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Almeida BK, Tran EH, Afkhami ME. Phyllosphere fungal diversity generates pervasive nonadditive effects on plant performance. THE NEW PHYTOLOGIST 2024; 243:2416-2429. [PMID: 38719779 DOI: 10.1111/nph.19792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/01/2024] [Indexed: 08/23/2024]
Abstract
Plants naturally harbor diverse microbiomes that can dramatically impact their health and productivity. However, it remains unclear how fungal microbiome diversity, especially in the phyllosphere, impacts intermicrobial interactions and consequent nonadditive effects on plant productivity. Combining manipulative experiments, field collections, culturing, microbiome sequencing, and synthetic consortia, we experimentally tested for the first time how foliar fungal community diversity impacts plant productivity. We inoculated morning glories (Ipomoea hederifolia L.) with 32 phyllosphere consortia of either low or high diversity or with single fungal taxa, and measured effects on plant productivity and allocation. We found the following: (1) nonadditive effects were pervasive with 56% of fungal consortia interacting synergistically or antagonistically to impact plant productivity, including some consortia capable of generating acute synergism (e.g. > 1000% increase in productivity above the additive expectation), (2) interactions among 'commensal' fungi were responsible for this nonadditivity in diverse consortia, (3) synergistic interactions were approximately four times stronger than antagonistic effects, (4) fungal diversity affected the magnitude but not frequency or direction of nonadditivity, and (5) diversity affected plant performance nonlinearly with the highest performance in low-diversity treatments. These findings highlight the importance of interpreting plant-microbiome interactions under a framework that incorporates intermicrobial interactions and nonadditive outcomes to understand natural complexity.
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Affiliation(s)
- Brianna K Almeida
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Elan H Tran
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
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2
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Jones GD, Insinga L, Droz B, Feinberg A, Stenke A, Smith J, Smith P, Winkel LHE. Emerging investigator series: predicted losses of sulfur and selenium in european soils using machine learning: a call for prudent model interrogation and selection. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2024. [PMID: 39101370 DOI: 10.1039/d4em00338a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Reductions in sulfur (S) atmospheric deposition in recent decades have been attributed to S deficiencies in crops. Similarly, global soil selenium (Se) concentrations were predicted to drop, particularly in Europe, due to increases in leaching attributed to increases in aridity. Given its international importance in agriculture, reductions of essential elements, including S and Se, in European soils could have important impacts on nutrition and human health. Our objectives were to model current soil S and Se levels in Europe and predict concentration changes for the 21st century. We interrogated four machine-learning (ML) techniques, but after critical evaluation, only outputs for linear support vector regression (Lin-SVR) models for S and Se and the multilayer perceptron model (MLP) for Se were consistent with known mechanisms reported in literature. Other models exhibited overfitting even when differences in training and testing performance were low or non-existent. Furthermore, our results highlight that similarly performing models based on RMSE or R2 can lead to drastically different predictions and conclusions, thus highlighting the need to interrogate machine learning models and to ensure they are consistent with known mechanisms reported in the literature. Both elements exhibited similar spatial patterns with predicted gains in Scandinavia versus losses in the central and Mediterranean regions of Europe, respectively, by the end of the 21st century for an extreme climate scenario. The median change was -5.5% for S (Lin-SVR) and -3.5% (MLP) and -4.0% (Lin-SVR) for Se. For both elements, modeled losses were driven by decreases in soil organic carbon, S and Se atmospheric deposition, and gains were driven by increases in evapotranspiration.
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Affiliation(s)
- Gerrad D Jones
- Department of Biological & Ecological Engineering, Oregon State University, Corvallis, Oregon, 97331, USA.
| | - Logan Insinga
- Department of Biological & Ecological Engineering, Oregon State University, Corvallis, Oregon, 97331, USA.
| | - Boris Droz
- Department of Biological & Ecological Engineering, Oregon State University, Corvallis, Oregon, 97331, USA.
