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Li D, Wang Y, Li X, Zhang Z, Wang G, Zhang Y, Chen L. Exploring microbial diversity and function in companion planting systems of white clover and orchard grass. Sci Rep 2024; 14:21609. [PMID: 39294312 PMCID: PMC11411128 DOI: 10.1038/s41598-024-72705-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 09/10/2024] [Indexed: 09/20/2024] Open
Abstract
Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.
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Affiliation(s)
- Daojie Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yili Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xi Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zimo Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Guoming Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yunhua Zhang
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Lijuan Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.
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Liu Y, Liu C, Wei L, Zhang X, Liu Q, Bai J, Wang X, Zhang S. Additional organic and bacterium fertilizer input regulated soybean root architecture and dry matter distribution for a sustainable yield in the semi-arid Region of China. PLoS One 2024; 19:e0305836. [PMID: 39018314 PMCID: PMC11253916 DOI: 10.1371/journal.pone.0305836] [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: 02/08/2024] [Accepted: 06/05/2024] [Indexed: 07/19/2024] Open
Abstract
In the dryland area of the Loess Plateau in northwest China, long-term excessive fertilization has led to soil compaction and nutrient loss, which in turn limits crop yield and soil productivity. To address this issue, we conducted experiments using environmentally friendly organic fertilizer and bacterium fertilizer. Our goal was to investigate the effects of additional organic and bacterium fertilizer inputs on soil water migration, crop root architecture, and yield formation. We implemented six different fertilizer strategies, namely: Nm (mulching, N 30 kg/ha), NPK1m (mulching, N 60 kg/ha; P 30 kg/ha; K 30 kg/ha), NPK2m (mulching, N 90 kg/ha; P 45 kg/ha; K 30 kg/ha), NPKOm (mulching, N 90 kg/ha; P 45 kg/ha; K 30 kg/ha; organic fertilizer 2 t/ha), NPKBm (mulching, N 60 kg/ha; P 30 kg/ha; K 30 kg/ha; bacterium fertilizer 10 kg/ha), and N (N 30 kg/ha; no mulching). The results revealed that the addition of bacterium fertilizer (NPKBm) had a positive impact on soybean root system development. Compared with the other treatments, it significantly increased the total root length, total root surface area, and total root length density by 25.96% ~ 94.89%, -19.63% ~ 36.28%, and 9.36% ~ 28.84%, respectively. Furthermore, NPKBm enhanced soil water consumption. In 2018, water storage during the flowering and podding periods decreased by 12.63% and 19.65%, respectively, while water consumption increased by 0.97% compared to Nm. In 2019, the flowering and harvest periods decreased by 23.49% and 11.51%, respectively, while water consumption increased by 0.65%. Ultimately, NPKBm achieved high grain yield and significantly increased water use efficiency (WUE), surpassing other treatments by 76.79% ~ 78.97% and 71.22% ~ 73.76%, respectively. Subsequently, NPK1m also exhibited significant increases in yield and WUE, with improvements of 35.58% ~ 39.27% and 35.26% ~ 38.16%, respectively. The use of bacterium fertilizer has a profound impact on soybean root architecture, leading to stable and sustainable grain yield production.
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Affiliation(s)
- Yu Liu
- College of Life Sciences, Yulin University, Yulin, China
| | - Chuhua Liu
- College of Life Sciences, Yulin University, Yulin, China
| | - Lichao Wei
- College of Life Sciences, Yulin University, Yulin, China
| | - Xudong Zhang
- College of Life Sciences, Yulin University, Yulin, China
| | - Qinhui Liu
- College of Life Sciences, Yulin University, Yulin, China
| | - Jiling Bai
- College of Life Sciences, Yulin University, Yulin, China
| | - Xiaolin Wang
- College of Life Sciences, Yulin University, Yulin, China
- Engineering and Technology Research Center of Water Saving for Crops in Arid Area of Northern Shaanxi, Yulin, China
| | - Suiqi Zhang
- State Key Laboratory of Soil Erosion and Dry Land Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
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Anderson MD, Taylor DL, Olson K, Ruess RW. Composition of soil Frankia assemblages across ecological drivers parallels that of nodule assemblages in Alnus incana ssp. tenuifolia in interior Alaska. Ecol Evol 2024; 14:e11458. [PMID: 38979008 PMCID: PMC11229434 DOI: 10.1002/ece3.11458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 07/10/2024] Open
Abstract
In root nodule symbioses (RNS) between nitrogen (N)-fixing bacteria and plants, bacterial symbionts cycle between nodule-inhabiting and soil-inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil-dwelling assemblages of the actinorhizal symbiont Frankia in sites with long-term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: (1) phylogenetic diversity of Frankia in soil versus nodules, (2) change in Frankia assemblages in soil versus nodules in response to environmental variation: both across succession, and in response to long-term fertilization with N and phosphorus, and (3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil-dwelling than nodule-dwelling assemblages and fell into two large clades not previously observed. The presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non-symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.
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Affiliation(s)
- M. D. Anderson
- Biology DepartmentMacalester CollegeSaint PaulMinnesotaUSA
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
| | - D. L. Taylor
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - K. Olson
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
| | - R. W. Ruess
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
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Martorelli I, Pooryousefi A, van Thiel H, Sicking FJ, Ramackers GJ, Merckx V, Verbeek FJ. Multiple graphical views for automatically generating SQL for the MycoDiversity DB; making fungal biodiversity studies accessible. Biodivers Data J 2024; 12:e119660. [PMID: 38933486 PMCID: PMC11199959 DOI: 10.3897/bdj.12.e119660] [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: 01/27/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Fungi is a highly diverse group of eukaryotic organisms that live under an extremely wide range of environmental conditions. Nowadays, there is a fundamental focus on observing how biodiversity varies on different spatial scales, in addition to understanding the environmental factors which drive fungal biodiversity. Metabarcoding is a high-throughput DNA sequencing technology that has positively contributed to observing fungal communities in environments. While the DNA sequencing data generated from metabarcoding studies are available in public archives, this valuable data resource is not directly usable for fungal biodiversity investigation. Additionally, due to its fragmented storage and distributed nature, it is not immediately accessible through a single user interface. We developed the MycoDiversity DataBase User Interface (https://mycodiversity.liacs.nl) to provide direct access and retrieval of fungal data that was previously inaccessible in the public domain. The user interface provides multiple graphical views of the data components used to reveal fungal biodiversity. These components include reliable geo-location terms, the reference taxonomic scientific names associated with fungal species and the standard features describing the environment where they occur. Direct observation of the public DNA sequencing data in association with fungi is accessible through SQL search queries created by interactively manipulating topological maps and dynamic hierarchical tree views. The search results are presented in configurable data table views that can be downloaded for further use. With the MycoDiversity DataBase User Interface, we make fungal biodiversity data accessible, assisting researchers and other stakeholders in using metabarcoding studies for assessing fungal biodiversity.
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Affiliation(s)
- Irene Martorelli
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
- Naturalis Biodiversity Center, Leiden, NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
| | - Aram Pooryousefi
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
| | - Haike van Thiel
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
| | - Floris J Sicking
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
| | - Guus J Ramackers
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
| | - Vincent Merckx
- Naturalis Biodiversity Center, Leiden, NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, NetherlandsInstitute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdamNetherlands
| | - Fons J Verbeek
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
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Decena BC, Dela Cruz TEE. Detection of Changes in Soil Microbial Community Physiological Profiles in Relation to Forest Types and Presence of Antibiotics Using BIOLOG EcoPlate. Indian J Microbiol 2024; 64:773-779. [PMID: 39011008 PMCID: PMC11246321 DOI: 10.1007/s12088-024-01294-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/21/2024] [Indexed: 07/17/2024] Open
Abstract
Soil is home to microbiota with diverse metabolic activities. These microorganisms play vital roles in many ecological processes. Thus, the assessment of microbial functional diversity is an important quality indicator of soil ecosystems. In this study, we collected soil samples from three distinct forest habitats, i.e., an agroforest, a primary forest (PF), and a secondary forest, within the Angat Watershed Reservation in Bulacan, Northern Philippines. Community-level physiological profiling (CLPP) was done with the BIOLOG EcoPlate™ to analyze the responses of the soil microbial communities from the three forest habitats in the absence or presence of antibiotics. The BIOLOG EcoPlate represents 31 utilizable carbon sources. Based on the CLPP analysis, soil samples from the PF showed significantly higher utilization of most carbon sources than the other forest types (p < 0.05). Thus, less disturbed forest types constitute more functionally diverse microbial communities. The presence of antibiotics significantly decreased the carbon utilization patterns of the soil microbial communities (p < 0.05), indicating the possible use of CLPP in monitoring contamination in soil.
