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Picariello E, De Nicola F. Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions. MICROBIAL ECOLOGY 2024; 87:86. [PMID: 38940921 PMCID: PMC11213729 DOI: 10.1007/s00248-024-02402-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.
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Affiliation(s)
- Enrica Picariello
- Department of Sciences and Technologies, University of Sannio, 82100, Benevento, Italy.
| | - Flavia De Nicola
- Department of Sciences and Technologies, University of Sannio, 82100, Benevento, Italy
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2
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Coleine C, Delgado-Baquerizo M, Zerboni A, Turchetti B, Buzzini P, Franceschi P, Selbmann L. Rock Traits Drive Complex Microbial Communities at the Edge of Life. ASTROBIOLOGY 2023; 23:395-406. [PMID: 36812458 DOI: 10.1089/ast.2022.0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Antarctic deserts are among the driest and coldest ecosystems of the planet; there, some microbes survive under these extreme conditions inside porous rocks, forming the so-called endolithic communities. Yet the contribution of distinct rock traits to support complex microbial assemblies remains poorly determined. Here, we combined an extensive Antarctic rock survey with rock microbiome sequencing and ecological networks and found that contrasting combinations of microclimatic and rock traits such as thermal inertia, porosity, iron concentration, and quartz cement can help explain the multiple complex microbial assemblies found in Antarctic rocks. Our work highlights the pivotal role of rocky substrate heterogeneity in sustaining contrasting groups of microorganisms, which is essential to understand life at the edge on Earth and for the search for life on other rocky planets such as Mars.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "A. Desio", Università degli Studi di Milano, Milano, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Pietro Franceschi
- Research and Innovation Center, Fondazione Edmund Mach, Trento, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
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Duan H, Wang H, Li S, Shen W, Zhuang Y, Zhang F, Li X, Zhai L, Liu H, Zhang L. Potential to mitigate nitrogen emissions from paddy runoff: A microbiological perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161306. [PMID: 36592915 DOI: 10.1016/j.scitotenv.2022.161306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/06/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Ditches and ponds are the basic units of agroecosystems that serve irrigation and drainage and also perform the natural ecological function of reducing nitrogen (N) emissions. To better enhance the design and advance management strategies in the paddy field ecosystem to minimize N emission, the N cycling microorganism in the paddy field ecosystem including interconnected fields with rice-wheat rotation, ditches, and ponds in central China was investigated by metagenomic techniques. Our results showed that ditches and ponds may be N removal hotspots by microorganisms in the rice and wheat seasons respectively. Given seasonal variation, the abundance of N-related microorganisms was high during the rice season. However, the Shannon and Simpson indices were lower and the microbial co-occurrence network was destabilized, which could make microbes in the rice season fragile and sensitive. Phytoplankton as key environmental factors affecting the N cycling microbial could promote more stable microbial communities through maintaining a good mutualistic symbiosis. While high algae concentration significantly promotes the abundance of norB than nosZ (P < 0.05), which may result in more N2O production. To trade off N removal and N2O emission, the algae concentration needs to be controlled. Our findings provide a systematic profile of N-related microorganisms in the paddy field ecosystem, and it would benefit in developing effective strategies for limiting N pollution in agriculture.
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Affiliation(s)
- He Duan
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Haodong Wang
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430078, China.
| | - Sisi Li
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wangzheng Shen
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yanhua Zhuang
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Fulin Zhang
- Institute of Plant Protection, Soil and Fertilizer Sciences, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Xudong Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Limei Zhai
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Hongbin Liu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Liang Zhang
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Beale DJ, Jones OA, Bose U, Broadbent JA, Walsh TK, van de Kamp J, Bissett A. Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience. Emerg Top Life Sci 2022; 6:185-199. [PMID: 35403668 PMCID: PMC9023019 DOI: 10.1042/etls20210261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022]
Abstract
Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of 'ecosurveillance', especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.