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
- Water and Environment Research Group, Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
| | - Aryeh Feinberg
- Institute for Data, Systems, and Society, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrea Stenke
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Jo Smith
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Pete Smith
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Lenny H E Winkel
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
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3
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Gatpatan IGT, Cabulong RB, Sadaba RB. Diversity and Screening of Cellulolytic Microorganisms from Mangrove Forests, Natural Parks, Paddy Field, and Sugarcane Plantation in Panay Island, Philippines. Int J Microbiol 2024; 2024:5573158. [PMID: 39081934 PMCID: PMC11288694 DOI: 10.1155/2024/5573158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 05/12/2024] [Accepted: 06/10/2024] [Indexed: 08/02/2024] Open
Abstract
Cellulolytic microorganisms secrete cellulase, which plays a crucial role in the conversion of lignocellulosic biomass into value-added products with diverse applications in industries, such as biofuel, healthcare, and agriculture. As the world transitions to a bioenergy future, cellulase demand is likely to expand. However, the high cost and low catalytic activity of cellulase hinder the commercialization of biorefineries. Searching for cellulase-producing microorganisms in different environments through bioprospecting can aid in broadening the range of cellulases that are currently available. Meanwhile, the cellulolytic activity of marine microorganisms remains largely unexplored, making it difficult to compare the cellulolytic activity of terrestrial and marine environments. Thus, this study aimed to investigate the diversity and activity of culturable cellulolytic microorganisms in four terrestrial and three marine sites within Panay Island, Philippines. The results showed that the cellulolytic microbial load was tenfold higher in the terrestrial sites than in the marine sites, possibly due to the dynamic mangrove environment. Out of the 42 isolates with a high cellulolytic index (CI) of ≥3.0, 36 were from terrestrial and 6 from marine habitats. The CMCase, Avicelase, and FPase activities were then tested on the 18 isolates with the highest CI. It was observed that many isolates had a high CI, but few exhibited high enzyme activities. Marine isolates showed higher CMCase and Avicelase activities, with comparable FPase activity to their terrestrial counterparts. Isolates S1ACP6B from a sugarcane field and MS1OMP2A from a mangrove site exhibited the highest cellulase activities at 0.41 and 0.29 U/mg, respectively, and were identified as Enterobacter roggenkampii and Rhodococcus erythropolis, respectively. Among the 18 identified isolates, three are resistant to chloramphenicol and three isolates are potentially new species of Halomonas sp. MS1ACP1B, Albirhodobacter sp. MP2ACP3B, and Saccharomycetaceae sp. B1CZP10A. Overall, this study provides an insight on the composition of cellulolytic microbial load and their activities among various habitats.
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Affiliation(s)
- Isabel Grace T. Gatpatan
- Division of Biological SciencesCollege of Arts and SciencesUniversity of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
| | - Rhudith B. Cabulong
- Division of Biological SciencesCollege of Arts and SciencesUniversity of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
| | - Resurreccion B. Sadaba
- Division of Biological SciencesCollege of Arts and SciencesUniversity of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
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4
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Mendonca C, Zhang L, Waldbauer JR, Aristilde L. Disproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11041-11052. [PMID: 38860668 PMCID: PMC11210201 DOI: 10.1021/acs.est.4c01328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024]
Abstract
Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide (CO2) budget. Partitioning of organic carbons into biomass relative to CO2 efflux, termed carbon-use efficiency (CUE), is widely used to characterize organic carbon cycling by soil microorganisms. Recent studies challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in Pseudomonas putida, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our 13C-metabolomics data captured substrate carbons into different metabolic pathways: cellulose-derived sugar carbons in glycolytic and pentose-phosphate pathways; lignin-related aromatic carbons in the tricarboxylic acid cycle. Subsequent 13C-metabolic flux analysis revealed a 3-fold lower investment of sugar carbons in CO2 efflux compared to aromatic carbons, in agreement with reported substrate-dependent CUE. Proteomics analysis revealed enzyme-level regulation only for substrate uptake and initial catabolism, which dictated downstream fluxes through CO2-producing versus biomass-synthesizing reactions. Metabolic partitioning as shown here explained the substrate-dependent CUE calculated from reported metabolic flux analyses of other bacteria, further supporting a metabolism-guided perspective for predicting the microbial conversion of accessible organic matter to CO2 efflux.
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Affiliation(s)
- Caroll
M. Mendonca
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Lichun Zhang
- Department
of the Geophysical Sciences, University
of Chicago, Chicago, Illinois 60637, United States
| | - Jacob R. Waldbauer
- Department
of the Geophysical Sciences, University
of Chicago, Chicago, Illinois 60637, United States
| | - Ludmilla Aristilde
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
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5
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Christel H, Bruelheide H, Cesarz S, Eisenhauer N, Hähn GJA, Beugnon R. The spatial distribution of tree-tree interaction effects on soil microbial biomass and respiration. Ecol Evol 2024; 14:e11530. [PMID: 38895566 PMCID: PMC11183910 DOI: 10.1002/ece3.11530] [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: 02/02/2024] [Revised: 04/05/2024] [Accepted: 05/13/2024] [Indexed: 06/21/2024] Open
Abstract
The capacity of forests to sequester carbon in both above- and belowground compartments is a crucial tool to mitigate rising atmospheric carbon concentrations. Belowground carbon storage in forests is strongly linked to soil microbial communities that are the key drivers of soil heterotrophic respiration, organic matter decomposition and thus nutrient cycling. However, the relationships between tree diversity and soil microbial properties such as biomass and respiration remain unclear with inconsistent findings among studies. It is unknown so far how the spatial configuration and soil depth affect the relationship between tree richness and microbial properties. Here, we studied the spatial distribution of soil microbial properties in the context of a tree diversity experiment by measuring soil microbial biomass and respiration in subtropical forests (BEF-China experiment). We sampled soil cores at two depths at five locations along a spatial transect between the trees in mono- and hetero-specific tree pairs of the native deciduous species Liquidambar formosana and Sapindus saponaria. Our analyses showed decreasing soil microbial biomass and respiration with increasing soil depth and distance from the tree in mono-specific tree pairs. We calculated belowground overyielding of soil microbial biomass and respiration - which is higher microbial biomass or respiration than expected from the monocultures - and analysed the distribution patterns along the transect. We found no general overyielding across all sampling positions and depths. Yet, we encountered a spatial pattern of microbial overyielding with a significant microbial overyielding close to L. formosana trees and microbial underyielding close to S. saponaria trees. We found similar spatial patterns across microbial properties and depths that only differed in the strength of their effects. Our results highlight the importance of small-scale variations of tree-tree interaction effects on soil microbial communities and functions and are calling for better integration of within-plot variability to understand biodiversity-ecosystem functioning relationships.