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Affiliation(s)
- Benjamin C Decena
- The Graduate School, University of Santo Tomas, Espana Blvd., 1015 Manila, Philippines
- Fungal Biodiversity, Ecogenomics and Systematics-Metabolomics (FBeS) Group, Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., 1015 Manila, Philippines
| | - Thomas Edison E Dela Cruz
- Department of Biological Sciences, College of Science, University of Santo Tomas, Espana Blvd., 1015 Manila, Philippines
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Liu J, Zhang W, Teng C, Pang Z, Peng Y, Qiu J, Lei J, Su X, Zhu W, Ding C. Intercropping changed the soil microbial community composition but no significant effect on alpha diversity. Front Microbiol 2024; 15:1370996. [PMID: 38572232 PMCID: PMC10988756 DOI: 10.3389/fmicb.2024.1370996] [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: 01/15/2024] [Accepted: 02/16/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Enhancing the planning of the forest-agricultural composite model and increasing the efficiency with which forest land is utilized could benefit from a thorough understanding of the impacts of intercropping between forests and agriculture on soil physicochemical properties and microbial communities. Methods Populus cathayana × candansis cv. Xinlin No.1 and Glycine max intercrop soils, along with their corresponding monocrops, were used in this study's llumina high-throughput sequencing analysis to determine the composition and diversity of soil bacterial and fungal communities. Results The findings indicated that intercropping considerably raised the soil's total phosphorus content and significantly lowered the soil's carbon nitrogen ratio when compared to poplar single cropping. Furthermore, the total carbon and nitrogen content of soil was increased and the soil pH was decreased. The sequencing results showed that intercropping had no significant effect on soil alpha diversity. Intercropping could increase the composition of fungal community and decrease the composition of bacterial community in poplar soil. At the phylum level, intercropping significantly increased the relative abundance of four dominant phyla, i.e., Patescibacteria, Proteobacteria, Patescibacteria and Deinococcus-Thermus. And the relative abundances of only two dominant phyla were significantly increased. It was found that soil total phosphorus and available phosphorus content had the strongest correlation with soil bacterial community diversity, and soil pH had the strongest correlation with soil fungal community diversity. Discussion The results of this study were similar to those of previous studies. This study can serve as a theoretical foundation for the development of a poplar and black bean-based forest-agricultural complex management system in the future.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Chao Teng
- Liaoning Non-Ferrous Geological Exploration and Research Institute Co., Ltd., Shenyang, China
| | | | | | - Jian Qiu
- State-owned Xinbin Manchu Autonomous County Douling Forest Farm, Fushun, China
| | - Jiawei Lei
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Sasi R, Suchithra TV. Wastewater microbial diversity versus molecular analysis at a glance: a mini-review. Braz J Microbiol 2023; 54:3033-3039. [PMID: 37723328 PMCID: PMC10689596 DOI: 10.1007/s42770-023-01130-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/10/2023] [Indexed: 09/20/2023] Open
Abstract
Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.
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Affiliation(s)
- R Sasi
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601
| | - T V Suchithra
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601.
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Zambrano-Romero A, Ramirez-Villacis DX, Barriga-Medina N, Sierra-Alvarez R, Trueba G, Ochoa-Herrera V, Leon-Reyes A. Comparative Methods for Quantification of Sulfate-Reducing Bacteria in Environmental and Engineered Sludge Samples. BIOLOGY 2023; 12:985. [PMID: 37508415 PMCID: PMC10375983 DOI: 10.3390/biology12070985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
This study aimed to compare microscopic counting, culture, and quantitative or real-time PCR (qPCR) to quantify sulfate-reducing bacteria in environmental and engineered sludge samples. Four sets of primers that amplified the dsrA and apsA gene encoding the two key enzymes of the sulfate-reduction pathway were initially tested. qPCR standard curves were constructed using genomic DNA from an SRB suspension and dilutions of an enriched sulfate-reducing sludge. According to specificity and reproducibility, the DSR1F/RH3-dsr-R primer set ensured a good quantification based on dsrA gene amplification; however, it exhibited inconsistencies at low and high levels of SRB concentrations in environmental and sulfate-reducing sludge samples. Ultimately, we conducted a qPCR method normalized to dsrA gene copies, using a synthetic double-stranded DNA fragment as a calibrator. This method fulfilled all validation criteria and proved to be specific, accurate, and precise. The enumeration of metabolically active SRB populations through culture methods differed from dsrA gene copies but showed a plausible positive correlation. Conversely, microscopic counting had limitations due to distinguishing densely clustered organisms, impacting precision. Hence, this study proves that a qPCR-based method optimized with dsrA gene copies as a calibrator is a sensitive molecular tool for the absolute enumeration of SRB populations in engineered and environmental sludge samples.
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Affiliation(s)
- Aracely Zambrano-Romero
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Dario X Ramirez-Villacis
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Noelia Barriga-Medina
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, The University of Arizona, P.O. Box 210011, Tucson, AZ 85721-0011, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Valeria Ochoa-Herrera
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Antonio Leon-Reyes
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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Adedayo AA, Fadiji AE, Babalola OO. Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum. PeerJ 2023; 11:e15432. [PMID: 37283894 PMCID: PMC10241170 DOI: 10.7717/peerj.15432] [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: 02/16/2023] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.
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Qiu Z, He X, Yu H, Zhu C, Shen W. Differential responses of soil bacterial communities to elevated CO 2 between strongly CO 2-responsive and weakly CO 2-responsive rice cultivars. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161843. [PMID: 36709908 DOI: 10.1016/j.scitotenv.2023.161843] [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: 12/03/2022] [Revised: 01/22/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Effects of elevated CO2 (eCO2) on paddy soil microbial communities remain unclear, particularly when different rice cultivars exposed to eCO2. We thus compared responses of soil bacterial communities to ambient CO2 (aCO2) and eCO2 (aCO2 + 200 μmol CO2 mol-1) between two weakly CO2-responsive (Wuyunjing27, W27; Huaidao5, H5) and two strongly CO2-responsive rice cultivars (Yongyou1540, Y1540; LongIIyou1988, L1988) throughout six growth stages (early tillering, late tillering, jointing, heading, grain filling and ripening) in a paddy field in Jiangdu, China in 2018. No significant changes in soil bacterial diversities were observed between eCO2 and aCO2 or between cultivars for any single growth stage at the OTU level, but α diversity significantly changed at the phylum level except for the ripening stage. For a single cultivar, particularly two strongly CO2-responsive cultivars, over their whole growth stage, eCO2 enhanced differences in bacterial β diversity at both OTU and phylum levels under H5, Y1540 and L1988. Soil bacterial community complexity at the phylum level under eCO2 was weakened under W27, H5 and Y1540, but enhanced under L1988. eCO2-induced changes in soil DOC under these four cultivars had significantly positive impact on bacterial abundances. However, structural equation modeling illustrated that changes in soil DOC induced by eCO2 significantly decreased soil bacterial community richness. eCO2 did not significantly affect relationships between soil bacterial community diversities and rice yields, but displayed significantly negative correlations between strongly CO2-responsive rice cultivars' yields and relative abundances of Proteobacteria at the ripening stage. Dynamics that how soil microbial communities can differentiate their eCO2 responses between strongly- and weakly-responsive rice cultivars will provide a new insight into promoting rice productivity and soil health.
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Affiliation(s)
- Zijian Qiu
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Xinhua He
- Centre of Excellence for Soil Biology, College of Resources and Environment, Southwest University, Chongqing 400715, China; School of Biological Sciences, University of Western Australia, Perth 6009, WA, Australia; Department of Land, Air and Water Resources, University of California at Davis, Davis, CA 95616, USA
| | - Haiyang Yu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315800, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Weishou Shen
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China.
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11
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Lashani E, Amoozegar MA, Turner RJ, Moghimi H. Use of Microbial Consortia in Bioremediation of Metalloid Polluted Environments. Microorganisms 2023; 11:microorganisms11040891. [PMID: 37110315 PMCID: PMC10143001 DOI: 10.3390/microorganisms11040891] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Metalloids are released into the environment due to the erosion of the rocks or anthropogenic activities, causing problems for human health in different world regions. Meanwhile, microorganisms with different mechanisms to tolerate and detoxify metalloid contaminants have an essential role in reducing risks. In this review, we first define metalloids and bioremediation methods and examine the ecology and biodiversity of microorganisms in areas contaminated with these metalloids. Then we studied the genes and proteins involved in the tolerance, transport, uptake, and reduction of these metalloids. Most of these studies focused on a single metalloid and co-contamination of multiple pollutants were poorly discussed in the literature. Furthermore, microbial communication within consortia was rarely explored. Finally, we summarized the microbial relationships between microorganisms in consortia and biofilms to remove one or more contaminants. Therefore, this review article contains valuable information about microbial consortia and their mechanisms in the bioremediation of metalloids.
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Affiliation(s)
- Elham Lashani
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran 14178-64411, Iran;
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran 14178-64411, Iran;
- Correspondence: (M.A.A.); (H.M.); Tel.: +98-21-66415495 (H.M.)
| | - Raymond J. Turner
- Microbial Biochemistry Laboratory, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada;
| | - Hamid Moghimi
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran 14178-64411, Iran
- Correspondence: (M.A.A.); (H.M.); Tel.: +98-21-66415495 (H.M.)
