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Adigoun RFR, Durand A, Tchokponhoué DA, Achigan-Dako EG, Aholoukpè HNS, Bokonon-Ganta AH, Benizri E. Drivers of the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] rhizosphere bacterial communities in Benin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173550. [PMID: 38810760 DOI: 10.1016/j.scitotenv.2024.173550] [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: 04/02/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024]
Abstract
Each plant species has its own rhizobacteriome, whose activities determine both soil biological quality and plant growth. Little knowledge exists of the rhizosphere bacterial communities associated with opportunity crops with high economic potential such as Synsepalum dulcificum. Native to West Africa, this shrub is famous for its red berries representing the only natural source of miraculin, a glycoprotein, with sweetening properties, but also playing a role in the treatment of cancer and diabetes. This study aimed to characterize the structure and diversity of rhizobacterial communities associated with S. dulcificum and to identify the parameters determining this diversity. An initial sampling stage allowed the collection of rhizosphere soils from 29 S. dulcificum accessions, belonging to three distinct phenotypes, from 16 municipalities of Benin, located either on farms or in home gardens. The bacterial diversity of these rhizosphere soils was assessed by Illumina sequencing of the 16S rRNA gene after DNA extraction from these soils. Furthermore, an analysis of the physicochemical properties of these soils was carried out. All accessions combined, the most represented phylum appeared to be Actinobacteriota, with an average relative abundance of 43.5 %, followed by Proteobacteria (14.8 %), Firmicutes (14.3 %) and Chloroflexi (12.2 %), yet the relative abundance of dominant phyla varied significantly among accessions (p < 0.05). Plant phenotype, habitat, climate and soil physicochemical properties affected the bacterial communities, but our study pointed out that soil physicochemical parameters were the main driver of rhizobacterial communities' structure and diversity. Among them, the assimilable phosphorus, lead, potassium, arsenic and manganese contents, texture and cation exchange capacity of rhizosphere soils were the major determinants of the composition and diversity of rhizosphere bacterial communities. These results suggested the possibility of improving the growth conditions and productivity of S. dulcificum, by harnessing its associated bacteria of interest and better managing soil physicochemical properties.
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Affiliation(s)
- Rabiath F R Adigoun
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France; Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin; Laboratoire d'Entomologie Agricole (LEAg), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, B.P. 526 Abomey-Calavi, Benin
| | - Alexis Durand
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
| | - Dèdéou A Tchokponhoué
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Enoch G Achigan-Dako
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Hervé N S Aholoukpè
- Centre de Recherches Agricoles Plantes Pérennes (CRA-PP), Institut National des Recherches Agricoles du Bénin, BP 01 Pobè, Benin
| | - Aimé H Bokonon-Ganta
- Laboratoire d'Entomologie Agricole (LEAg), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, B.P. 526 Abomey-Calavi, Benin
| | - Emile Benizri
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
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Cai X, Chen C, Singh AK, Zhu X, Liu W. Anthropogenic restoration exhibits more complex and stable microbial co-occurrence patterns than natural restoration in rubber plantations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174935. [PMID: 39053530 DOI: 10.1016/j.scitotenv.2024.174935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/05/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Forest restoration is an effective method for restoring degraded soil ecosystems (e.g., converting primary tropical forests into rubber monoculture plantations; RM). The effects of forest restoration on microbial community diversity and composition have been extensively studied. However, how rubber plantation-based forest restoration reshapes soil microbial communities, networks, and inner assembly mechanisms remains unclear. Here, we explored the effects of jungle rubber mixed (JRM; secondary succession and natural restoration of RM) plantation and introduction of rainforest species (AR; anthropogenic restoration established by mimicking the understory and overstory tree species of native rainforests) to RM stands on soil physico-chemical properties and microbial communities. We found that converting tropical rainforest (RF) to RM decreased soil fertility and simplified microbial composition and co-occurrence patterns, whereas the conversion of RM to JRM and AR exhibited opposite results. These changes were significantly correlated with pH, soil moisture content (SMC), and soil nutrients, suggesting that vegetation restoration can provide a favorable soil microenvironment that promotes the development of soil microorganisms. The complexity and stability of the bacterial-fungal cross-kingdom, bacterial, and fungal networks increased with JRM and AR. Bacterial community assembly was primarily governed by stochastic (78.79 %) and deterministic (59.09 %) processes in JRM and AR, respectively, whereas stochastic processes (limited dispersion) predominantly shaped fungal assembly across all forest stands. AR has more significant benefits than JRM, such as a relatively slower and natural vegetation succession with more nutritive soil conditions, microbial diversity, and complex and stable microbial networks. These results highlight the importance of sustainable forest management to restore soil biodiversity and ecosystem functions after extensive soil degradation and suggest that anthropogenic restoration can more effectively improve soil quality and microbial communities than natural restoration in degraded rubber plantations.