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Affiliation(s)
- Henriette Christel
- German Center for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology, Leipzig UniversityLeipzigGermany
| | - Helge Bruelheide
- German Center for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle‐WittenbergHalleGermany
| | - Simone Cesarz
- German Center for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology, Leipzig UniversityLeipzigGermany
| | - Nico Eisenhauer
- German Center for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology, Leipzig UniversityLeipzigGermany
| | - Georg J. A. Hähn
- BIOME Lab, Department of Biological, Geological and Environmental Sciences (BiGeA)Alma Mater Studiorum University of BolognaBolognaItaly
| | - Rémy Beugnon
- German Center for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute for Meteorology, Leipzig UniversityLeipzigGermany
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellier Cedex 5France
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6
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Zampolli J, De Giani A, Rossi M, Finazzi M, Di Gennaro P. Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas. Front Microbiol 2024; 15:1380953. [PMID: 38863750 PMCID: PMC11165352 DOI: 10.3389/fmicb.2024.1380953] [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: 02/02/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.
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Affiliation(s)
| | | | | | | | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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7
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Hassan A, Hamid FS, Pariatamby A, Ossai IC, Ahmed A, Barasarathi J, Auta HS. Influence of bioaugmented fungi on tolerance, growth and phytoremediation ability of Prosopis juliflora Sw. DC in heavy metal-polluted landfill soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:28671-28694. [PMID: 38561536 DOI: 10.1007/s11356-024-33018-1] [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: 09/19/2023] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
The research aimed to determine the influence of endophytic fungi on tolerance, growth and phytoremediation ability of Prosopis juliflora in heavy metal-polluted landfill soil. A consortium of 13 fungal isolates as well as Prosopis juliflora Sw. DC was used to decontaminate heavy metal-polluted landfill soil. Enhanced plant growth (biomass and root and shoot lengths) and production of carotenoids, chlorophyll and amino acids L-phenylalanine and L-leucine that are known to enhance growth were found in the treated P. juliflora. Better accumulations of heavy metals were observed in fungi-treated P. juliflora over the untreated one. An upregulated activity of peroxidase, catalase and ascorbate peroxidase was recorded in fungi-treated P. juliflora. Additionally, other metabolites, such as glutathione, 3,5,7,2',5'-pentahydroxyflavone, 5,2'-dihydroxyflavone and 5,7,2',3'-tetrahydroxyflavone, and small peptides, which include Lys Gln Ile, Ser Arg Ala, Asp Arg Gly, Arg Ser Ser, His His Arg, Arg Thr Glu, Thr Arg Asp and Ser Pro Arg, were also detected. These provide defence supports to P. juliflora against toxic metals. Inoculating the plant with the fungi improved its growth, metal accumulation as well as tolerance against heavy metal toxicity. Such a combination can be used as an effective strategy for the bioremediation of metal-polluted soil.