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Affiliation(s)
- David J. Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park QLD 4102, Australia
| | - Oliver A.H. Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, Bundoora West Campus, PO Box 71, Bundoora, VIC 3083, Australia
| | - Utpal Bose
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - James A. Broadbent
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Thomas K. Walsh
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT 2601, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
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Naidoo Y, Valverde A, Pierneef RE, Cowan DA. Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils. MICROBIAL ECOLOGY 2022; 83:689-701. [PMID: 34105010 DOI: 10.1007/s00248-021-01785-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Angel Valverde
- IRNASA-CSIC, C/Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
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6
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Functional soil mycobiome across ecosystems. J Proteomics 2022; 252:104428. [PMID: 34818587 DOI: 10.1016/j.jprot.2021.104428] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/17/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospholipid fatty acids, PLFA), community composition (by metabarcoding of the 18S rRNA gene from extracted DNA) and functional profile (by metaproteomics) to investigate soil fungi and their relation to edaphic and environmental variables across three ecosystems (forests, grasslands, and shrublands) distributed across the globe. We found that protein richness of soil fungi was significantly higher in forests than in shrublands. Among a wide suite of edaphic and environmental variables, we found that soil carbon content and plant cover shaped evenness and diversity of fungal soil proteins while protein richness correlated to mean annual temperature and pH. Functions shifted from metabolism in forests to information processing and storage in shrublands. The differences between the biomes highlight the utility of metaproteomics to investigate functional microbiomes in soil. SIGNIFICANCE: Understanding the structure and the function of fungal communities and the driving factors is crucial to determine the contribution to ecosystem services of fungi and what effect future climate has. While there is considerable knowledge on the ecosystem processes provided by fungi such as decomposition of organic matter and plant-soil relationships, our understanding of the driving factors of the fungal metaproteome is scarce. Here we present the first estimates of fungal topsoil protein diversity in a wide range of soils across global biomes. We report taxonomic differences for genes delivered by amplicon sequencing of the 18S rRNA gene and differences of the functional microbiome based on metaproteomics. Both methods gave a complementary view on the fungal topsoil communities, unveiling both taxonomic and functional changes with changing environments. Such a comprehensive multi-omic analysis of fungal topsoil communities has never been performed before, to our knowledge.
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Simopoulos CMA, Figeys D, Lavallée-Adam M. Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies. Methods Mol Biol 2022; 2456:319-338. [PMID: 35612752 DOI: 10.1007/978-1-0716-2124-0_22] [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] [Indexed: 10/18/2022]
Abstract
Constant improvements in mass spectrometry technologies and laboratory workflows have enabled the proteomics investigation of biological samples of growing complexity. Microbiomes represent such complex samples for which metaproteomics analyses are becoming increasingly popular. Metaproteomics experimental procedures create large amounts of data from which biologically relevant signal must be efficiently extracted to draw meaningful conclusions. Such a data processing requires appropriate bioinformatics tools specifically developed for, or capable of handling metaproteomics data. In this chapter, we outline current and novel tools that can perform the most commonly used steps in the analysis of cutting-edge metaproteomics data, such as peptide and protein identification and quantification, as well as data normalization, imputation, mining, and visualization. We also provide details about the experimental setups in which these tools should be used.
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Affiliation(s)
- Caitlin M A Simopoulos
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
- School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.
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Mishra B, Varjani S, Kumar G, Awasthi MK, Awasthi SK, Sindhu R, Binod P, Rene ER, Zhang Z. Microbial approaches for remediation of pollutants: Innovations, future outlook, and challenges. ENERGY & ENVIRONMENT 2021; 32:1029-1058. [DOI: 10.1177/0958305x19896781] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Environmental contamination with persistent organic pollutants has emerged as a serious threat of pollution. Bioremediation is a key to eliminate these harmful pollutants from the environment and has gained the interest of researchers during the past few decades. Scientific knowledge upon microbial interactions with individual pollutants over the past decades has helped to abate environmental pollution. Traditional bioremediation approaches have limitations for their applications; hence, it is essential to discover new bioremediation approaches with biotechnological interventions for best results. The developments in various methodologies are expected to increase the efficiency of bioremediation techniques and provide environmentally sound strategies. This paper deals with the profiling of microorganisms present in polluted sites using various techniques such as culture-based approaches and omics-based approaches. Besides this, it also provides up-to-date scientific literature on the microbial electrochemical technologies which are nowadays considered as the best approach for remediation of pollutants. Detailed information about future outlook and challenges to evaluate the effect of various treatment technologies for remediation of pollutants has been discussed.