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Affiliation(s)
- Xiaoyi Cai
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunfeng Chen
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Ashutosh Kumar Singh
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Xiai Zhu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Wenjie Liu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
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Li S, Zhang L, Fang W, Shen Z. Variations in bacterial community succession and assembly mechanisms with mine age across various habitats in coal mining subsidence water areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174822. [PMID: 39029748 DOI: 10.1016/j.scitotenv.2024.174822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
Microorganisms play a pivotal role as catalysts in the biogeochemical cycles of aquatic ecosystems within coal mining subsidence areas. Despite their importance, the succession of microbial communities with increasing mine age, particularly across different habitats, and variations in phylogenetically-based community assembly mechanisms are not well understood. To address this knowledge gap, we collected 72 samples from lake sediments, water, and surrounding topsoil (0-20 cm) at various mining stages (early: 16 years, middle: 31 years, late: 40 years). We analyzed these samples using 16S rRNA gene sequencing and multivariate statistical methods to explore the dynamics and assembly mechanisms of bacterial communities. Our findings reveal that increases in phosphorus and organic matter in sediments, correlating with mining age, significantly enhance bacterial alpha diversity while reducing species richness (P < 0.001). Homogenizing selection (49.9 %) promotes species asynchrony-complementarity, augmenting the bacterial community's ability to metabolize sulfur, phosphorus, and organic matter, resulting in more complex-stable co-occurrence networks. In soil, elevated nitrogen and organic carbon levels markedly influence bacterial community composition (Adonis R2 = 0.761), yet do not significantly alter richness or diversity (P > 0.05). The lake's high connectivity with surrounding soil leads to substantial species drift and organic matter accumulation, thereby increasing bacterial richness in later stages (P < 0.05) and enhancing the ability to metabolize dissolved organic matter, including humic-like substances, fulvic acids, and protein-like materials. The assembly of soil bacterial communities is largely governed by stochastic processes (79.0 %) with species drift (35.8 %) significantly shaping these communities over a broad spatial scale, also affecting water bacterial communities. However, water bacterial community assembly is primarily driven by stochastic processes (51.2 %), with a substantial influence from habitat quality (47.6 %). This study offers comprehensive insights into the evolution of microbial community diversity within coal mining subsidence water areas, with significant implications for enhancing environmental management and protection strategies for these ecosystems.
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Affiliation(s)
- Shuo Li
- School of Earth and Environment, Anhui University of Science and Technology, Huainan, 232001, China
| | - Lei Zhang
- College of Civil and Architecture Engineering, Chuzhou University, Chuzhou, 239000, China.