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Meta-Analysis of the Effects of Biochar Application on the Diversity of Soil Bacteria and Fungi. Microorganisms 2023; 11:microorganisms11030641. [PMID: 36985214 PMCID: PMC10057247 DOI: 10.3390/microorganisms11030641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Biochar is increasingly being used for soil improvement, but the effects on microbial diversity in soil are still ambiguous due to contrasting results reported in the literature. We conducted a meta-analysis to clarify the effect of biochar addition on soil bacterial and fungal diversity with an increase in Shannon or Chao1 index as the outcome. Different experimental setups, quantitative levels of biochar addition, various biochar source materials and preparation temperatures, and the effect of natural precipitation in field experiments were the investigated variables. From a total of 95 publications identified for analysis, 384 datasets for Shannon index and 277 datasets for Chao1 index were extracted that described the bacterial diversity in the soils, of which field experiments and locations in China dominated. The application of biochar in soil significantly increased the diversity of soil bacteria but it had no significant effect on the diversity of fungi. Of the different experimental setups, the largest increase in bacterial diversity was seen for field experiments, followed by pot experiments, but laboratory and greenhouse settings did not report a significant increase. In field experiments, natural precipitation had a strong effect, and biochar increased bacterial diversity most in humid conditions (mean annual precipitation, MAP > 800 mm), followed by semi-arid conditions (MAP 200–400 mm). Biochar prepared from herbaceous materials was more effective to increase bacterial diversity than other raw materials and the optimal pyrolysis temperature was 350–550 °C. Addition of biochar at various levels produced inconclusive data for Chao1 and Shannon indices, and its effect was less strong than that of the other assessed variables.
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Atreya M, Desousa S, Kauzya J, Williams E, Hayes A, Dikshit K, Nielson J, Palmgren A, Khorchidian S, Liu S, Gopalakrishnan A, Bihar E, Bruns CJ, Bardgett R, Quinton JN, Davies J, Neff JC, Whiting GL. A Transient Printed Soil Decomposition Sensor Based on a Biopolymer Composite Conductor. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205785. [PMID: 36507571 PMCID: PMC9929122 DOI: 10.1002/advs.202205785] [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: 10/05/2022] [Revised: 11/19/2022] [Indexed: 06/18/2023]
Abstract
Soil health is one of the key factors in determining the sustainability of global agricultural systems and the stability of natural ecosystems. Microbial decomposition activity plays an important role in soil health; and gaining spatiotemporal insights into this attribute is critical for understanding soil function as well as for managing soils to ensure agricultural supply, stem biodiversity loss, and mitigate climate change. Here, a novel in situ electronic soil decomposition sensor that relies on the degradation of a printed conductive composite trace utilizing the biopolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) as a binder is presented. This material responds selectively to microbially active environments with a continuously varying resistive signal that can be readily instrumented with low-cost electronics to enable wide spatial distribution. In soil, a correlation between sensor response and intensity of microbial decomposition activity is observed and quantified by comparison with respiration rates over 14 days, showing that devices respond predictably to both static conditions and perturbations in general decomposition activity.
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Affiliation(s)
- Madhur Atreya
- Paul M. Rady Department of Mechanical EngineeringUniversity of Colorado Boulder1111 Engineering Drive, UCB 427BoulderCO80309‐0427USA
| | - Stacie Desousa
- Environmental StudiesUniversity of Colorado Boulder4001 Discovery Drive, 397 UCBBoulderCO80303‐0397USA
| | - John‐Baptist Kauzya
- Paul M. Rady Department of Mechanical EngineeringUniversity of Colorado Boulder1111 Engineering Drive, UCB 427BoulderCO80309‐0427USA
| | - Evan Williams
- Department of ElectricalComputerand Energy EngineeringUniversity of Colorado Boulder1111 Engineering Dr, 425 UCBBoulderCO80309USA
| | - Austin Hayes
- Paul M. Rady Department of Mechanical EngineeringUniversity of Colorado Boulder1111 Engineering Drive, UCB 427BoulderCO80309‐0427USA
| | - Karan Dikshit
- Materials Science and Engineering ProgramUniversity of Colorado Boulder4001 Discovery Dr, 613 UCBBoulderCO80303USA
| | - Jenna Nielson
- Department of Chemical and Biological EngineeringUniversity of Colorado Boulder1111 Engineering Dr, 596 UCBBoulderCO80309USA
| | - Abigail Palmgren
- Department of Chemical and Biological EngineeringUniversity of Colorado Boulder1111 Engineering Dr, 596 UCBBoulderCO80309USA
| | - Sara Khorchidian
- Paul M. Rady Department of Mechanical EngineeringUniversity of Colorado Boulder1111 Engineering Drive, UCB 427BoulderCO80309‐0427USA
| | - Shangshi Liu
- Department of Earth and Environmental SciencesThe University of ManchesterWilliamson BuildingManchesterM13 9PYUK
| | - Anupam Gopalakrishnan
- Materials Science and Engineering ProgramUniversity of Colorado Boulder4001 Discovery Dr, 613 UCBBoulderCO80303USA
| | - Eloise Bihar
- Paul M. Rady Department of Mechanical EngineeringUniversity of Colorado Boulder1111 Engineering Drive, UCB 427BoulderCO80309‐0427USA
| | - Carson J. Bruns
- Paul M. Rady Department of Mechanical EngineeringUniversity of Colorado Boulder1111 Engineering Drive, UCB 427BoulderCO80309‐0427USA
| | - Richard Bardgett
- Department of Earth and Environmental SciencesThe University of ManchesterWilliamson BuildingManchesterM13 9PYUK
| | - John N. Quinton
- Lancaster Environment CentreLancaster UniversityUniversityLibrary Ave, BailriggLancasterLA1 4YQUK
| | - Jessica Davies
- Lancaster Environment CentreLancaster UniversityUniversityLibrary Ave, BailriggLancasterLA1 4YQUK
| | - Jason C. Neff
- Environmental StudiesUniversity of Colorado Boulder4001 Discovery Drive, 397 UCBBoulderCO80303‐0397USA
| | - Gregory L. Whiting
- Paul M. Rady Department of Mechanical EngineeringUniversity of Colorado Boulder1111 Engineering Drive, UCB 427BoulderCO80309‐0427USA
- Materials Science and Engineering ProgramUniversity of Colorado Boulder4001 Discovery Dr, 613 UCBBoulderCO80303USA
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Rojas-Solis D, Larsen J, Lindig-Cisneros R. Arsenic and mercury tolerant rhizobacteria that can improve phytoremediation of heavy metal contaminated soils. PeerJ 2023; 11:e14697. [PMID: 36650835 PMCID: PMC9840862 DOI: 10.7717/peerj.14697] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023] Open
Abstract
Background Mining deposits often contain high levels of toxic elements such as mercury (Hg) and arsenic (As) representing strong environmental hazards. The purpose of this study was the isolation for plant growth promoting bacteria (PGPBs) that can improve phytoremediation of such mine waste deposits. Methods We isolated native soil bacteria from the rhizosphere of plants of mine waste deposits and agricultural land that was previously mine tailings from Tlalpujahua Michoacán, Mexico, and were identified by their fatty acid profile according to the MIDI Sherlock system. Plant growth promoting traits of all bacterial isolates were examined including production of 3-indoleacetic acid (IAA), siderophores, biofilm formation, and phosphate solubilization. Finally, the response of selected bacteria to mercury and arsenic was examined an in-vitro assay. Results A total 99 bacterial strains were isolated and 48 identified, representing 34 species belonging to 23 genera. Sixty six percent of the isolates produced IAA of which Pseudomonas fluorescens TL97 produced the most. Herbaspirillum huttiense TL36 performed best in terms of phosphate solubilization and production of siderophores. In terms of biofilm formation, Bacillus atrophaeus TL76 was the best. Discussion Most of the bacteria isolates showed high level of tolerance to the arsenic (as HAsNa2O4 and AsNaO2), whereas most isolates were susceptible to HgCl2. Three of the selected bacteria with PGP traits Herbispirillum huttiense TL36, Klebsiella oxytoca TL49 and Rhizobium radiobacter TL52 were also tolerant to high concentrations of mercury chloride, this might could be used for restoring or phytoremediating the adverse environmental conditions present in mine waste deposits.
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Rai A, Saha SP, Manvar T, Bhattacharjee A. A shotgun approach to explore the bacterial diversity and a brief insight into the glycoside hydrolases of Samiti lake located in the Eastern Himalayas. J Genet Eng Biotechnol 2022; 20:162. [PMID: 36469176 PMCID: PMC9723087 DOI: 10.1186/s43141-022-00444-y] [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: 04/19/2022] [Accepted: 11/12/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Himalayas have always been an enigma and, being biodiversity hotspots, are considered extremely important from an ecological point of view. Recent advances in studies regarding high-altitude lakes have garnered relevant importance as these habitats could harbor potential psychrophilic and psychrotrophic microbes with bio-prospective applications. Contemplating the above scenario, the present study has been undertaken to understand the diversity and the functional capacities of the microbes thriving in this lake. RESULTS In our present study on Samiti Lake, the abundance of Proteobacteria as the major phylum was seen in both the soil and water samples. Incase of the ABSLW (water) and ABS1 (soil) sample, 148,066 and 239,754 predicted genes, were taken for functional analysis. The KEGG analysis showed that ABSLW and ABS1 had 122,911 and 160,268, genes assigned to KO terms respectively. Whereas in case of COG functional analysis, 104,334 and 130,191 genes were assigned to different COG classes for ABSLW and ABS1 respectively. Further, on studying the glycoside hydrolases, an abundance of GH13, GH2, GH3, GH43, and GH23 in both the soil and water samples were seen. CONCLUSION Our study has provided a comprehensive report about the bacterial diversity and functional capacities of microbes thriving in Samiti Lake. It has also thrown some light on the occurrence of glycoside hydrolases in this region, as they have numerous biotechnological applications in different sectors.