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Affiliation(s)
- Bishwambhar Mishra
- Department of Biotechnology, Chaitanya Bharathi Institute of Technology, Hyderabad, India
| | - Sunita Varjani
- Paryavaran Bhavan, Gujarat Pollution Control Board, Gandhinagar, India
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A& F University, Shaanxi Province, PR China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A& F University, Shaanxi Province, PR China
| | - Raveendran Sindhu
- CSIR–National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum, India
| | - Parameswaran Binod
- CSIR–National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum, India
| | - Eldon R Rene
- Department of Environmental Engineering and Water Technology, IHE Delft Institute of Water Education, Delft, The Netherlands
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A& F University, Shaanxi Province, PR China
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Kim SY, Lopez-Vazquez CM, Curko J, Matosic M, Svetec IK, Štafa A, Milligan C, Herrera A, Maestre JP, Kinney KA, Brdjanovic D, Garcia HA. Supersaturated-oxygen aeration effects on a high-loaded membrane bioreactor (HL-MBR): Biological performance and microbial population dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144847. [PMID: 33548701 DOI: 10.1016/j.scitotenv.2020.144847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Conventional diffused aeration systems (such as fine-bubble diffusers) exhibit a poor oxygen transfer in wastewater treatment plants (WWTPs), particularly when operating at sludge concentrations higher than 15 g L-1. The supersaturated dissolved oxygen (SDOX) system has been proposed as an alternative for supplying dissolved oxygen (DO) at high mixed liquor suspended solids (MLSS) concentrations. The advantages introduced by such technology include the possibility of operating WWTPs at much higher than usual MLSS concentrations, increasing the treatment capacity of WWTPs. Recent studies have demonstrated that the SDOX system has higher oxygen transfer rates (OTRs) and oxygen transfer efficiencies (OTEs) relative to fine-bubble diffusers. However, it is unknown if the high-pressure conditions introduced by SDOX may possibly impact the biological performance of WWTPs. In this study, the effects of SDOX technology on the biological performance of a membrane bioreactor (MBR) were evaluated. The MBR was operated at an MLSS concentration of approximately 15 g L-1 in four phases as follows: (P1) with bubble diffusers, (P2) with an SDOX unit, (P3) with the bubble diffusers, and (P4) with the SDOX unit. The performance of the MBR was assessed by monitoring the sludge concentration, as well as changes in the particle size distribution (PSD), sludge activity, organic matter removal and nitrification performance, and changes in the microbial community within the MBR. The operational conditions exerted by the SDOX technology did not affect the concentration of active biomass during the study period. The biological performance of the MBR was not affected by the introduction of the SDOX technology. Finally, the microbial community was relatively stable although some variations at the family and genus level were evident during each of the study phases. Therefore, the SDOX system can be proposed as an alternative technology for DO supply in WWTPs increasing the overall treatment capacity.
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Affiliation(s)
- Sang Yeob Kim
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Carlos M Lopez-Vazquez
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands
| | - Josip Curko
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Marin Matosic
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ivan K Svetec
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Kršnjavoga 25, 10000 Zagreb, Croatia
| | - Anamarija Štafa
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Kršnjavoga 25, 10000 Zagreb, Croatia
| | - Chris Milligan
- BlueInGreen, LLC, 700 W. Research Center Blvd. Suite 1208, Fayetteville, AR 72701, United States
| | - Aridai Herrera
- HAC Group, LLC, 8111 Hicckma Mills Dr, Kansas City, MO 64132, United States
| | - Juan Pedro Maestre
- Civil, Architectural and Environmental Engineering Department, University of Texas at Austin, Austin, TX, United States
| | - Kerry A Kinney
- Civil, Architectural and Environmental Engineering Department, University of Texas at Austin, Austin, TX, United States
| | - Damir Brdjanovic
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Hector A Garcia
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands.