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Affiliation(s)
- Auwalu Hassan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Center for Research in Waste Management, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Biological Sciences, Faculty of Science, Federal University of Kashere, Kashere, Gombe State, Nigeria.
| | - Fauziah Shahul Hamid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Center for Research in Waste Management, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Agamuthu Pariatamby
- Jeffrey Sachs Center On Sustainable Development, Sunway University, Sunway, Malaysia
| | - Innocent Chukwunonso Ossai
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Center for Research in Waste Management, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Aziz Ahmed
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Center for Research in Waste Management, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Faculty of Marine Sciences, Lasbela University of Agriculture, Water and Marine Sciences, Uthal, Balochistan, Pakistan
| | - Jayanthi Barasarathi
- Faculty of Health and Life Sciences (FHLS), INTI International University, Pesiaran Perdana BBN, Nilai, Negeri Sambilan, Malaysia
| | - Helen Shnada Auta
- Department of Microbiology, Federal University of Technology, Minna, Niger State, Nigeria
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Hassett E, Bohrer G, Kinsman-Costello L, Onyango Y, Pope T, Smith C, Missik J, Eberhard E, Villa J, McMurray SE, Morin T. Changes in inundation drive carbon dioxide and methane fluxes in a temperate wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170089. [PMID: 38224896 DOI: 10.1016/j.scitotenv.2024.170089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/18/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024]
Abstract
Wetlands cycle carbon by being net sinks for carbon dioxide (CO2) and net sources of methane (CH4). Daily and seasonal temporal patterns, dissolved oxygen (DO) availability, inundation status (flooded or dry/partially flooded), water depth, and vegetation can affect the magnitude of carbon uptake or emissions, but the extent and interactive effects of these variables on carbon gas fluxes are poorly understood. We characterized the linkages between carbon fluxes and these environmental and temporal drivers at the Old Woman Creek National Estuarine Research Reserve (OWC), OH. We measured diurnal gas flux patterns in an upstream side channel (called the cove) using chamber measurements at six sites (three vegetated and three non-vegetated). We sampled hourly from 7 AM to 7 PM and monthly from July to October 2022. DO concentrations and water levels were measured monthly. Water inundation status had the most influential effect on carbon fluxes with flooded conditions supporting higher CH4 fluxes (0.39 μmol CH4 m-2 s-1; -1.23 μmol CO2 m-2 s-1) and drier conditions supporting higher CO2 fluxes (0.03 μmol CH4 m-2 s-1; 0.86 μmol CO2 m-2 s-1). When flooded, the wetland was a net CO2 sink; however, it became a source for both CH4 and CO2 when water levels were low. We compared chamber-based gas fluxes from the cove in flooded (July) and dry (August) months to fluxes measured with an eddy covariance tower whose footprint covers flooded portions of the wetland. The diurnal pattern of carbon fluxes at the tower did not vary with changing water levels but remained a CO2 sink and a CH4 source even when the cove where we performed the chamber measurements dried out. These results emphasize the role of inundation status on wetland carbon cycling and highlight the importance of fluctuating hydrologic patterns, especially hydrologic drawdowns, under changing climatic conditions.
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Affiliation(s)
- Erin Hassett
- SUNY College of Environmental Science and Forestry, Syracuse, NY, United States of America.
| | - Gil Bohrer
- Ohio State University, Columbus, OH, United States of America
| | | | - Yvette Onyango
- Ohio State University, Columbus, OH, United States of America
| | - Talia Pope
- Kent State University, Akron, OH, United States of America
| | - Chelsea Smith
- Kent State University, Akron, OH, United States of America
| | - Justine Missik
- Ohio State University, Columbus, OH, United States of America
| | - Erin Eberhard
- Kent State University, Akron, OH, United States of America
| | - Jorge Villa
- University of Louisiana at Lafayette, Lafayette, LA, United States of America
| | | | - Tim Morin
- SUNY College of Environmental Science and Forestry, Syracuse, NY, United States of America
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9
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Liu Z, Shao Y, Cui Q, Ye X, Huang Z. 'Fertile island' effects on the soil microbial community beneath the canopy of Tetraena mongolica, an endangered and dominant shrub in the West Ordos Desert, North China. BMC PLANT BIOLOGY 2024; 24:178. [PMID: 38454326 PMCID: PMC10921620 DOI: 10.1186/s12870-024-04873-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND The fertile islands formed by shrubs are major drivers of the structure and function of desert ecosystems, affecting seedling establishment, plant-plant interactions, the diversity and productivity of plant communities, and microbial activity/diversity. Although an increasing number of studies have shown the critical importance of soil microbes in fertile island formation, how soil microbial community structure and function are affected by the different fertile island effect intensities is still unknown. As an endangered and dominant shrub species in the West Ordos Desert, Tetraena mongolica was selected for further exploration of its fertile island effect on the soil microbial community in the present study to test the following two hypotheses: (1) T. mongolica shrubs with different canopy sizes exert fertile island effects of different strengths; (2) the soil microbial community structure and function beneath the T. mongolica canopy are affected by the fertile island, and the strength of these effects varies depending on the shrub canopy size. RESULTS The contents of soil total nitrogen (TN) and available phosphorus (AVP) were significantly greater beneath T. mongolica shrub canopy than outside the shrub canopy. With increasing shrub canopy size, the enrichment of soil TN and AVP increased, indicating a stronger fertile island effect. The structure and function of soil microbial communities, including fungal, archaeal and bacterial communities, are affected by the fertile island effect. An increase in canopy size increased the relative abundance of Ascomycota (Fungi) and Thaumarchaeota (Archaea). For the soil microbial functional groups, the relative abundance of endophytes in the fungal functional groups; steroid hormone biosynthesis, sphingolipid metabolism, and steroid biosynthesis genes in the bacterial functional groups; and nonhomologous end-joining and bisphenol degradation functional genes in the archaeal functional groups increased significantly with increasing T. mongolica canopy size. CONCLUSIONS These results revealed that T. mongolica had a fertile island effect, which affected the soil microbial community structure and functions, and that the fertile island effect might increase with increasing shrub canopy size. The fertile island effect may strengthen the interaction between T. mongolica shrubs and microbes, which may be beneficial to the growth and maintenance of T. mongolica.
