of soil metabolome with bacterial community diversity and co-occurrence patterns in root-associated soils across different land types on the Tibetan Plateau. The soil metabolome mainly encompassed a range of organic acids, and sugars and sugar derivatives, which were widely negatively correlated with bacterial alpha-diversity. Compared to the investigated environmental variables, metabolites accounted more for the variations in the Shannon diversity and bacterial community compositions. Compared to sugars, organic acids accounted more for bacterial community compositions at high taxonomic ranks, while reversed at genus and species levels. The relative abundances of some bacterial genera and metabolites were closely linked to soil types and plant genotypes. The differential compounds were significantly correlated with the distinctive bacterial taxa across land types and plant genotypes. Keystone species in co-occurrence network, such as Bradyrhizobium, Bryobacter, and Microvirga were significantly correlated with sugars and organic acids. Structural equation modeling revealed that sugar metabolism can play a crucial role in altering the bacterial community diversity. This study provides new insights into the ecological mechanism that maintains bacterial community in the root-associated soils on the Tibetan Plateau.
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Affiliation(s)
- Kaihui Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Xiaowei Ding
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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Pan C, Bao Y, Guo A, Ma J. Environmentally Relevant-Level CeO 2 NP with Ferrous Amendment Alters Soil Bacterial Community Compositions and Metabolite Profiles in Rice-Planted Soils. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8172-8184. [PMID: 32663007 DOI: 10.1021/acs.jafc.0c03507] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The environmental risks and benefits associated with the introduction of CeO2 nanoparticle (NP) in agricultural soil must be carefully assessed. The ferrous ion is rich in rhizosphere soil of rice due to the reduction states underground. The aim of this study was to investigate the effects of environmentally relevant-level CeO2 NP (25 mg·kg-1) in the absence or presence of ferrous (30 mg·kg-1) amendment on soil bacterial communities and soil metabolomics in rice-planted soil over 150 days. Results showed that CeO2 NP exposure changed soil bacterial community compositions and soil metabolomics, and the above changes were further shifted with the ferrous amendment. Several functionally significant bacterial phyla containing Proteobacteria and Bacteroidetes abundances, which were associated with carbon and nitrogen cycling, were promoted after CeO2 NP exposure with ferrous amendment. However, CeO2 NP inhibited plant-growth-promoting rhizobacteria containing genera Bacillus and Arthrobacter irrespective of the presence or absence of ferrous. Among rhizosphere soil enzyme activities, cellulose activity was the most sensitive for CeO2 NP exposure. NP decreased Firmicutes and increased Chloroflexi, Rokubacteria, and Thaumarchaeota abundances at the phylum level, which contributed to reduce soil cellulose activity. Additionally, CeO2 NP positively or negatively affected soil pH, Ce accumulation in root, and rice physiological properties (root-POD, stem-POD). As a result, the above factors were related to the changes of Chloroflexi, Gemmatimonadetes, Rokubacteria, Thaumarchaeota, and Nitrospirae at the phylum level. After adding CeO2 NP with ferrous or not, the main metabolic changes were concentrated on fluctuations in starch and sucrose metabolism, nitrogen metabolism, sulfur metabolism, propanoate metabolism, fatty acid metabolism, and urea cycle. The eight changed metabolites containing glycerol monstearate, boric acid, monopalmitin, palmitic acid, alkane, ethanol, dicarboximide, and stearic acid accounted for the separation of different treatments with CeO2 NP exposure. Activities of soil enzymes (urease, invertase, and cellulose), pH, and soil organic matter affected dominant metabolites containing fatty acids, inorganic acid, and sugar. Network analysis showed that the influence of soil bacterial community on metabolites varied with metabolites and bacteria species. The presence of CeO2 NP mainly promoted fatty acids (hexanoic acid, nonanoic acid) and amino acid (oxoproline) and amine (diethanolamine) concentrations, which could be from the increased Proteobacteria abundance after CeO2 NP exposure. Phylum Proteobacteria had the most genus species containing 13 genera affecting soil metabolite profiles. These results provide valuable information for understanding the impact of environmentally relevant-level CeO2 NP exposure on soil microbial communities and metabolites with or without ferrous, which is needed to understand the ecological risk posed by long-term CeO2 NP exposure in rice-planted soil with rich ferrous.