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Extending Natural Limits to Address Water Scarcity? The Role of Non-Conventional Water Fluxes in Climate Change Adaptation Capacity: A Review. SUSTAINABILITY 2021. [DOI: 10.3390/su13052473] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Water consumption continues to grow globally, and it is estimated that more than 160% of the total global water volume will be needed to satisfy the water requirements in ten years. In this context, non-conventional water resources are being considered to overcome water scarcity and reduce water conflicts between regions and sectors. A bibliometric analysis and literature review of 81 papers published between 2000 and 2020 focused on south-east Spain were conducted. The aim was to examine and re-think the benefits and concerns, and the inter-connections, of using reclaimed and desalinated water for agricultural and urban-tourist uses to address water scarcity and climate change impacts. Results highlight that: (1) water use, cost, quality, management, and perception are the main topics debated by both reclaimed and desalinated water users; (2) water governance schemes could be improved by including local stakeholders and water users in decision-making; and (3) rainwater is not recognized as a complementary option to increase water supply in semi-arid regions. Furthermore, the strengths–weaknesses–opportunities–threats (SWOT) analysis identifies complementary concerns such as acceptability and investment in reclaimed water, regulation (cost recovery principle), and environmental impacts of desalinated water.
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Tartaglia M, Bastida F, Sciarrillo R, Guarino C. Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights. Int J Mol Sci 2020; 21:ijms21228455. [PMID: 33187080 PMCID: PMC7697097 DOI: 10.3390/ijms21228455] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Soil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptomics and less on metaproteomics studies. Metaproteomic allows total extraction of intracellular and extracellular proteins from soil samples, providing a complete picture of the physiological and functional state of the “soil community”. The advancement of high-performance mass spectrometry technologies was more rapid than the development of ad hoc extraction techniques for soil proteins. The protein extraction from environmental samples is biased due to interfering substances and the lower amount of proteins in comparison to cell cultures. Soil sample preparation and extraction methodology are crucial steps to obtain high-quality resolution and yields of proteins. This review focuses on the several soil protein extraction protocols to date to highlight the methodological challenges and critical issues for the application of proteomics to soil samples. This review concludes that improvements in soil protein extraction, together with the employment of ad hoc metagenome database, may enhance the identification of proteins with low abundance or from non-dominant populations and increase our capacity to predict functional changes in soil.
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Affiliation(s)
- Maria Tartaglia
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
| | - Felipe Bastida
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain;
| | - Rosaria Sciarrillo
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
| | - Carmine Guarino
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
- Correspondence: ; Tel.: +39-824-305145
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12
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Ananbeh H, Merlos Rodrigo MA, Jelinkova P, Strmiska V, Splichal Z, Jehmlich N, Michalkova H, Stojanović M, Voberkova S, Adam V, Moulick A. Soil protein as a potential antimicrobial agent against methicillin -resistant Staphylococcus aureus. ENVIRONMENTAL RESEARCH 2020; 188:109320. [PMID: 32540568 DOI: 10.1016/j.envres.2020.109320] [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: 06/18/2019] [Revised: 02/04/2020] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
Recently, the interest is increasing to find alternatives to replace the usage of antibiotics since their massive and improper usage enhance the antibiotic resistance in human pathogens. In this study, for the first time we showed that the soil proteins have very high antibacterial activity (98% of growth inhibition) against methicillin resistant Staphylococcus aureus (MRSA), one of the most threatening human pathogens. We found that the protein extract (C3) from the forest with past intensive management showed higher antibacterial activity than that of unmanaged forest. The MIC and IC50 were found to be 30 and 15.0 μg protein g-1 dry soil respectively. C3 was found to kill the bacteria by cell wall disruption and genotoxicity which was confirmed by optical and fluorescent microscopy and comet assay. According to qPCR study, the mecA (the antibiotic resistant gene) expression in MRSA was found to be down-regulated after C3 treatment. In contrast, C3 showed no hemolytic toxicity on human red blood cells which was confirmed by hemolytic assay. According to ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS), 144 proteins were identified in C3 among which the majority belonged to Gram negative bacteria (45.8%). Altogether, our results will help to develop novel, cost-effective, non-toxic and highly efficient antibacterial medicines from natural sources against antibiotic resistant infections.