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Affiliation(s)
- Zhangkai Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Science, Beijng, 100093, China
- University of Chinese Academy of Science, Beijng, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yuying Shao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Science, Beijng, 100093, China
- University of Chinese Academy of Science, Beijng, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Qingguo Cui
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Science, Beijng, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Xuehua Ye
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Science, Beijng, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
| | - Zhenying Huang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Science, Beijng, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
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10
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Kilner CL, Carrell AA, Wieczynski DJ, Votzke S, DeWitt K, Yammine A, Shaw J, Pelletier DA, Weston DJ, Gibert JP. Temperature and CO 2 interactively drive shifts in the compositional and functional structure of peatland protist communities. GLOBAL CHANGE BIOLOGY 2024; 30:e17203. [PMID: 38433341 DOI: 10.1111/gcb.17203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024]
Abstract
Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2 levels could alter the structure and function of peatland microbial food webs-a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.
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Affiliation(s)
- Christopher L Kilner
- Department of Biology, Duke University, Durham, North Carolina, USA
- Bird Conservancy of the Rockies, Fort Collins, Colorado, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Samantha Votzke
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Katrina DeWitt
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Andrea Yammine
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jean P Gibert
- Department of Biology, Duke University, Durham, North Carolina, USA
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11
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Alvarez-Aponte ZI, Govindaraju AM, Hallberg ZF, Nicolas AM, Green MA, Mok KC, Fonseca-García C, Coleman-Derr D, Brodie EL, Carlson HK, Taga ME. Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates. THE ISME JOURNAL 2024; 18:wrae068. [PMID: 38648288 PMCID: PMC11287214 DOI: 10.1093/ismejo/wrae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/15/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids-the vitamin B12 family of cofactors-are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.
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Affiliation(s)
- Zoila I Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alekhya M Govindaraju
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alexa M Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Myka A Green
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Citlali Fonseca-García
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, United States
| | - Devin Coleman-Derr
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Hans K Carlson
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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12
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Muscatt G, Cook R, Millard A, Bending GD, Jameson E. Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile. mBio 2023; 14:e0224623. [PMID: 38032184 PMCID: PMC10746233 DOI: 10.1128/mbio.02246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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13
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Siebert J, Sünnemann M, Hautier Y, Risch AC, Bakker JD, Biederman L, Blumenthal DM, Borer ET, Bugalho MN, Broadbent AAD, Caldeira MC, Cleland E, Davies KF, Eskelinen A, Hagenah N, Knops JMH, MacDougall AS, McCulley RL, Moore JL, Power SA, Price JN, Seabloom EW, Standish R, Stevens CJ, Zimmermann S, Eisenhauer N. Drivers of soil microbial and detritivore activity across global grasslands. Commun Biol 2023; 6:1220. [PMID: 38040868 PMCID: PMC10692199 DOI: 10.1038/s42003-023-05607-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023] Open
Abstract
Covering approximately 40% of land surfaces, grasslands provide critical ecosystem services that rely on soil organisms. However, the global determinants of soil biodiversity and functioning remain underexplored. In this study, we investigate the drivers of soil microbial and detritivore activity in grasslands across a wide range of climatic conditions on five continents. We apply standardized treatments of nutrient addition and herbivore reduction, allowing us to disentangle the regional and local drivers of soil organism activity. We use structural equation modeling to assess the direct and indirect effects of local and regional drivers on soil biological activities. Microbial and detritivore activities are positively correlated across global grasslands. These correlations are shaped more by global climatic factors than by local treatments, with annual precipitation and soil water content explaining the majority of the variation. Nutrient addition tends to reduce microbial activity by enhancing plant growth, while herbivore reduction typically increases microbial and detritivore activity through increased soil moisture. Our findings emphasize soil moisture as a key driver of soil biological activity, highlighting the potential impacts of climate change, altered grazing pressure, and eutrophication on nutrient cycling and decomposition within grassland ecosystems.