| | - Wangkai Fang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan, 232001, China
| | - Zhen Shen
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
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Wu J, Xiong L, Huang X, Li C, Li F, Wong JWC. Silver sulfide nanoparticles eliminate the stimulative effects of earthworms on nutrient uptake by soybeans in high organic matter soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174433. [PMID: 38960153 DOI: 10.1016/j.scitotenv.2024.174433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 06/03/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
A significant knowledge gap exists regarding the impact of soil organic matter on the bioavailability of Ag2S-NPs (environmentally relevant forms of Ag-NPs) in soil-earthworm-plant systems. This study used two soils with varying organic matter content, both with and without earthworms, to investigate the bioavailability of Ag2S-NPs. The findings revealed an 80 % increase in Ag bioaccessibility to soybeans in soils with high organic matter content compared to soils with low organic matter. Additionally, the presence of earthworms significantly increased Cl concentrations from 24.3-62.2 mg L-1 to 80.1-147.2 mg L-1, triggering the elevated bioavailability of Ag. Interestingly, Ag2S-NPs eliminated the stimulative effects of earthworms on plant nutrient uptake. In the presence of earthworms, the high organic matter soil amended with Ag2S-NPs exhibited lower concentrations of essential elements (Ca, Cu, Fe, K, and P) in plant tissues compared to soils without earthworms. Our study presents evidence of the transformation of Ag2S-NPs into Ag-NPs across various soil solutions, resulting in the formation of Ag nanoparticle complexes. Particularly noteworthy is the significant reduction in particle sizes in soils incubated with earthworms and high organic matter content, from 85.0 nm to 40.2 nm. Notably, in the rhizosphere soil, a decrease in the relative abundance of nutrient cycling-related phyla was observed, with reductions of 18.5 % for Proteobacteria and 30.0 % for Actinobacteriota. These findings offer valuable insights into the biological and biochemical consequences of Ag2S-NP exposure on earthworm-mediated plant nutrient acquisition.
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Affiliation(s)
- Jingtao Wu
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, PR China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Lei Xiong
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia; Smart Water Affairs Research Center, Shenzhen University, Shenzhen 518000, China
| | - Xingyun Huang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Cui Li
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia; Northwestern Polytechnical University, Research Centre for Ecology and Environmental Sciences, Xi'an 710072, China
| | - Feng Li
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, PR China; College of Chemistry & Biology and Environmental Engineering, Xiangnan University, Chenzhou 423043, Hunan, PR China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Jonathan W C Wong
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, PR China
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Bereczki K, Tóth EG, Szili-Kovács T, Megyes M, Korponai K, Lados BB, Illés G, Benke A, Márialigeti K. Soil Parameters and Forest Structure Commonly Form the Microbiome Composition and Activity of Topsoil Layers in Planted Forests. Microorganisms 2024; 12:1162. [PMID: 38930544 PMCID: PMC11205539 DOI: 10.3390/microorganisms12061162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way, plant succession processes. Conversely, vegetation type influences microbial soil life. The present study compared the bacterial microbiome composition, diversity and catabolic activity profile of topsoil samples collected under three different forest types (a twice-coppiced black locust stand, a young, naturally reforested, and a middle-aged mixed pedunculate oak stand) planted on former arable land in the early 20th century. Diversity indices determined during 16S ribosomal RNA sequencing-based metagenome analysis indicated that the black locust stand had the highest soil bacterial community diversity. At the phylum level, Acidobacteriota, Actinobacteriota, Proteobacteria, Verrucomicrobiota, Bacteroidota, and Gemmatimonadota were the most abundant taxa in the forest soils. Concerning soil parameters, redundancy analysis revealed that pH had the highest impact on bacterial community structure and pH, and soil organic carbon content on the samples' respiration patterns. As for catabolic activity, the recently clearcut oak forest showed the lowest substrate-induced respiration, and citrate was the main driver for the inter-stand variability of microbial activity. Our results confirm that soil parameters and forest type influence the composition and functioning of the soil bacterial microbiome.