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Affiliation(s)
- Hanadi Ananbeh
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Miguel Angel Merlos Rodrigo
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Pavlina Jelinkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Vladislav Strmiska
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Zbynek Splichal
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Hana Michalkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Marko Stojanović
- Global Change Research Institute, Academy of Sciences of the Czech Republic, Bělidla 4a, 603 00, Brno, Czech Republic
| | - Stanislava Voberkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic; Central European Institute of Technology, Mendel University in Brno, Zemedelska 1, 61300, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic.
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13
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Chen J, Arafat Y, Ud Din I, Yang B, Zhou L, Wang J, Letuma P, Wu H, Qin X, Wu L, Lin S, Zhang Z, Lin W. Nitrogen Fertilizer Amendment Alter the Bacterial Community Structure in the Rhizosphere of Rice ( Oryza sativa L.) and Improve Crop Yield. Front Microbiol 2019; 10:2623. [PMID: 31798559 PMCID: PMC6868037 DOI: 10.3389/fmicb.2019.02623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/28/2019] [Indexed: 01/01/2023] Open
Abstract
Availability of nitrogen (N) in soil changes the composition and activities of microbial community, which is critical for the processing of soil organic matter and health of crop plants. Inappropriate application of N fertilizer can alter the rhizosphere microbial community and disturb the soil N homeostasis. The goal of this study was to assess the effect of different ratio of N fertilizer at various early to late growth stages of rice, while keeping the total N supply constant on rice growth performance, microbial community structure, and soil protein expression in rice rhizosphere. Two different N regimes were applied, i.e., traditional N application (NT) consists of three sessions including 60, 30 and 10% at pre-transplanting, tillering and panicle initiation stages, respectively, while efficient N application (NF) comprises of four sessions, i.e., 30, 30, 30, and 10%), where the fourth session was extended to anthesis stage. Soil metaproteomics combined with Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to determine the rhizosphere biological process. Under NF application, soil enzymes, nitrogen utilization efficiency and rice yield were significantly higher compared to NT application. T-RFLP and qPCR analysis revealed differences in rice rhizosphere bacterial diversity and structure. NF significantly decreased the specific microbes related to denitrification, but opposite result was observed for bacteria associated with nitrification. Furthermore, soil metaproteomics analysis showed that 88.28% of the soil proteins were derived from microbes, 5.74% from plants, and 6.25% from fauna. Specifically, most of the identified microbial proteins were involved in carbohydrate, amino acid and protein metabolisms. Our experiments revealed that NF positively regulates the functioning of the rhizosphere ecosystem and further enabled us to put new insight into microbial communities and soil protein expression in rice rhizosphere.
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Affiliation(s)
- Jun Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yasir Arafat
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Genetic Breeding and Comprehensive Utilization of the Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Israr Ud Din
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Bo Yang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liuting Zhou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juanying Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Puleng Letuma
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongmiao Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xianjin Qin
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Linkun Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhixing Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
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14
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Anselmann SEL, Löffler C, Stärk HJ, Jehmlich N, von Bergen M, Brüls T, Boll M. The class II benzoyl-coenzyme A reductase complex from the sulfate-reducing Desulfosarcina cetonica. Environ Microbiol 2019; 21:4241-4252. [PMID: 31430028 DOI: 10.1111/1462-2920.14784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/06/2019] [Accepted: 08/18/2019] [Indexed: 12/17/2022]
Abstract
Benzoyl-CoA reductases (BCRs) catalyse a key reaction in the anaerobic degradation pathways of monocyclic aromatic substrates, the dearomatization of benzoyl-CoA (BzCoA) to cyclohexa-1,5-diene-1-carboxyl-CoA (1,5-dienoyl-CoA) at the negative redox potential limit of diffusible enzymatic substrate/product couples (E°' = -622 mV). A 1-MDa class II BCR complex composed of the BamBCDEGHI subunits has so far only been isolated from the Fe(III)-respiring Geobacter metallireducens. It is supposed to drive endergonic benzene ring reduction at an active site W-pterin cofactor by flavin-based electron bifurcation. Here, we identified multiple copies of putative genes encoding the structural components of a class II BCR in sulfate reducing, Fe(III)-respiring and syntrophic bacteria. A soluble 950 kDa Bam[(BC)2 DEFGHI]2 complex was isolated from extracts of Desulfosarcina cetonica cells grown with benzoate/sulfate. Metal and cofactor analyses together with the identification of conserved binding motifs gave rise to 4 W-pterins, two selenocysteines, six flavin adenine dinucleotides, four Zn, and 48 FeS clusters. The complex exhibited 1,5-dienoyl-CoA-, NADPH- and ferredoxin-dependent oxidoreductase activities. Our results indicate that high-molecular class II BCR metalloenzyme machineries are remarkably conserved in strictly anaerobic bacteria with regard to subunit architecture and cofactor content, but their subcellular localization and electron acceptor preference may differ as a result of adaptations to variable energy metabolisms.