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Affiliation(s)
- Julia Siebert
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
| | - Marie Sünnemann
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany.
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany.
| | - Yann Hautier
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Anita C Risch
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Community Ecology, Zuercherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Jonathan D Bakker
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Lori Biederman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50010, USA
| | - Dana M Blumenthal
- USDA-ARS Rangeland Resources & Systems Research Unit, Fort Collins, CO, 80526, USA
| | - Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior; University of Minnesota, St. Paul, MN, 55108, USA
| | - Miguel N Bugalho
- Centre for Applied Ecology "Prof. Baeta Neves", School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Arthur A D Broadbent
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Maria C Caldeira
- Forest Research Centre, School of Agriculture, University of Lisbon, Lisbon, Portugal
| | - Elsa Cleland
- Ecology, Behavior and Evolution Section, University of California San Diego, 9500 Gilman Dr. #0116, La Jolla, California, 92093-0116, USA
| | - Kendi F Davies
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Anu Eskelinen
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
- Ecology and Genetics Unit, University of Oulu, P.O. Box 8000, FI-90014 University of Oulu, Oulu, Finland
- Helmholtz Center for Environmental Research - UFZ, Department of Physiological Diversity, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Nicole Hagenah
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Johannes M H Knops
- Health & Environmental Sciences Department, Xi'an Jiatong-Liverpool University, Suzhou, China
| | - Andrew S MacDougall
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Rebecca L McCulley
- Department of Plant & Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Joslin L Moore
- Arthur Rylah Institute for Environmental Research, 123 Brown Street, Heidelberg, VIC, 3084, Australia
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Clayton, VIC, 3800, Australia
| | - Sally A Power
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Jodi N Price
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Albury, NSW, 2640, Australia
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior; University of Minnesota, St. Paul, MN, 55108, USA
| | - Rachel Standish
- Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Carly J Stevens
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Stephan Zimmermann
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Forest Soils and Biogeochemistry, Zuercherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
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14
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Xia H, Zhang T, Li X, He T, Wang X, Zhang J, Zhang K. Effects of drought and nutrient deficiencies on the allocation of recently fixed carbon in a plant-soil-microbe system. TREE PHYSIOLOGY 2023; 43:1903-1916. [PMID: 37584459 DOI: 10.1093/treephys/tpad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/18/2023] [Accepted: 08/08/2023] [Indexed: 08/17/2023]
Abstract
Carbon (C) allocation plays an important role in plant adaptation to water and nutrient stresses. However, the effects of drought and nutrient deficiencies on the allocation of recently fixed C in the plant-soil-microbe system remain largely unknown. Herein, we studied the response of C allocation of Sophora moorcroftiana (an indigenous pioneer shrub in Tibet) to drought, nitrogen (N) deficiency and phosphorus (P) deficiency using a microcosm experiment. The 13CO2 continuous labeling was used to trace C allocation in the plant-soil-microbe system. We found that drought significantly reduced plant 13C, but it increased 13C accumulation in soil. The decreased plant 13C under drought was attributed to the decrease of 13C in stem and root rather than that in leaf. The excess 13C fraction in the microbial biomass (MB13C) was reduced by N deficiency, but it was not affected by the combination of drought and N deficiency, indicating that drought weakened the effects of N deficiency on MB13C. By contrast, MB13C increased under the combination of drought and P deficiency, suggesting that drought enhanced the effects of P deficiency on MB13C. Drought and nutrient deficiencies regulated the belowground 13C allocation. Specifically, drought and P deficiency increased the allocation of 13C to root and N deficiency regulated the allocation of 13C to microbial biomass C and dissolved organic C in soil. Notably, soil 13C decreased with increasing plant 13C, while MB13C first decreased and then increased with increasing plant 13C. Overall, our study demonstrated that drought and nutrient deficiencies interactively affected C allocation in a plant-soil-microbe system and provided insights into C allocation strategies in response to multiple resource (water and nutrient) stresses under environmental changes.