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Affiliation(s)
- Aditi Rai
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
| | - Shyama Prasad Saha
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
| | - Toral Manvar
- Xcelris Labs Ltd, Ahmedabad, Gujarat 380006 India
| | - Arindam Bhattacharjee
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
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van der Heyde M, Bunce M, Nevill P. Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157617. [PMID: 35901901 DOI: 10.1016/j.scitotenv.2022.157617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Ecological restoration of terrestrial environments is a globally important process to combat the loss of biodiversity and ecosystem services. Holistic monitoring of restored biota and active management of restoration is necessary to improve restoration processes and outcomes, and provide evidence to stakeholders that targets are being achieved. Increasingly, environmental DNA (eDNA) metabarcoding is used as a restoration monitoring tool because it is able to generate biodiversity data rapidly, accurately, non-destructively, and reliably, on a wide breadth of organisms from soil microbes to mammals. The overall objective of this review is to discuss the key factors to consider in the use of environmental DNA for monitoring of restored terrestrial ecosystems, hopefully improving monitoring, and ultimately, restoration outcomes. We identified that the majority of eDNA based studies of ecosystem restoration are currently conducted in Europe, North America, and Australia, and that almost half of total studies were published in 2021-22. Soil was the most popular sample substrate, soil microbial communities the most targeted taxa, and forests the most studied ecosystem. We suggest there is no 'one size fits all' approach to restoration monitoring using eDNA, and discuss survey design. Factors to consider include substrate selection, sample collection and storage, assay selection, and data interpretation, all of which require careful planning to obtain reliable, and accurate information that can be used for restoration monitoring and decision making. We explore future directions for research and argue that eDNA metabarcoding can be a useful tool in the restoration monitoring 'toolkit', but requires informed application and greater accessibility to data by a wide spectrum of stakeholders.
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Affiliation(s)
- Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia.
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia; Institute of Environmental Science and Research (ESR), Kenepuru, Porirua 5022, New Zealand
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia
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Orozco-Mosqueda MDC, Fadiji AE, Babalola OO, Glick BR, Santoyo G. Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 2022; 263:127137. [PMID: 35905581 DOI: 10.1016/j.micres.2022.127137] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.
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Affiliation(s)
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico.
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A first report on the identification of a novel archaea, Methanospirillum lacunae from spoilt paints in Lagos, Nigeria using a metagenomic approach. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2021.e01029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Structural Selectivity of PAH Removal Processes in Soil, and the Effect of Metal Co-Contaminants. ENVIRONMENTS 2022. [DOI: 10.3390/environments9020023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) form a convenient structural series of molecules with which to examine the selectivity exerted on their removal by soil microbiota. It is known that there is an inverse relationship between PAH molecular size and degradation rates in soil. In this paper, we look at how the magnitude of the slope for this relationship, m, can be used as an indicator of the effect of metal co-contaminants on degradation rates across a range of PAH molecular weights. The analysis utilises data collected from our previous microcosm study (Deary, M.E.; Ekumankama, C.C.; Cummings, S.P. Development of a novel kinetic model for the analysis of PAH biodegradation in the presence of lead and cadmium co-contaminants. Journal of Hazard Materials 2016, 307, 240–252) in which we followed the degradation of the 16 US EPA PAHs over 40 weeks in soil microcosms taken from a high organic matter content woodland soil. The soil was amended with a PAH mixture (total concentration of 2166 mg kg−1) and with a range of metal co-contaminant concentrations (lead, up to 782 mg kg−1; cadmium up to 620 mg kg−1; and mercury up to 1150 mg kg−1). It was found that the magnitude of m increases in relation to the applied concentration of metal co-contaminant, indicating a more adverse effect on microbial communities that participate in the removal of higher molecular weight PAHs. We conclude that m is a useful parameter by which we might measure the differential effects of environmental contaminants on the PAH removal. Such information will be useful in planning and implementing remediation strategies.
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Bonomo MG, Calabrone L, Scrano L, Bufo SA, Di Tomaso K, Buongarzone E, Salzano G. Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:48. [PMID: 34978609 PMCID: PMC8724107 DOI: 10.1007/s10661-021-09637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/20/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (- 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between - 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between - 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between - 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between - 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.
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Affiliation(s)
| | - Luana Calabrone
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Laura Scrano
- Department of European Cultures, University of Basilicata, Potenza, Italy
| | - Sabino Aurelio Bufo
- Department of Sciences, University of Basilicata, Potenza, Italy
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Katia Di Tomaso
- Department of Sciences, University of Basilicata, Potenza, Italy
| | | | - Giovanni Salzano
- Department of Sciences, University of Basilicata, Potenza, Italy
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Sivojiene D, Kacergius A, Baksiene E, Maseviciene A, Zickiene L. The Influence of Organic Fertilizers on the Abundance of Soil Microorganism Communities, Agrochemical Indicators, and Yield in East Lithuanian Light Soils. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122648. [PMID: 34961119 PMCID: PMC8703430 DOI: 10.3390/plants10122648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 06/02/2023]
Abstract
Soil microorganisms are one of the main indicators used for assessing the stability of the soil ecosystem, the metabolism in the soil, and its fertility. The most important are the active soil microorganisms and the influence of the fertilizer applied to the soil on the abundance of these microorganisms. We aimed to investigate how the applied organic fertilizers affect the most active soil microorganisms, which determine the soil fertility and stability. Fungi, yeast-like fungi abundance, and abundance of three physiological groups of bacteria were analyzed: non-symbiotic diazotrophic, organotrophic, and mineral nitrogen assimilating. This study is valuable because relatively few similar studies have been performed on infertile Lithuanian soils. The first results of a long-term study were obtained. The results show the effect of fertilizers on trends in the changes of microorganism community diversity; however, more analysis is needed to assess the impact of organic fertilizers on the most active soil microorganisms. Therefore, the investigation was continued. The results of the 2020 quantitative analysis of culturable soil microorganisms show that the highest abundance of organotrophic and non-symbiotic diazotrophic bacteria were recorded during the summer season. Meanwhile, the abundance of bacteria assimilating mineral nitrogen and fungi was higher in autumn. Agrochemical parameters were determined at the beginning of the experiment. The highest concentration of Nmin in the soil was determined after fertilizing the plants with the combination of granulated poultry manure (N170) + biological substance Azotobacter spp. The yield of barley was calculated. It was found that the highest yield of spring barley in 2020 was obtained by fertilizing the experimental field with organic in combination with mineral fertilizers.
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Affiliation(s)
- Diana Sivojiene
- Lithuanian Research Centre for Agriculture and Forestry, Vokė Branch of Institute of Agriculture, Žalioji Sq. 2, LT-02232 Vilnius, Lithuania; (A.K.); (E.B.)
| | - Audrius Kacergius
- Lithuanian Research Centre for Agriculture and Forestry, Vokė Branch of Institute of Agriculture, Žalioji Sq. 2, LT-02232 Vilnius, Lithuania; (A.K.); (E.B.)
| | - Eugenija Baksiene
- Lithuanian Research Centre for Agriculture and Forestry, Vokė Branch of Institute of Agriculture, Žalioji Sq. 2, LT-02232 Vilnius, Lithuania; (A.K.); (E.B.)
| | - Aiste Maseviciene
- Agrochemical Research Laboratory of Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Savanoriu Av. 287, LT-50127 Kaunas, Lithuania; (A.M.); (L.Z.)
| | - Lina Zickiene
- Agrochemical Research Laboratory of Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Savanoriu Av. 287, LT-50127 Kaunas, Lithuania; (A.M.); (L.Z.)
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Seydametova E, Zainol N. Morphological, physiological, biochemical and molecular characterization of statin-producing Penicillium microfungi isolated from little-explored tropical ecosystems. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100044. [PMID: 34841335 PMCID: PMC8610345 DOI: 10.1016/j.crmicr.2021.100044] [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: 04/26/2021] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 12/01/2022] Open
Abstract
Natural statins produced by microfungi are extremely successful drugs. Fungal producers of statins were isolated from soils of unique tropical habitats. Three novel statin-producing Penicillium strains were characterized and identified. Pravastatin was produced by the identified fungal cultures directly.
As hypercholesterolemia is a primary risk factor for coronary artery disease and stroke, there is now an increasing demand for cholesterol-lowering drugs. Statins are a group of extremely successful drugs that lower the cholesterol level in the blood. Natural statins are produced by fermentation using different species of microorganisms. The overall aim of the present study was to identify statin-producing microfungi, which were isolated from different types of little-explored mangrove and oil palm plantation soils. Isolated fungal cultures were characterized on the basis of morphological, physiological, biochemical, and molecular features. Morphological variability was detected amongst the fungal isolates in regard to colony morphology, conidiophores structures, and conidia coloration. Based on their physiological properties and enzyme assays, rapid differentiation of statin-producing isolates was achieved. Further molecular characterization allowed reliable identification of the selected Penicillium microfungi up to the species level. The identified Penicillium cintrinum ESF2M, Penicillium brefeldianum ESF21P, and Penicillium janthinellum ESF26P strains have a scientific interest as novel wild-type producers of natural statins.