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Affiliation(s)
| | - Claudia Löffler
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Hans-Joachim Stärk
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany.,Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, 04103, Leipzig, Germany
| | - Thomas Brüls
- CEA, DRF, IBFJ, Genoscope, Evry, France.,CNRS-UMR8030, Université d'Evry Val d'Essonne and Université Paris-Saclay, Evry, France
| | - Matthias Boll
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
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15
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Starke R, Jehmlich N, Alfaro T, Dohnalkova A, Capek P, Bell SL, Hofmockel KS. Incomplete cell disruption of resistant microbes. Sci Rep 2019; 9:5618. [PMID: 30948770 PMCID: PMC6449382 DOI: 10.1038/s41598-019-42188-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/22/2019] [Indexed: 11/08/2022] Open
Abstract
Biomolecules for OMIC analysis of microbial communities are commonly extracted by bead-beating or ultra-sonication, but both showed varying yields. In addition to that, different disruption pressures are necessary to lyse bacteria and fungi. However, the disruption efficiency and yields comparing bead-beating and ultra-sonication of different biological material have not yet been demonstrated. Here, we show that ultra-sonication in a bath transfers three times more energy than bead-beating over 10 min. TEM imaging revealed intact gram-positive bacterial and fungal cells whereas the gram-negative bacterial cells were destroyed beyond recognition after 10 min of ultra-sonication. DNA extraction using 10 min of bead-beating revealed higher yields for fungi but the extraction efficiency was at least three-fold lower considering its larger genome. By our critical viewpoint, we encourage the review of the commonly used extraction techniques as we provide evidence for a potential underrepresentation of resistant microbes, particularly fungi, in ecological studies.
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Affiliation(s)
- Robert Starke
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Praha, Czech Republic.
| | - Nico Jehmlich
- Helmholtz-Center for Environmental Research, UFZ, Leipzig, Germany
| | - Trinidad Alfaro
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Alice Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Petr Capek
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sheryl L Bell
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kirsten S Hofmockel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Iowa, USA
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16
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Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics. J Proteomics 2019; 198:50-58. [DOI: 10.1016/j.jprot.2018.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
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17
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Moreno JL, Torres IF, García C, López-Mondéjar R, Bastida F. Land use shapes the resistance of the soil microbial community and the C cycling response to drought in a semi-arid area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:1018-1030. [PMID: 30340250 DOI: 10.1016/j.scitotenv.2018.08.214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
The aim of this study was to understand the responses of the microbial community of soil under different land uses to drought in a semi-arid Mediterranean area. In a laboratory incubation, soil samples from different land uses (natural forest, drip-irrigated orchard, rain-fed almond tree cultivation and abandoned area) were maintained at 20% and 60% of the WHC. The microbial biomass and potential enzyme activities were determined after four and fifty days of soil incubation. The diversity and composition of the microbial community were studied after 50 days of incubation. The total mineralisation of soil organic C (SOC), as well as, the mineralisation of fresh organic matter (FOM) and the "priming effect" were analysed after addition of 13C-enriched plant tissue. Both land use and drought had significant effects in the soil microbial community, but the effect of land use was stronger than that of drought. The PLFA content (microbial biomass) of the forests soil was greater under drought. After 50 days of soil incubation, the microbial biomass and most of potential enzyme activities of the almond tree and abandoned soil samples were not significantly affected by drought contrary to those in orchard soil. The total and FOM mineralisation were on average lower in soil under drought than under optimal moisture for all land uses. However, the responses of the priming effect to drought were dependent on the land use. Overall, we conclude that the resistance to drought of the soil microbial community from an agroecosystem having a semi-arid climate is strongly influenced by the previous land use.