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Affiliation(s)
- Katalin Bereczki
- Doctoral School of Environmental Sciences, Eötvös Loránd University, 1117 Budapest, Hungary;
- Department of Forest Management and Ecology, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary;
| | - Endre György Tóth
- National Coalition of Independent Scholars (NCIS), Brattleboro, VT 05301, USA;
| | - Tibor Szili-Kovács
- Institute for Soil Sciences, Centre for Agricultural Research, 1022 Budapest, Hungary;
| | - Melinda Megyes
- Doctoral School of Environmental Sciences, Eötvös Loránd University, 1117 Budapest, Hungary;
| | - Kristóf Korponai
- Department of Plant Molecular Biology, Agricultural Institute, Centre for Agricultural Research, 2462 Martonvásár, Hungary;
| | - Botond Boldizsár Lados
- Department of Forestry Breeding, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary; (B.B.L.); (A.B.)
| | - Gábor Illés
- Department of Forest Management and Ecology, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary;
| | - Attila Benke
- Department of Forestry Breeding, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary; (B.B.L.); (A.B.)
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, 1117 Budapest, Hungary;
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Li YM, Wang YM, Qiu GW, Yu HJ, Liu FM, Wang GL, Duan Y. Conservation tillage facilitates the accumulation of soil organic carbon fractions by affecting the microbial community in an eolian sandy soil. Front Microbiol 2024; 15:1394179. [PMID: 38881670 PMCID: PMC11176501 DOI: 10.3389/fmicb.2024.1394179] [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: 03/01/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024] Open
Abstract
Conservation tillage (CT) is an important agronomic measure that facilitates soil organic carbon (SOC) accumulation by reducing soil disturbance and plant residue mulching, thus increasing crop yields, improving soil fertility and achieving C neutrality. However, our understanding of the microbial mechanism underlying SOC fraction accumulation under different tillage practices is still lacking. Here, a 6-year in situ field experiment was carried out to explore the effects of CT and traditional tillage (CK) practices on SOC fractions in an eolian sandy soil. Compared with CK, CT increased the particulate OC (POC) content in the 0-30 cm soil layer and the mineral-associated OC (MAOC) content in the 0-20 cm soil layer. Moreover, tillage type and soil depth had significant influences on the bacterial, fungal and protistan community compositions and structures. The co-occurrence network was divided into 4 ecological modules, and module 1 exhibited significant correlations with the POC and MOC contents. After determining their topological roles, we identified the keystone taxa in the network. The results indicated that the most common bacterial taxa may result in SOC loss due to low C use efficiency, while specific fungal (Cephalotrichum) and protistan (Cercozoa) species could facilitate SOC fraction accumulation by promoting macroaggregate formation and predation. Therefore, the increase in keystone fungi and protists, as well as the reduction in bacteria, drove module 1 community function, which in turn promoted SOC sequestration under CT. These results strengthen our understanding of microbial functions in the accrual of SOC fractions, which contributes to the development of conservation agriculture on the Northeast China Plain.
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Affiliation(s)
- Yu-Mei Li
- Heilongjiang Black Soil Conservation and Utilization Research Institute, Harbin, China
| | - Yu-Ming Wang
- The Centre for Ion Beam Bioengineering Green Agriculture, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Science Island Branch, Graduate School of USTC, Hefei, China
| | - Guang-Wei Qiu
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Hong-Jiu Yu
- Heilongjiang Black Soil Conservation and Utilization Research Institute, Harbin, China
| | - Feng-Man Liu
- Heilongjiang Black Soil Conservation and Utilization Research Institute, Harbin, China
| | - Gen-Lin Wang
- Heilongjiang Black Soil Conservation and Utilization Research Institute, Harbin, China
| | - Yan Duan
- The Centre for Ion Beam Bioengineering Green Agriculture, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
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Meyneng M, Lemonnier H, Le Gendre R, Plougoulen G, Antypas F, Ansquer D, Serghine J, Schmitt S, Siano R. Subtropical coastal microbiome variations due to massive river runoff after a cyclonic event. ENVIRONMENTAL MICROBIOME 2024; 19:10. [PMID: 38291506 PMCID: PMC10829310 DOI: 10.1186/s40793-024-00554-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024]