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Affiliation(s)
- Emine Seydametova
- College of Engineering, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Kuantan 26300, Malaysia.,Institute of Microbiology, Academy of Sciences of Uzbekistan, Tashkent 100128, Uzbekistan
| | - Norazwina Zainol
- College of Engineering, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Kuantan 26300, Malaysia
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Ghosh S, Pramanik S. Structural diversity, functional aspects and future therapeutic applications of human gut microbiome. Arch Microbiol 2021; 203:5281-5308. [PMID: 34405262 PMCID: PMC8370661 DOI: 10.1007/s00203-021-02516-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023]
Abstract
The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.
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Affiliation(s)
- Soma Ghosh
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute, i-8 Sector-C, East Kolkata Township, Kolkata, 700107, India.
| | - Sreemanta Pramanik
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute, i-8 Sector-C, East Kolkata Township, Kolkata, 700107, India
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Spatial and temporal differences in the community structure of endophytic fungi in the carnivorous plant Pinguicula moranensis (Lentibulariaceae). FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Reiß F, Kiefer N, Noll M, Kalkhof S. Application, release, ecotoxicological assessment of biocide in building materials and its soil microbial response. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112707. [PMID: 34461316 DOI: 10.1016/j.ecoenv.2021.112707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Biocides are used in building materials to protect the building against microbial colonization and biodeterioration. However, these biocides are introduced by gradual leaching into soils in proximity of the buildings. This review discusses the aspects and characteristics of biocides from building materials in terms of (i) in-situ leaching and simulation thereof in-vitro and in-field tests, (ii) persistence, as well as photolytic and biodegradation, and its influence on toxicological evaluation, and (iii) evaluation of terrestrial toxicity by conventional ecotoxicological tests and novel holistic testing approaches. These aspects are influenced by multiple parameters, out of which water availability, physicochemical properties of microhabitats, combination of biocidal building materials, soil parameters, and composition of the soil microbiome are of utmost relevance. Deeper understanding of this multiparametric system and development of comprehensive characterization methodologies remains crucial, as to facilitate realistic assessment of the environmental impact of biocides used in construction materials and the corresponding degradation byproducts.
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Affiliation(s)
- Fabienne Reiß
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - Nadine Kiefer
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
| | - Stefan Kalkhof
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; Proteomics Unit, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany.
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26
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Effect of Saline Water for Drip Irrigation on Microbial Diversity and on Fertility of Aeolian Sandy Soils. DIVERSITY 2021. [DOI: 10.3390/d13080379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Saline water is widely distributed in the arid environment and sometimes represents the only source of irrigation water to restore and reconstruct vegetation. However, the effects of saline water on the bacterial diversity and fertility level of aeolian sandy soil are not well understood. In this study, we investigated a vegetation belt along the Tarim Desert Highway that has been constructed as a windbreak and consists of desert shrubs and was irrigated with saline water at six levels of salinity along the Tarim Desert Highway. The bacterial diversity was studied using Biolog Eco, a phospholipid fatty acid analysis, and a polymerase chain reaction–denaturing gradient gel electrophoresis, and the soil fertility was calculated and expressed as the integrated fertility index. The soil bacterial diversity (in terms of carbon metabolism, genes, and fatty acid species) was significantly affected by the level of salinity, and the microbial activity was low under high salinity. Fertility was also markedly affected by the degree of salinity and by the depth of soil, being lower at higher salinity levels and in the top layer (0–5 cm), and was also correlated to both the metabolic diversity index of soil microorganisms and the diversity index of fatty acids of soil microorganisms. The genetic diversity index of soil microorganisms shared a polynomial relation with fertility and contributed to it positively and significantly. Therefore, using less saline water for drip irrigation could avoid salt accumulation in soil and arrest its compaction, promote the formation of soil aggregates and the build-up of nutrients, and increase microbial activity, thus playing a crucial role in promoting the circulation, conversion, and utilization of nutrients in aeolian sandy soils and improving the soil quality. The judicious use of saline water, therefore, deserves serious consideration in irrigation practices.
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Fan L, Tarin MWK, Zhang Y, Han Y, Rong J, Cai X, Chen L, Shi C, Zheng Y. Patterns of soil microorganisms and enzymatic activities of various forest types in coastal sandy land. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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28
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Zhang H, Serwah Boateng NA, Ngolong Ngea GL, Shi Y, Lin H, Yang Q, Wang K, Zhang X, Zhao L, Droby S. Unravelling the fruit microbiome: The key for developing effective biological control strategies for postharvest diseases. Compr Rev Food Sci Food Saf 2021; 20:4906-4930. [PMID: 34190408 DOI: 10.1111/1541-4337.12783] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Fruit-based diets are recognized for their benefits to human health. The safety of fruit is a global concern for scientists. Fruit microbiome represents the whole microorganisms that are associated with a fruit. These microbes are either found on the surfaces (epiphytes) or in the tissues of the fruit (endophytes). The recent knowledge gained from these microbial communities is considered relevant to the field of biological control in prevention of postharvest fruit pathology. In this study, the importance of the microbiome of certain fruits and how it holds promise for solving the problems inherent in biocontrol and postharvest crop protection are summarized. Research needs on the fruit microbiome are highlighted. Data from DNA sequencing and "meta-omics" technologies very recently applied to the study of microbial communities of fruits in the postharvest context are also discussed. Various fruit parameters, management practices, and environmental conditions are the main determinants of the microbiome. Microbial communities can be classified according to their structure and function in fruit tissues. A critical mechanism of microbial biological control agents is to reshape and interact with the microbiome of the fruit. The ability to control the microbiome of any fruit is a great potential in postharvest management of fruits. Research on the fruit microbiome offers important opportunities to develop postharvest biocontrol strategies and products, as well as the health profile of the fruit.
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Affiliation(s)
- Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | | | - Guillaume Legrand Ngolong Ngea
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China.,Institute of Fisheries Sciences, University of Douala, Douala, Cameroon
| | - Yu Shi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Hetong Lin
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Kaili Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xiaoyun Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Lina Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Samir Droby
- Department of Postharvest Science, ARO, the Volcani Center, Rishon LeZion, Israel
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Lewe N, Hermans S, Lear G, Kelly LT, Thomson-Laing G, Weisbrod B, Wood SA, Keyzers RA, Deslippe JR. Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data. J Microbiol Methods 2021; 188:106271. [PMID: 34146605 DOI: 10.1016/j.mimet.2021.106271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023]
Abstract
Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. Quantitative estimates of the biomass of different taxonomic groups in samples were made through the analysis of PLFAs, and these were compared to the relative abundances of microbial taxa estimated from metabarcoding. Furthermore, we used the PLFA-based quantitative estimates of the biomass to adjust relative abundances of microbial groups determined by metabarcoding to provide insight into how the biomass of microbial taxa from PLFA analysis can improve understanding of microbial communities from environmental DNA samples. We used two sets of PLFA biomarkers that differed in their number of PLFAs to evaluate how PLFA biomarker selection influences biomass estimates. Metabarcoding and PLFA analysis provided significantly different views of bacterial composition, and these differences varied among substrates. We observed the most notable differences for the Gram-negative bacteria, which were overrepresented by metabarcoding in comparison to PLFA analysis. In contrast, the relative biomass and relative sequence abundances aligned reasonably well for Cyanobacteria across the tested freshwater substrates. Adjusting relative abundances of microbial taxa estimated by metabarcoding with PLFA-based quantification estimates of the microbial biomass led to significant changes in the microbial community compositions in all substrates. We recommend including independent estimates of the biomass of microbial groups to increase comparability among metabarcoding libraries from environmental samples, especially when comparing communities associated with different substrates.
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Affiliation(s)
- Natascha Lewe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Syrie Hermans
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Laura T Kelly
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Georgia Thomson-Laing
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Barbara Weisbrod
- Human and Environmental Toxicology, Department of Biology, Universität Konstanz, 78457 Konstanz, Germany
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Robert A Keyzers
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Julie R Deslippe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand.