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Affiliation(s)
- José Luis Moreno
- CEBAS-CSIC, Campus Universitario de Espinardo, PO Box 164, CP 30100 Murcia, Spain.
| | - Irene F Torres
- CEBAS-CSIC, Campus Universitario de Espinardo, PO Box 164, CP 30100 Murcia, Spain
| | - Carlos García
- CEBAS-CSIC, Campus Universitario de Espinardo, PO Box 164, CP 30100 Murcia, Spain
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Praha 4, Czech Republic
| | - Felipe Bastida
- CEBAS-CSIC, Campus Universitario de Espinardo, PO Box 164, CP 30100 Murcia, Spain
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18
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Gurdeep Singh R, Tanca A, Palomba A, Van der Jeugt F, Verschaffelt P, Uzzau S, Martens L, Dawyndt P, Mesuere B. Unipept 4.0: Functional Analysis of Metaproteome Data. J Proteome Res 2018; 18:606-615. [PMID: 30465426 DOI: 10.1021/acs.jproteome.8b00716] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Unipept ( https://unipept.ugent.be ) is a web application for metaproteome data analysis, with an initial focus on tryptic-peptide-based biodiversity analysis of MS/MS samples. Because the true potential of metaproteomics lies in gaining insight into the expressed functions of complex environmental samples, the 4.0 release of Unipept introduces complementary functional analysis based on GO terms and EC numbers. Integration of this new functional analysis with the existing biodiversity analysis is an important asset of the extended pipeline. As a proof of concept, a human faecal metaproteome data set from 15 healthy subjects was reanalyzed with Unipept 4.0, yielding fast, detailed, and straightforward characterization of taxon-specific catalytic functions that is shown to be consistent with previous results from a BLAST-based functional analysis of the same data.
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Affiliation(s)
- Robbert Gurdeep Singh
- Department of Applied Mathematics, Computer Science and Statistics , Ghent University , Ghent B-9000 , Belgium
| | - Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia , Tramariglio, Alghero 07041 , Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia , Tramariglio, Alghero 07041 , Italy
| | - Felix Van der Jeugt
- Department of Applied Mathematics, Computer Science and Statistics , Ghent University , Ghent B-9000 , Belgium
| | - Pieter Verschaffelt
- Department of Applied Mathematics, Computer Science and Statistics , Ghent University , Ghent B-9000 , Belgium
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of Sardinia , Tramariglio, Alghero 07041 , Italy
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology , VIB , Ghent B-9000 , Belgium.,Department of Biochemistry , Ghent University , Ghent B-9000 , Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics , Ghent University , Ghent B-9000 , Belgium
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics , Ghent University , Ghent B-9000 , Belgium.,VIB-UGent Center for Medical Biotechnology , VIB , Ghent B-9000 , Belgium.,Department of Biochemistry , Ghent University , Ghent B-9000 , Belgium
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19
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Bastida F, Crowther TW, Prieto I, Routh D, García C, Jehmlich N. Climate shapes the protein abundance of dominant soil bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:18-21. [PMID: 29852443 DOI: 10.1016/j.scitotenv.2018.05.288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/23/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Sensitive models of climate change impacts would require a better integration of multi-omics approaches that connect the abundance and activity of microbial populations. Here, we show that climate is a fundamental driver of the protein abundance of Actinobacteria, Planctomycetes and Proteobacteria, supporting the hypothesis that metabolic activity of some dominant phyla may be closely linked to climate. These results may improve our capacity to construct microbial models that better predict the impact of climate change in ecosystem processes.
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Affiliation(s)
- Felipe Bastida
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain.
| | - Tom W Crowther
- Institute of Integrative Biology, ETH Zürich, Univeritätstrasse 16, 8006 Zürich, Switzerland
| | - Iván Prieto
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - Devin Routh
- Institute of Integrative Biology, ETH Zürich, Univeritätstrasse 16, 8006 Zürich, Switzerland
| | - Carlos García
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstr. 15, 04318 Leipzig, Germany
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