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Affiliation(s)
- Huijuan Xia
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, No. 201 Jiufeng 1 Road, East Lake High-Tech Development Zone, Wuhan 430074, P.R. China
| | - Tiantian Zhang
- College of Science, Tibet University, No. 10 Zangda East Road, Chengguan District, Lhasa 850000, P.R. China
| | - Xinshuai Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, No. 201 Jiufeng 1 Road, East Lake High-Tech Development Zone, Wuhan 430074, P.R. China
| | - Tiehu He
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, No. 201 Jiufeng 1 Road, East Lake High-Tech Development Zone, Wuhan 430074, P.R. China
| | - Xia Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, No. 201 Jiufeng 1 Road, East Lake High-Tech Development Zone, Wuhan 430074, P.R. China
| | - Jiehao Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, No. 201 Jiufeng 1 Road, East Lake High-Tech Development Zone, Wuhan 430074, P.R. China
| | - Kerong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, No. 201 Jiufeng 1 Road, East Lake High-Tech Development Zone, Wuhan 430074, P.R. China
- College of Science, Tibet University, No. 10 Zangda East Road, Chengguan District, Lhasa 850000, P.R. China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, No. 201 Jiufeng 1 Road, East Lake High-Tech Development Zone, Wuhan 430074, P.R. China
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15
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Kumari A, Dash M, Singh SK, Jagadesh M, Mathpal B, Mishra PK, Pandey SK, Verma KK. Soil microbes: a natural solution for mitigating the impact of climate change. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1436. [PMID: 37940796 DOI: 10.1007/s10661-023-11988-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023]
Abstract
Soil microbes are microscopic organisms that inhabit the soil and play a significant role in various ecological processes. They are essential for nutrient cycling, carbon sequestration, and maintaining soil health. Importantly, soil microbes have the potential to sequester carbon dioxide (CO2) from the atmosphere through processes like carbon fixation and storage in organic matter. Unlocking the potential of microbial-driven carbon storage holds the key to revolutionizing climate-smart agricultural practices, paving the way for sustainable productivity and environmental conservation. A fascinating tale of nature's unsung heroes is revealed by delving into the realm of soil microbes. The guardians of the Earth are these tiny creatures that live beneath our feet and discreetly work their magic to fend off the effects of climate change. These microbes are also essential for plant growth enhancement through their roles in nutrient uptake, nitrogen fixation, and synthesis of growth-promoting chemicals. By understanding and managing soil microbial communities, it is possible to improve soil health, soil water-holding capacity, and promote plant growth in agricultural and natural ecosystems. Added to it, these microbes play an important role in biodegradation, bioremediation of heavy metals, and phytoremediation, which in turn helps in treating the contaminated soils. Unfortunately, climate change events affect the diversity, composition, and metabolism of these microbes. Unlocking the microbial potential demands an interdisciplinary endeavor spanning microbiology, ecology, agronomy, and climate science. It is a call to arms for the scientific community to recognize soil microbes as invaluable partners in the fight against climate change. By implementing data-driven land management strategies and pioneering interventions, we possess the means to harness their capabilities, paving the way for climate mitigation, sustainable agriculture, and promote ecosystem resilience in the imminent future.
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Affiliation(s)
- Aradhna Kumari
- College of Agriculture, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Ganj Basoda, Vidisha, Madhya Pradesh, 464221, India
| | - Munmun Dash
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
| | - Santosh Kumar Singh
- Dr Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India.
| | - M Jagadesh
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
| | - Bhupendra Mathpal
- School of Agriculture, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - P K Mishra
- College of Agriculture, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Ganj Basoda, Vidisha, Madhya Pradesh, 464221, India
| | - Sunil Kumar Pandey
- College of Agriculture, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Narmadapuram, Madhya Pradesh, 461110, India
| | - Krishan K Verma
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China.
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16
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Wang S, Heal KV, Zhang Q, Yu Y, Tigabu M, Huang S, Zhou C. Soil microbial community, dissolved organic matter and nutrient cycling interactions change along an elevation gradient in subtropical China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118793. [PMID: 37619380 DOI: 10.1016/j.jenvman.2023.118793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/27/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
To identify possible dominating processes involved in soil microbial community assembly, dissolved organic matter (DOM) and multi-nutrient cycling (MNC) interactions and contribute to understanding of climate change effects on these important cycles, we investigated the interaction of soil chemistry, DOM components and microbial communities in five vegetation zones - ranging from evergreen broad-leaved forest to alpine meadow - along an elevation gradient of 290-1960 m in the Wuyi Mountains, Fujian Province, China. Soil DOM composition and microbial community assembly were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and Illumina MiSeq high-throughput sequencing, respectively. Sloan's neutral model and the modified stochasticity ratio were used to infer community assembly processes. Key microbial drivers of the soil MNC index were identified from partial least squares path models. Our results showed that soil DOM composition is closely related to the vegetation types along an elevation gradient, the structure and composition of the microbial community, and soil nutrient status. Overall, values of the double bond equivalent (DBE), modified aromaticity index (AImod) increased, and H/C ratio and molecular lability boundary (MLBL) percentage decreased with elevation. Lignins/CRAM-like structures compounds dominated soil DOM in each vegetation type and its relative abundance decreased with elevation. Aliphatic/protein and lipids components also decreased, but the relative abundance of aromatic structures and tannin increased with elevation. The alpha diversity index of soil bacteria gradually decreased with elevation, with deterministic processes dominating the microbial community assembly in the highest elevation zone. Bacterial communities were conducive to the decomposition of labile degradable DOM compounds (H/C ≥ 1.5) at low elevation. In the cooler and wetter conditions at higher-elevation sites the relative abundance of potentially resistant soil DOM components (H/C < 1.5) gradually increased. Microbial community diversity and composition were important predictors of potential soil nutrient cycling. Although higher elevation sites have higher nutrient cycling potential, soil DOM was assessed to be a more stable carbon store, with apparent lower lability and bioavailability than at lower elevation sites. Overall, this study increases understanding of the potential linkage between soil microbial community, multiple nutrient cycling and DOM fate in subtropical mountain ecosystems that can help predict the effect of climate change on soil carbon sequestration and thus inform ecosystem management.