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Studying greenhouse gas emissions through interactions between phospholipid fatty acid content and soil properties of alpine grassland soil in Northern Tibet, China. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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31
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Yadav AN, Kour D, Kaur T, Devi R, Yadav A, Dikilitas M, Abdel-Azeem AM, Ahluwalia AS, Saxena AK. Biodiversity, and biotechnological contribution of beneficial soil microbiomes for nutrient cycling, plant growth improvement and nutrient uptake. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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32
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Bodenhausen N, Deslandes-Hérold G, Waelchli J, Held A, van der Heijden MGA, Schlaeppi K. Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi. MYCORRHIZA 2021; 31:137-148. [PMID: 33475800 PMCID: PMC7910240 DOI: 10.1007/s00572-020-01014-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/15/2020] [Indexed: 05/13/2023]
Abstract
Arbuscular mycorrhiza fungi (AMF) are beneficial soil fungi that can promote the growth of their host plants. Accurate quantification of AMF in plant roots is important because the level of colonization is often indicative of the activity of these fungi. Root colonization is traditionally measured with microscopy methods which visualize fungal structures inside roots. Microscopy methods are labor-intensive, and results depend on the observer. In this study, we present a relative qPCR method to quantify AMF in which we normalized the AMF qPCR signal relative to a plant gene. First, we validated the primer pair AMG1F and AM1 in silico, and we show that these primers cover most AMF species present in plant roots without amplifying host DNA. Next, we compared the relative qPCR method with traditional microscopy based on a greenhouse experiment with Petunia plants that ranged from very high to very low levels of AMF root colonization. Finally, by sequencing the qPCR amplicons with MiSeq, we experimentally confirmed that the primer pair excludes plant DNA while amplifying mostly AMF. Most importantly, our relative qPCR approach was capable of discriminating quantitative differences in AMF root colonization and it strongly correlated (Spearman Rho = 0.875) with quantifications by traditional microscopy. Finally, we provide a balanced discussion about the strengths and weaknesses of microscopy and qPCR methods. In conclusion, the tested approach of relative qPCR presents a reliable alternative method to quantify AMF root colonization that is less operator-dependent than traditional microscopy and offers scalability to high-throughput analyses.
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Affiliation(s)
- Natacha Bodenhausen
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, Switzerland
| | - Gabriel Deslandes-Hérold
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Jan Waelchli
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Alain Held
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Klaus Schlaeppi
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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Tong AZ, Liu W, Liu Q, Xia GQ, Zhu JY. Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages. BMC Microbiol 2021; 21:18. [PMID: 33419388 PMCID: PMC7792351 DOI: 10.1186/s12866-020-02081-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Background Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored. Methods Amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions were analyzed for microbial community composition and diversity. Results The obtained sequencing data were reasonable for estimating soil microbial diversity. We observed significant variations in richness, diversity, and relative abundances of microbial taxa between farmland, deforestation field, and different cultivation years. The bacterial communities of LCK (forest soil where P. ginseng was not grown) had a much higher richness and diversity than those in NCK (farmland soil where P. ginseng was not grown). The increase in cultivation years of P. ginseng in farmland and deforestation field significantly changed the diversity of soil microbial communities. In addition, the accumulation of P. ginseng soil-borne pathogens (Monographella cucumerina, Ilyonectria mors-panacis, I. robusta, Fusarium solani, and Nectria ramulariae) varied with the cropping age of P. ginseng. Conclusion Soil microbial diversity and function were significantly poorer in farmland than in the deforestation field and were affected by P. ginseng planting years. The abundance of common soil-borne pathogens of P. ginseng increased with the cultivation age and led to an imbalance in the microbial community. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02081-2.
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Affiliation(s)
- Ai-Zi Tong
- School of Life Science, Tonghua Normal University, No.950 Yu Cai Road, Dongchang District, Tonghua, 134002, China
| | - Wei Liu
- School of Life Science, Tonghua Normal University, No.950 Yu Cai Road, Dongchang District, Tonghua, 134002, China.
| | - Qiang Liu
- Chinese Institute of Jilin Ginseng, Tonghua, 134002, China
| | - Guang-Qing Xia
- School of Life Science, Tonghua Normal University, No.950 Yu Cai Road, Dongchang District, Tonghua, 134002, China
| | - Jun-Yi Zhu
- School of Life Science, Tonghua Normal University, No.950 Yu Cai Road, Dongchang District, Tonghua, 134002, China
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Sangannavar PA, Kumar JS, Subrahmanyam G, Kutala S. Genomics and omics tools to assess complex microbial communities in silkworms: A paradigm shift towards translational research. J Microbiol Methods 2021. [DOI: 10.1016/bs.mim.2021.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Jayaraman S, Naorem A, Lal R, Dalal RC, Sinha N, Patra A, Chaudhari S. Disease-Suppressive Soils-Beyond Food Production: a Critical Review. JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION 2021; 21:1437-1465. [PMID: 33746349 PMCID: PMC7953945 DOI: 10.1007/s42729-021-00451-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/21/2021] [Indexed: 05/09/2023]
Abstract
In the pursuit of higher food production and economic growth and increasing population, we have often jeopardized natural resources such as soil, water, vegetation, and biodiversity at an alarming rate. In this process, wider adoption of intensive farming practices, namely changes in land use, imbalanced fertilizer application, minimum addition of organic residue/manure, and non-adoption of site-specific conservation measures, has led to declining in soil health and land degradation in an irreversible manner. In addition, increasing use of pesticides, coupled with soil and water pollution, has led the researchers to search for an environmental-friendly and cost-effective alternatives to controlling soil-borne diseases that are difficult to control, and which significantly limit agricultural productivity. Since the 1960s, disease-suppressive soils (DSS) have been identified and studied around the world. Soil disease suppression is the reduction in the incidence of soil-borne diseases even in the presence of a host plant and inoculum in the soil. The disease-suppressive capacity is mainly attributed to diverse microbial communities present in the soil that could act against soil-borne pathogens in multifaceted ways. The beneficial microorganisms employ some specific functions such as antibiosis, parasitism, competition for resources, and predation. However, there has been increasing evidence on the role of soil abiotic factors that largely influence the disease suppression. The intricate interactions of the soil, plant, and environmental components in a disease triangle make this process complex yet crucial to study to reduce disease incidence. Increasing resistance of the pathogen to presently available chemicals has led to the shift from culturable microbes to unexplored and unculturable microbes. Agricultural management practices such as tillage, fertilization, manures, irrigation, and amendment applications significantly alter the soil physicochemical environment and influence the growth and behaviour of antagonistic microbes. Plant factors such as age, type of crop, and root behaviour of the plant could stimulate or limit the diversity and structure of soil microorganisms in the rhizosphere. Further, identification and in-depth of disease-suppressive soils could lead to the discovery of more beneficial microorganisms with novel anti-microbial and plant promoting traits. To date, several microbial species have been isolated and proposed as key contributors in disease suppression, but the complexities as well as the mechanisms of the microbial and abiotic interactions remain elusive for most of the disease-suppressive soils. Thus, this review critically explores disease-suppressive attributes in soils, mechanisms involved, and biotic and abiotic factors affecting DSS and also briefly reviewing soil microbiome for anti-microbial drugs, in fact, a consequence of DSS phenomenon.
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Affiliation(s)
- Somasundaram Jayaraman
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - A.K. Naorem
- ICAR– Central Arid Zone Research Institute, Regional Research Station-Kukma, Bhuj, Gujarat 370105 India
| | - Rattan Lal
- Carbon Management Sequestration Center, The Ohio State University, 2021 Coffey Rd, Columbus, OH USA
| | - Ram C. Dalal
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD 4072 Australia
| | - N.K. Sinha
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - A.K. Patra
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - S.K. Chaudhari
- Indian Council of Agricultural Research, KAB-II, New Delhi, India
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Phosphate-Solubilizing Fungi: Current Perspective and Future Need for Agricultural Sustainability. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Rajagopal G, Jeyavani J, Ilango S. Larvicidal and histopathological efficacy of inhabitant pathogenic bacterial strains to reduce the dengue vector competence. PEST MANAGEMENT SCIENCE 2020; 76:3587-3595. [PMID: 32400956 DOI: 10.1002/ps.5892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/26/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Aedes aegypti is a primary vector of dengue virus, and the causative agent of dengue is emerging globally as one of the most important arboviral diseases currently threatening human populations. Therefore, vector control is presently the primary intervention method of population reduction, in which natural A. aegypti populations would be reduced with inhabitant bacterial strains that are unable to transmit dengue virus. RESULT Based on the pathogenicity of strains, only four isolates effectively show larvicidal activity. The 16S rRNA gene sequences and the phylogeny depicted that the potential isolates were Bacillus firmus (MK791255), Bacillus paramycoides (MK788268), Bacillus siamensis (MK788212), and Bacillus licheniformis (MK791256). After 24 and 48 hours exposure, the B. licheniformis strain (cell mass of 2.2 × 107 CFU mL-1 ) showed potent larvicidal activity with LC50 of 16.22 μg mL-1 and 9.57 μg mL-1 and the B. paramycoides (cell mass of 3.1 × 107 CFU mL-1 ) strain inhibits the larval and pupal development with LC50 of 42.62 μg mL-1 and 26.97 μg mL-1 . Intermittent stages and causes of abscess in the gut and siphon regions were observed through histopathological studies. These two bacterial strains extend larval duration up to 15-16 days as well as reduce development. CONCLUSION These studies demonstrate the challenge for dengue vector in reducing developmental and reproduction competence. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Gopalan Rajagopal
- Department of Zoology, Ayya Nadar Janaki Ammal College, Sivakasi, India
| | - Jeyaraj Jeyavani
- Department of Zoology, Ayya Nadar Janaki Ammal College, Sivakasi, India
| | - Sakkanan Ilango
- Department of Zoology, Ayya Nadar Janaki Ammal College, Sivakasi, India
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Diversity and characterization of culturable haloalkaliphilic bacteria from two distinct hypersaline lakes in northern Egypt. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00609-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Tsang KSW, Cheung MK, Lam RYC, Kwan HS. A preliminary examination of the bacterial, archaeal, and fungal rhizosphere microbiome in healthy and Phellinus noxius-infected trees. Microbiologyopen 2020; 9:e1115. [PMID: 32969600 PMCID: PMC7568256 DOI: 10.1002/mbo3.1115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/02/2020] [Accepted: 08/18/2020] [Indexed: 01/07/2023] Open
Abstract
Phellinus noxius is a pathogenic fungus that causes brown root rot disease, resulting in a widespread tree and crop mortality in the tropics and subtropics. Early stages of this disease are largely asymptomatic, hindering early diagnosis and effective treatment. We hypothesized that P. noxius infection would alter the rhizosphere microbiome of infected trees, based on which diagnostic biomarkers could be developed. Here, we examined for the first time the bacterial, archaeal, and fungal rhizosphere microbiome in four species of healthy and P. noxius‐infected trees (Ficus microcarpa, Celtis sinensis, Mallotus paniculatus, and Cinnamomum camphora) using high‐throughput amplicon sequencing. Results revealed the dominance of Proteobacteria and Actinobacteria in bacteria, Crenarchaeota and Euryarchaeota in archaea, and Ascomycota and Basidiomycota in fungi. Phellinus noxius infection did not affect the alpha diversity of the bacterial rhizosphere microbiome in all four tree species but affected that of archaea and fungi in a tree species‐dependent manner. Infection with P. noxius only affected the bacterial rhizosphere composition in M. paniculatus but not the other three tree species. By contrast, P. noxius infection affected the composition of the archaeal and fungal rhizosphere microbiome in all four tree species. Collectively, these results suggest that potential diagnostic biomarkers for brown root rot disease are tree species‐specific and should be developed based on different taxonomic groups. Our study has provided insights into the rhizosphere microbiome in healthy and P. noxius‐infected trees and laid a solid foundation for future comprehensive studies.