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Affiliation(s)
- Chengrong Pan
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, P. R. China
| | - Yanyu Bao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, P. R. China
| | - Aiyun Guo
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, P. R. China
| | - Jinyu Ma
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, P. R. China
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Liu Y, Luo M, Ye R, Huang J, Xiao L, Hu Q, Zhu A, Tong C. Impacts of the rhizosphere effect and plant species on organic carbon mineralization rates and pathways, and bacterial community composition in a tidal marsh. FEMS Microbiol Ecol 2020; 95:5538758. [PMID: 31344237 DOI: 10.1093/femsec/fiz120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/18/2019] [Indexed: 11/13/2022] Open
Abstract
Despite the growing recognition regarding the carbon cycle in the rhizosphere of upland ecosystems, little is known regarding the rhizosphere effect on soil organic carbon (SOC) mineralization in tidal marsh soils. In the current study, in situ rhizobox experiments (including rhizosphere and inner and outer bulk soil) were conducted in an estuarine tidal marsh. Our results showed that a higher abundance of total bacteria, Geobacter, dsrA and mcrA and lower α-diversity were observed in the rhizosphere relative to the bulk soil. Rhizosphere effects shifted the partition of terminal metabolic pathways from sulfate reduction in the bulk soil to the co-dominance of microbial Fe(III) and sulfate reduction in the rhizosphere. Although the rhizosphere effect promoted the rates of three terminal metabolic pathways, it showed greater preference towards microbial Fe(III) reduction in the tidal marsh soils. Plant species had little impact on the partitioning of terminal metabolic pathways, but did affect the potential of total SOC mineralization together with the abundance and diversity of total bacteria. Both the rhizosphere effect and plant species influenced the bacterial community composition in the tidal marsh soils; however, plant species had a less pronounced impact on the bacterial community compared with that of the rhizosphere effect.
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Affiliation(s)
- Yuxiu Liu
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Min Luo
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China.,School of Environment and Resource, Fuzhou University, Fuzhou 350116, China
| | - Rongzhong Ye
- Pee Dee Research & Education Centers, Clemson University, Florence, SC 29506, USA
| | - Jiafang Huang
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Leilei Xiao
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Qikai Hu
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China.,School of Environment and Resource, Fuzhou University, Fuzhou 350116, China
| | - Aijv Zhu
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Chuan Tong
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
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34
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Similar but Not Identical Resuscitation Trajectories of the Soil Microbial Community Based on Either DNA or RNA after Flooding. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10040502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Both drought and flooding are unfavorable for soil microorganisms, but nevertheless, are highly relevant to the extreme weather events that have been predicted to increase in the future. The switch of soil water status from drought to flooding can happen rapidly and microbial activity might be either stimulated or further inhibited, but we have insufficient understanding of the underlying microbial processes. Here, we tracked the changes in soil bacterial and fungal abundance and their community structures, assaying the total (DNA-based) and potentially active (RNA-based) communities in response to abrupt flooding of dry soil. Also, rates of soil respiration and enzyme activity were measured after flooding. Results showed that the bacterial community was found to be more responsive than the fungal community to flooding. The bacterial community responses were clearly classified into three distinct patterns in which the intermediate pattern displayed highly phylogenetic clustering. A transient flourish of Bacilli which belongs to Firmicutes was detected at 8–48 h of flooding, suggesting its potential importance in the microbial assemblage and subsequent ecosystem functioning. Finally, the accumulative amount of CO2 released was more closely related than enzyme activity to the change in structure of the bacterial community after flooding. In conclusion, these findings extended our understanding of the underlying soil microbial processes following abrupt water condition changes.
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Iliev I, Marhova M, Kostadinova S, Gochev V, Tsankova M, Ivanova A, Yahubyan G, Baev V. Metagenomic analysis of the microbial community structure in protected wetlands in the Maritza River Basin. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1697364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Ivan Iliev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Mariana Marhova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Sonya Kostadinova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Velizar Gochev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Marinela Tsankova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Angelina Ivanova
- Institute of Fisheries and Aquaculture, Agriculture Academy, Plovdiv, Bulgaria
| | - Galina Yahubyan
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Vesselin Baev
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
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Bacterial Diversity and Community Structure in Typical Plant Rhizosphere. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11100179] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacteria play a vital role in the quality of soil, health, and the production of plants. This has led to several studies in understanding the diversity and structure in the plant rhizosphere. Over the years, there have been overwhelming advances in molecular biology which have led to the development of omics techniques which utilize RNA, DNA, or proteins as biomolecules; these have been gainfully used in plant–microbe interactions. The bacterial community found in the rhizosphere is known for its colonization around the roots due to availability of nutrients, and composition, and it affects the plant growth directly or indirectly. Metabolic fingerprinting enables a snapshot of the metabolic composition at a given time. We review metabolites with ample information on their benefit to plants and which are found in rhizobacteria such as Pseudomonas spp. and Bacillus spp. Exploring plant-growth-promoting rhizobacteria using omics techniques can be a true success story for agricultural sustainability.