Abstract
BACKGROUND Coastal ecosystem variability at tropical latitudes is dependent on climatic conditions. During the wet, rainy season, extreme climatic events such as cyclones, precipitation, and winds can be intense over a short period and may have a significant impact on the entire land‒sea continuum. This study focused on the effect of river runoff across the southwest coral lagoon ecosystem of Grand Terre Island of New Caledonia (South Pacific) after a cyclonic event, which is considered a pulse disturbance at our study site. The variability of coastal microbiomes, studied by the metabarcoding of V4 18S (protists) and V4-V5 16S (bacteria) rDNA genes, after the cyclone passage was associated with key environmental parameters describing the runoff impact (salinity, organic matter proxies, terrestrial rock origin metals) and compared to community structures observed during the dry season. RESULTS Microbiome biodiversity patterns of the dry season were destructured because of the runoff impact, and land-origin taxa were observed in the coastal areas. After the rainy event, different daily community dynamics were observed locally, with specific microbial taxa explaining these variabilities. Plume dispersal modeling revealed the extent of low salinity areas up to the coral reef area (16 km offshore), but a rapid (< 6 days) recovery to typical steady conditions of the lagoon's hydrology was observed. Conversely, during the same time, some biological components (microbial communities, Chl a) and biogeochemical components (particulate nickel, terrigenous organic matter) of the ecosystem did not recover to values observed during the dry season conditions. CONCLUSION The ecosystem resilience of subtropical ecosystems must be evaluated from a multidisciplinary, holistic perspective and over the long term. This allows evaluating the risk associated with a potential continued and long-term disequilibrium of the ecosystem, triggered by the change in the frequency and intensity of extreme climatic events in the era of planetary climatic changes.
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Affiliation(s)
- M Meyneng
- IFREMER, DYNECO, BP70, Plouzané, France
| | - H Lemonnier
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - R Le Gendre
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - G Plougoulen
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - F Antypas
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - D Ansquer
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | | | - S Schmitt
- IFREMER, DYNECO, BP70, Plouzané, France
| | - R Siano
- IFREMER, DYNECO, BP70, Plouzané, France.
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Kang W, Xiao Y, Li W, Cheng A, Cheng C, Jia Z, Yu L. Paddy cultivation in degraded karst wetland soil can significantly improve the physiological and ecological functions of carbon-fixing resident microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168187. [PMID: 37972785 DOI: 10.1016/j.scitotenv.2023.168187] [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: 07/04/2023] [Revised: 10/10/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023]
Abstract
Microorganisms play an important role in carbon fixation in karst wetland soils. However, the carbon fixation capacity of karst wetland soils and active microorganisms involved in the carbon fixation process are poorly understood. In this study, carbon fixation capacity and active microorganisms involved in the fixation of inorganic carbon into organic carbon were studied in native, naturally degraded, and reclaimed karst wetland soils by the combination of stable isotope probing (SIP) and high-throughput sequencing. Under light conditions, the soil carbon fixation capacity ranked: the reclaimed wetland soil (1.58 mg C kg-1 day-1) > native wetland soil (1.43 mg C kg-1 day-1) > degraded wetland soil (0.62 mg C kg-1 day-1). In the dark, the soils ranked: the native wetland soil (0.24 mg C kg-1 day-1) > reclaimed wetland soil (0.18 mg C kg-1 day-1) > degraded wetland soil (0.06 mg C kg-1 day-1). Active microorganisms fixing inorganic carbon in the karst wetland soils were mainly Sulfurovum, Thermovirga, Dethiosulfatibacter, Allochromatium, Methylorubrum, and Bradyrhizobium. Thus, paddy cultivation can restore the carbon fixation capacity of microorganisms in the degraded karst wetland soil. This study provides an experimental basis for improving soil carbon fixation capacity and repairing degraded soil in karst wetlands.