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Affiliation(s)
| | - Man Kit Cheung
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Regent Yau Ching Lam
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Muni Arborist Limited, Lam Tsuen, Hong Kong
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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Kirubakaran R, ArulJothi KN, Revathi S, Shameem N, Parray JA. Emerging priorities for microbial metagenome research. BIORESOURCE TECHNOLOGY REPORTS 2020; 11:100485. [PMID: 32835181 PMCID: PMC7319936 DOI: 10.1016/j.biteb.2020.100485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.
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Affiliation(s)
| | - K N ArulJothi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, India
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | | | - Nowsheen Shameem
- Department of Environmental Science, Cluster University Srinagar, J&K, India
| | - Javid A Parray
- Department of Environmental Science, Govt SAM Degree College Budgam, J&K, India
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Nelson A, Vandegrift R, Carroll GC, Roy BA. Double lives: transfer of fungal endophytes from leaves to woody substrates. PeerJ 2020; 8:e9341. [PMID: 32923176 PMCID: PMC7457945 DOI: 10.7717/peerj.9341] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 05/20/2020] [Indexed: 01/09/2023] Open
Abstract
Fungal endophytes are a ubiquitous feature of plants, yet for many fungi the benefits of endophytism are still unknown. The Foraging Ascomycete (FA) hypothesis proposes that saprotrophic fungi can utilize leaves both as dispersal vehicles and as resource havens during times of scarcity. The presence of saprotrophs in leaf endophyte communities has been previously observed but their ability to transfer to non-foliar saprobic substrates has not been well investigated. To assess this ability, we conducted a culture study by placing surface-sterilized leaves from a single tropical angiosperm tree (Nectandra lineatifolia) directly onto sterile wood fragments and incubating them for 6 weeks. Fungi from the wood were subsequently isolated in culture and identified to the genus level by ITS sequences or morphology. Four-hundred and seventy-seven fungal isolates comprising 24 taxa were cultured from the wood. Of these, 70.8% of taxa (82.3% of isolates) belong to saprotrophic genera according to the FUNGuild database. Furthermore, 27% of OTUs (6% of isolates) were basidiomycetes, an unusually high proportion compared to typical endophyte communities. Xylaria flabelliformis, although absent in our original isolations, formed anamorphic fruiting structures on the woody substrates. We introduce the term viaphyte (literally, "by way of plant") to refer to fungi that undergo an interim stage as leaf endophytes and, after leaf senescence, colonize other woody substrates via hyphal growth. Our results support the FA hypothesis and suggest that viaphytism may play a significant role in fungal dispersal.
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Affiliation(s)
- Aaron Nelson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Roo Vandegrift
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - George C. Carroll
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Bitty A. Roy
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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Li M, Yang F, Wu X, Yan H, Liu Y. Effects of continuous cropping of sugar beet (Beta vulgaris L.) on its endophytic and soil bacterial community by high-throughput sequencing. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01583-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
As a major sugar crop, sugar beet (Beta vulgaris L.) plays an important role in both sugar industry and feed products. Soil, acts as the substrate for plant growth, provides not only nutrients to plants but also a habitat for soil microorganisms. High soil fertility and good micro-ecological environment are basic requirements for obtaining high-yield and high-sugar sugar beets. This study aimed at exploring the effects of continuous cropping of sugar beet on its endophytic, soil bacterial community structures, and diversity.
Methods
Using high-throughput sequencing technology which is based on Illumina Hiseq 2500 platform, the seeds of sugar beet (sample S), non-continuous cropping sugar beet (sample Bn) with its rhizosphere soil (sample Sr), and planting soil (sample Sn), continuous cropping sugar beet (sample Bc) with its planting soil (sample Sc), were collected as research materials.
Result
The results showed that the bacterial communities and diversity in each sample exhibited different OTU richness; 67.9% and 63.8% of total endophytic OTUs from samples Bc and Bn shared with their planting soil samples Sc and Sn, while sharing 36.4% and 31.8% of total OTUs with their seed sample S. Pseudarthrobacter and Bacillus as the two major groups coexisted among all samples, and other shared groups belonged to Achromobacter, Sphingomonas, Novosphingobium, Terribacillus, Planococcus, Paracoccus, Nesterenkonia, Halomonas, and Nocardioides. Genera, including Pantoea, Pseudomonas, Stenotrophomonas, Weissella, Leuconostoc, and Acinetobacter, were detected in each sugar beet sample but not in their corresponding soil sample. In this study, the bacterial community structures and soil compositions have significantly changed before and after continuous cropping; however, the effects of continuous cropping on endophytic bacteria of sugar beet were not statistically significant.
Conclusion
This study would provide a scientific basis and reference information for in-depth research on correlations between continuous cropping and micro-ecological environment of sugar beet plant.
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Kumar G, Mathimani T, Sivaramakrishnan R, Shanmugam S, Bhatia SK, Pugazhendhi A. Application of molecular techniques in biohydrogen production as a clean fuel. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137795. [PMID: 32208247 DOI: 10.1016/j.scitotenv.2020.137795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Considering the future energy demand and pollution to the environment, biohydrogen, a biofuel, produced from biological sources have garnered increased attention. The present review emphasis the various techniques and methods employed to enumerate the microbial community and enhancement of hydrogen production by dark fermentation. Notably, molecular techniques such as terminal restriction fragment length polymorphism (T-RFLP), quantitative real-time PCR (q-PCR), fluorescent in-situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis (RISA), and next generation sequencing (NGS) have been extensively discussed on identifying the microbial population in hydrogen production. Further, challenges and merits of the molecular techniques have been elaborated.
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Affiliation(s)
- Gopalakrishnan Kumar
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea; Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Thangavel Mathimani
- Department of Energy and Environment, National Institute of Technology, Tiruchirappalli - 620015, Tamil Nadu, India
| | - Ramachandran Sivaramakrishnan
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sabarathinam Shanmugam
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044 China; Institute of Engineering Thermophysics, Chongqing University, Chongqing 400044, China
| | - Shashi Kant Bhatia
- Department of Biological Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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Martorelli I, Helwerda LS, Kerkvliet J, Gomes SIF, Nuytinck J, van der Werff CRA, Ramackers GJ, Gultyaev AP, Merckx VSFT, Verbeek FJ. Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB). J Integr Bioinform 2020; 17:jib-2019-0046. [PMID: 32463383 PMCID: PMC7734503 DOI: 10.1515/jib-2019-0046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 04/20/2020] [Indexed: 11/15/2022] Open
Abstract
Fungi have crucial roles in ecosystems, and are important associates for many organisms. They are adapted to a wide variety of habitats, however their global distribution and diversity remains poorly documented. The exponential growth of DNA barcode information retrieved from the environment is assisting considerably the traditional ways for unraveling fungal diversity and detection. The raw DNA data in association to environmental descriptors of metabarcoding studies are made available in public sequence read archives. While this is potentially a valuable source of information for the investigation of Fungi across diverse environmental conditions, the annotation used to describe environment is heterogenous. Moreover, a uniform processing pipeline still needs to be applied to the available raw DNA data. Hence, a comprehensive framework to analyses these data in a large context is still lacking. We introduce the MycoDiversity DataBase, a database which includes public fungal metabarcoding data of environmental samples for the study of biodiversity patterns of Fungi. The framework we propose will contribute to our understanding of fungal biodiversity and aims to become a valuable source for large-scale analyses of patterns in space and time, in addition to assisting evolutionary and ecological research on Fungi.