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Nawaz A, Purahong W, Herrmann M, Küsel K, Buscot F, Wubet T. DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors. Microorganisms 2019; 7:microorganisms7090341. [PMID: 31514383 PMCID: PMC6780912 DOI: 10.3390/microorganisms7090341] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
Recent advances in high-throughput sequencing (HTS) technologies have revolutionized our understanding of microbial diversity and composition in relation to their environment. HTS-based characterization of metabolically active (RNA-derived) and total (DNA-derived) fungal communities in different terrestrial habitats has revealed profound differences in both richness and community compositions. However, such DNA- and RNA-based HTS comparisons are widely missing for fungal communities of groundwater aquifers in the terrestrial biogeosphere. Therefore, in this study, we extracted DNA and RNA from groundwater samples of two pristine aquifers in the Hainich CZE and employed paired-end Illumina sequencing of the fungal nuclear ribosomal internal transcribed spacer 2 (ITS2) region to comprehensively test difference/similarities in the “total” and “active” fungal communities. We found no significant differences in the species richness between the DNA- and RNA-derived fungal communities, but the relative abundances of various fungal operational taxonomic units (OTUs) appeared to differ. We also found the same set of environmental parameters to shape the “total” and “active” fungal communities in the targeted aquifers. Furthermore, our comparison also underlined that about 30%–40% of the fungal OTUs were only detected in RNA-derived communities. This implies that the active fungal communities analyzed by HTS methods in the subsurface aquifers are actually not a subset of supposedly total fungal communities. In general, our study highlights the importance of differentiating the potential (DNA-derived) and expressed (RNA-derived) members of the fungal communities in aquatic ecosystems.
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Affiliation(s)
- Ali Nawaz
- Helmholtz Centre for Environmental Research-UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany.
- Helmholtz Centre for Environmental Research-UFZ, Department of Community Ecology, 06120 Halle (Saale), Germany.
- Institute of Biology, University of Leipzig, 04103 Leipzig, Germany.
| | - Witoon Purahong
- Helmholtz Centre for Environmental Research-UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany.
| | - Martina Herrmann
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - François Buscot
- Helmholtz Centre for Environmental Research-UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Tesfaye Wubet
- Helmholtz Centre for Environmental Research-UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany.
- Helmholtz Centre for Environmental Research-UFZ, Department of Community Ecology, 06120 Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
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Li H, Su JQ, Yang XR, Zhou GW, Lassen SB, Zhu YG. RNA Stable Isotope Probing of Potential Feammox Population in Paddy Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4841-4849. [PMID: 30978017 DOI: 10.1021/acs.est.8b05016] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Anaerobic ammonium oxidation coupled to iron reduction (Feammox) is a recently discovered pathway contributing to nitrogen loss in various ecosystems such as paddy soils and sediments. However, little is known about the microbes driving Feammox in an agricultural ecosystem. Here, we demonstrated the occurrence of Feammox in paddy soils of Southern China using a 15N isotopic tracing technique, and examined the microbial communities associated with Feammox using RNA based stable isotope probing (RNA-SIP) combined with Illumina sequencing. Feammox was detected in all collected soils with direct N2 production as the dominant Feammox pathway. It was estimated that approximately 6.91% of the applied nitrogen fertilizers were lost through Feammox in the paddy soils. RNA-SIP results showed that the composition of enriched active microbial communities were dependent on soil properties, especially the soil pH and grain size. Geobacter were enriched in most soils across various properties. The abundance of enriched GOUTA19 were significantly higher in soils with low pH than those in soils with medium pH and high pH, and the relative abundance of active Nitrososphaeraceae and Pseudomonas only increased in soils with medium and high pH during 4-day of incubation. These results suggested Feammox is a ubiquitous and important process for N loss. Geobacter, GOUTA19, Nitrososphaeraceae and Pseudomonas were active during the incubation that favored Feammox and the growth of Feammox microbes, suggesting these microbes were potentially associated with Feammox in natural agricultural soils.
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Affiliation(s)
- Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , P. R. China
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , P. R. China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , P. R. China
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , P. R. China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , P. R. China
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , P. R. China
| | - Guo-Wei Zhou
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
| | - Simon Bo Lassen
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , P. R. China
- Department of Plant and Environmental Sciences, Faculty of Science , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , P. R. China
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , P. R. China
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
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