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Affiliation(s)
- Weihua Kang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yutian Xiao
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wei Li
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan 430074, China.
| | - Aoqi Cheng
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Congyu Cheng
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan 430074, China
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9
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Tokumoto Y, Katayama A. Effects of Pieris japonica (Ericaceae) dominance on cool temperate forest altered-understory environments and soil microbiomes in Southern Japan. PLoS One 2024; 19:e0296692. [PMID: 38206984 PMCID: PMC10783712 DOI: 10.1371/journal.pone.0296692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/17/2023] [Indexed: 01/13/2024] Open
Abstract
The number of plants unpalatable to deer increases with increasing deer numbers. In the Kyushu Mountain area of Southern Japan, Pieris japonica (Ericaceae), an unpalatable shrub, has become the monodominant vegetation under evergreen conifer and deciduous broad-leaved tree stands. The monodominance of unpalatable plants in the understory has potential advantages and drawbacks; however, the effects of Pieris dominance are not well understood. To assess the effects of P. japonica dominances on forest environments and ecosystems, we investigated understory environments and soil microbiomes in Pieris-dominant sites. Under the deciduous broad-leaved trees, Pieris dominance leads to considerable Pieris leaf litter and humus weights and low soil bulk density and canopy openness. In the soil fungal community and fungal functional groups, the relative abundance of symbiotrophic fungi, particularly ectomycorrhizal fungi in Pieris-dominant sites were lower than in other-vegetation understory sites and saprotrophic fungi vice versa. Because few seedlings and saplings were found under Pieris shrubs, Pieris dominance in the understory might exclude other plant species. The results of this study will contribute to the Pieris population and forest management following deer overgrazing.
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Affiliation(s)
- Yuji Tokumoto
- Institute for Tenure Track Promotion, University of Miyazaki, Miyazaki, Japan
| | - Ayumi Katayama
- Shiiba Research Forest, Kyushu University, Shiiba, Miyazaki, Japan
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10
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Fang C, He Y, Yang Y, Fu B, Pan S, Jiao F, Wang J, Yang H. Laboratory tidal microcosm deciphers responses of sediment archaeal and bacterial communities to microplastic exposure. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131813. [PMID: 37339576 DOI: 10.1016/j.jhazmat.2023.131813] [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: 04/03/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Microplastics (MPs) are 1-5 mm plastic particles that are serious global contaminants distributed throughout marine ecosystems. However, their impact on intertidal sediment microbial communities is poorly understood. In this study, we conducted a 30-day laboratory tidal microcosm experiment to investigate the effects of MPs on microbial communities. Specifically, we used the biodegradable polymers polylactic acid (PLA) and polybutylene succinate (PBS), as well as the conventional polymers polyethylene terephthalate (PET), polycarbonate (PC), and polyethylene (PE). Treatments with different concentrations (1-5%, w/w) of PLA- and PE-MPs were also included. We analyzed taxonomic variations in archaeal and bacterial communities using 16S rRNA high-throughput sequencing. PLA-MPs at concentrations of 1% (w/w) rapidly altered microbiome composition. Total organic carbon and nitrite nitrogen were the key physicochemical factors and urease was the major enzyme shaping MP-exposed sediment microbial communities. Stochastic processes predominated in microbial assembly and the addition of biodegradable MPs enhanced the contribution of ecological selections. The major keystone taxa of archaea and bacteria were Nitrososphaeria and Alphaproteobacteria, respectively. MPs exposure had less effect on archaeal functions while nitrogen cycling decreased in PLA-MPs treatments. These findings expanded the current understanding of the mechanism and pattern that MPs affect sediment microbial communities.
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Affiliation(s)
- Chang Fang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Yinglin He
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Yuting Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Bing Fu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Sentao Pan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Fang Jiao
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China.