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Affiliation(s)
- Irene Martorelli
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Leon S. Helwerda
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
| | - Jesse Kerkvliet
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Sofia I. F. Gomes
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Jorinde Nuytinck
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Guus J. Ramackers
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
| | - Alexander P. Gultyaev
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
| | - Vincent S. F. T. Merckx
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Fons J. Verbeek
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
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Molecular Characterization of Mycobiota and Aspergillus Species from Eupolyphaga sinensis Walker Based on High-Throughput Sequencing of ITS1 and CaM. J FOOD QUALITY 2020. [DOI: 10.1155/2020/1752415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eupolyphaga sinensis Walker is a valuable traditional Chinese animal medicine first recorded in Shennong Bencao. Previous research has shown that E. sinensis is easily contaminated by aflatoxins (AFs), which are highly toxic mycotoxins, during harvest, storage, and transport, thereby posing a considerable threat to consumer health. Most often, these AFs are produced by Aspergillus species. In this study, we contrast the traditional culture-based dilution plating method to the high-throughput sequencing (HTS) technology for fungal identification in TCM E. sinensis. Both of the methods used internal transcribed spacer 1 (ITS1) and calmodulin (CaM) sequencing for fungal molecular identification. The new CaM primer we designed in the study is suitable for MiSeq PE300 sequencing used for identification of Aspergillus species in community DNA samples. More fungal species were found in the E. sinensis samples based on HTS than those found using the culture-based dilution plating method. Overall, combining the sequencing power of ITS1 and CaM is an effective method for the detection and monitoring of potential toxigenic Aspergillus species in E. sinensis. In conclusion, HTS can be used to obtain a large amount of sequencing data about fungi contaminating animal medicine, allowing earlier detection of potential toxigenic fungi and ensuring the efficient production and safety of E. sinensis.
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Karikari-Yeboah O, Skinner W, Addai-Mensah J. Microbial diversity and functional response to the redox dynamics of pyrite-rich sediment and the impact of preload surcharge. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:226. [PMID: 32152784 DOI: 10.1007/s10661-020-8169-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
Microbial diversity and activities play pivotal biogeochemical roles in a redox-sensitive, pyrite-rich sediment's ecosystem. However, very little is known about the microbial community composition and distribution among the redox zones of pyrite-rich sediment and their response to changes caused by the burial of the sediment beneath compacted fill. In the present work, culture-independent, molecular phylogenetic investigations of the prokaryotic population and its diversity in a naturally occurring pyrite-rich sediment were undertaken to determine the microbial community composition, richness, diversity and distributions among the varying redox zones and their functional response to the imposition of surface surcharge, in the form of compacted fill. It was established that the pyrite-rich sediment is a redox-sensitive environment consisting of microhabitats with distinct and discontinuous physico-chemical characteristics, including DO, pH, Eh, temperature, electrical conductivity and salinity. It is a favourable environment for cyclic transformation of inorganic sulphur compounds and a unique environment for the habitation and growth of various microorganisms. Microbes adapted to the microhabitat and lived together in consortia, in response to their physiological and functional requirements. Microbes involved in the sulphur cycle had their populations concentrated in the oxic zone, while those involved in iron and carbon cycles were prevalent in the anoxic zones. As a result, highly diverse microbial populations occurred in isolated peaks within the sediment. The physico-chemical differences within the sediment changed in response to changes in the sediment redox dynamics. Imposition of the surcharge resulted in significant changes in the pH, temperature, Eh, DO, EC and salinity, reflecting marked re-distribution of the microbial population within the ecosystem. The cable bacteria phenomenon was evident in the sediment studied; however, there were doubt regarding their filamentous occurrence.
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Affiliation(s)
| | - W Skinner
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, South Australia
| | - J Addai-Mensah
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, South Australia
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Zhu J, Ren Z, Huang B, Cao A, Wang Q, Yan D, Ouyang C, Wu J, Li Y. Effects of Fumigation with Allyl Isothiocyanate on Soil Microbial Diversity and Community Structure of Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1226-1236. [PMID: 31922739 DOI: 10.1021/acs.jafc.9b07292] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
As a substitute for methyl bromide, effects of allyl isothiocyanate (AITC) on nontarget microorganisms in soil are poorly understood. This study measured the half-life of AITC in the soil as well as its effects on the soil substrate-induced respiration (SIR) and on communities of soil bacteria and fungi. The results showed that AITC had a short half-life and a short-term inhibition of SIR; high-throughput sequencing analysis showed that AITC had less effect on bacterial than fungal communities. Fumigation reduced the diversity of soil bacteria temporarily, but stimulated the diversity of soil fungi in the long-term and significantly changed the structure of the fungal community. Following AITC fumigation there were significant increases in the relative abundance of probiotics such as Sphingomonas, Streptomyces, Hypocreales, Acremonium, Aspergillus, and Pseudallescheria that help to control plant diseases. Our study provided useful information for assessing the ecological safety of AITC.
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Affiliation(s)
- Jiahong Zhu
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Zongjie Ren
- National Agricultural Technology Extension Service Center , Ministry of Agriculture and Rural Affairs , Beijing 100125 , China
| | - Bin Huang
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Aocheng Cao
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Qiuxia Wang
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Dongdong Yan
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Canbin Ouyang
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Jiajia Wu
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Yuan Li
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
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Microbial diversity changes and enrichment of potential petroleum hydrocarbon degraders in crude oil-, diesel-, and gasoline-contaminated soil. 3 Biotech 2020; 10:42. [PMID: 31988836 DOI: 10.1007/s13205-019-2027-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
This study investigated the impacts of crude oil, diesel, and gasoline on the diversity of indigenous microbial communities as well as culturable microorganisms in the studied soil. Oil contamination led to shifts in the diversity of the soil's microbial communities, regardless of the contaminant applied. Unpolluted soils were more diverse and evenly distributed than contaminated samples. The domain Bacteria accounted for 65.15% of the whole microbial community. The bacterial phylum Proteobacteria dominated in all samples, followed by Actinobacteria and Acidobacteria. Pseudomonas with 28.15% of reads dominated in Proteobacteria, while Rhodococcus (3.07%) dominated in Actinobacteria, and Blastocatella (2.53%) dominated in Acidobacteria. The dominant fungal phyla across all samples were Ascomycota dominated by Penicillium (50.48% of sequences), and Zygomycota dominated by Mortierella (16.87%). Sequences similar to the archaeal phyla, Euryarchaeota and Thaumarchaeota, were also detected. The number of culturable microorganisms increased following the contamination and was higher in contaminated samples than in clean samples. Oil contamination also resulted in the enrichment of oil-degrading strains. Two bacteria, Serratia marcescens strain PL and Raoultella ornithinolytica PS, which were isolated from crude oil-contaminated soil, exhibited strong crude oil degradation ability. Strain PL was the most efficient strain and degraded 75.10% of crude oil, while strain PL degraded 65.48%, after 20 days of incubation. However, the mixed culture of the two strains was more effective than single strain and could achieve up to 96.83% of crude oil degradation, with a complete abatement of straight-chain hydrocarbons (from C12 to C25), and more than 91% removal of highly branched hydrocarbons, phytane and pristane, which are known to be more recalcitrant to biodegradation. Strains PS and PL are two newly isolated crude oil degraders that are not among the most prominent crude oil-degrading strains referenced in the literature. Therefore, their high degradation capacity makes them perfect candidates for the bioremediation of petroleum hydrocarbon contaminated environments.
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49
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Liu L, Zhu K, Wurzburger N, Zhang J. Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales. Ecosphere 2020. [DOI: 10.1002/ecs2.2999] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Lan Liu
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station & Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration School of Ecological and Environmental Sciences East China Normal University Shanghai 200241 China
- Department of Environmental Studies University of California Santa Cruz California 95064 USA
- Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092 China
| | - Kai Zhu
- Department of Environmental Studies University of California Santa Cruz California 95064 USA
| | - Nina Wurzburger
- Odum School of Ecology University of Georgia Athens Georgia 30602 USA
| | - Jian Zhang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station & Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration School of Ecological and Environmental Sciences East China Normal University Shanghai 200241 China
- Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092 China
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Madariaga-Mazón A, Hernández-Alvarado RB, Noriega-Colima KO, Osnaya-Hernández A, Martinez-Mayorga K. Toxicity of secondary metabolites. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Abstract
Secondary metabolites, commonly referred to as natural products, are produced by living organisms and usually have pharmacological or biological activities. Secondary metabolites are the primary source for the discovery of new drugs. Furthermore, secondary metabolites are also used as food preservatives, biopesticides or as research tools. Although secondary metabolites are mainly used by their beneficial biological activity, the toxicity of some of them may limit their use. The toxicity assessment of any compound that is prone to be used in direct contact with human beings is of vital importance. There is a vast spectrum of experimental methods for toxicity evaluation, including in vitro and in vivo methodologies. In this work, we present an overview of the different sources, bioactivities, toxicities and chemical classification of secondary metabolites, followed by a sketch of the role of toxicity assessment in drug discovery and agrochemistry.
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