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11
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Christel A, Dequiedt S, Chemidlin-Prevost-Bouré N, Mercier F, Tripied J, Comment G, Djemiel C, Bargeot L, Matagne E, Fougeron A, Mina Passi JB, Ranjard L, Maron PA. Urban land uses shape soil microbial abundance and diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163455. [PMID: 37062324 DOI: 10.1016/j.scitotenv.2023.163455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
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Affiliation(s)
- Amélie Christel
- AgroParisTech, 75732 Paris, France; Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Florian Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julie Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Gwendoline Comment
- Platforme GenoSol, INRAE-Université de Bourgogne, CMSE, 21000 Dijon, France
| | - Christophe Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Eric Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - Agnès Fougeron
- Jardin de l'Arquebuse Mairie de Dijon, CS 73310, 21033 Dijon Cedex, France
| | | | - Lionel Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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12
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Wong SK, Cui Y, Chun SJ, Kaneko R, Masumoto S, Kitagawa R, Mori AS, Lim AS, Uchida M. Vegetation as a key driver of the distribution of microbial generalists that in turn shapes the overall microbial community structure in the low Arctic tundra. ENVIRONMENTAL MICROBIOME 2023; 18:41. [PMID: 37165459 PMCID: PMC10173506 DOI: 10.1186/s40793-023-00498-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/27/2023] [Indexed: 05/12/2023]
Abstract
Understanding the variability of microbial niches and their interaction with abiotic and biotic factors in the Arctic can provide valuable insights into microbial adaptations to extreme environments. This study investigates the structure and diversity of soil bacterial communities obtained from sites with varying vegetation coverage and soil biogeochemical properties in the low Arctic tundra and explores how bacteria interact under different environmental parameters. Our findings reveal differences in bacterial composition and abundance among three bacterial niche breadths (specialists, common taxa, and generalists). Co-occurrence network analysis revealed Rhizobiales and Ktedonobacterales as keystone taxa that connect and support other microbes in the habitat. Low-elevation indicators, such as vascular plants and moisture content, were correlated with two out of three generalist modular hubs and were linked to a large proportion of generalists' distribution (18%). Structural equation modeling revealed that generalists' distribution, which influenced the remaining microbial communities, was mainly regulated by vegetation coverage as well as other abiotic and biotic factors. These results suggest that elevation-dependent environmental factors directly influence microbial community structure and module formation through the regulation of generalists' distribution. Furthermore, the distribution of generalists was mainly affected by macroenvironment filtering, whereas the distribution of specialists was mainly affected by microenvironment filtering (species-engineered microbial niche construction). In summary, our findings highlight the strong top-down control exerted by vegetation on generalists' distribution, which in turn shapes the overall microbial community structure in the low Arctic tundra.
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Affiliation(s)
- Shu-Kuan Wong
- Research Organization of Information and Systems, National Institute of Polar Research, 10-3, Midori-cho, Tachikawa, Tokyo, Japan
| | - Yingshun Cui
- Division of Life Science and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Seong-Jun Chun
- LMO Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon, Republic of Korea.
| | - Ryo Kaneko
- Research Organization of Information and Systems, National Institute of Polar Research, 10-3, Midori-cho, Tachikawa, Tokyo, Japan
| | - Shota Masumoto
- Graduate School of Environment and Information Sciences, Yokohama National University, 79-7, Tokiwadai, Hodogaya, Yokohama, Japan
| | - Ryo Kitagawa
- Kansai Research Center, Forestry and Forest Products Research Institute, 68, Nagaikyutaroh, Momoyama, Fushimi, Kyoto, Japan
| | - Akira S Mori
- Graduate School of Environment and Information Sciences, Yokohama National University, 79-7, Tokiwadai, Hodogaya, Yokohama, Japan
| | - An Suk Lim
- Division of Life Science and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Masaki Uchida
- Research Organization of Information and Systems, National Institute of Polar Research, 10-3, Midori-cho, Tachikawa, Tokyo, Japan.
- Department of Polar Science, School of Multidisciplinary Sciences, The Graduate University for Advanced Studies, SOKENDAI, 10-3, Midori-cho, Tachikawa, Tokyo, Japan.
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