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Affiliation(s)
- Shuzhen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China; Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Kate V Heal
- School of GeoSciences, The University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Qin Zhang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Yuanchun Yu
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
| | - Mulualem Tigabu
- Swedish University of Agricultural Sciences, Faculty of Forest Science, Southern Swedish Forest Research Centre, P.O. Box 190, SE-234 22, Lomma, Sweden
| | - Shide Huang
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354315, Fujian Province, China
| | - Chuifan Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China; Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.
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17
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Raza T, Qadir MF, Khan KS, Eash NS, Yousuf M, Chatterjee S, Manzoor R, Rehman SU, Oetting JN. Unrevealing the potential of microbes in decomposition of organic matter and release of carbon in the ecosystem. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118529. [PMID: 37418912 DOI: 10.1016/j.jenvman.2023.118529] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/25/2023] [Indexed: 07/09/2023]
Abstract
Organic matter decomposition is a biochemical process with consequences affecting climate change and ecosystem productivity. Once decomposition begins, C is lost as CO2 or sequestered into more recalcitrant carbon difficult to further degradation. As microbial respiration releases carbon dioxide into the atmosphere, microbes act as gatekeepers in the whole process. Microbial activities were found to be the second largest CO2 emission source in the environment after human activities (industrialization), and research investigations suggest that this may have affected climate change over the past few decades. It is crucial to note that microbes are major contributors in the whole C cycle (decomposition, transformation, and stabilization). Therefore, imbalances in the C cycle might be causing changes in the entire carbon content of the ecosystem. The significance of microbes, especially soil bacteria in the terrestrial carbon cycle requires more attention. This review focuses on the factors that affect microorganism behavior during the breakdown of organic materials. The key factors affecting the microbial degradation processes are the quality of the input material, nitrogen, temperature, and moisture content. In this review, we suggest that to address global climate change and its effects on agricultural systems and vice versa, there is a need to double-up on efforts and conduct new research studies to further evaluate the potential of microbial communities to reduce their contribution to terrestrial carbon emission.
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Affiliation(s)
- Taqi Raza
- The Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, USA.
| | - Muhammad Farhan Qadir
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad 38040, Pakistan
| | - Khuram Shehzad Khan
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Neal S Eash
- The Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, USA
| | - Muhammad Yousuf
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad 38040, Pakistan
| | - Sumanta Chatterjee
- USDA ARS, Hydrology and Remote Sensing Laboratory, 10300 Baltimore Avenue, Beltsville, MD 20705, USA; ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Rabia Manzoor
- Land Resources Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Sana Ur Rehman
- National Research Center of Intercropping, The Islamia University of Bahawalpur, Pakistan
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18
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Li C, Wu Y, Li L, Zhao C, Li B, Wu Y, Wang H, Yan Z. Different techniques reveal the difference of community structure and function of fungi from root and rhizosphere of Salvia miltiorrhiza Bunge. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:848-859. [PMID: 37394812 DOI: 10.1111/plb.13556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/23/2023] [Indexed: 07/04/2023]
Abstract
Fungi have essential functions in plant health and performance. However, the plant-associated functions of many cultured fungi have not been established in detail. Here, the fungal species diversity in Salvia miltiorrhiza roots and rhizosphere was assessed for the first time using culturomics and high-throughput sequencing. We present a comprehensive functional metagenomic analysis of these fungi and verified activity of cellulase and chitinase predicted in the metagenomic analysis. We first collected and cultured fungi from the root and rhizosphere of S. miltiorrhiza. We found 92 species across 37 families and five phyla, with Ascomycota being dominant. Many rDNA internal transcribed spacer sequences could not be assigned to lower taxonomic levels. There were 19 genera of endophytic fungi and 37 genera of rhizosphere fungi. The culturomics approach had lower taxonomic diversity than high-throughput sequencing, but some fungi were only found in cultures. Structural analyses indicated that the dominant species differed in cultured and non-cultured samples at other levels, apart from the phylum level. Functional analysis mapped 223 carbohydrate enzyme families and 393 pathways in the CAZy and KEGG databases, respectively. The most abundant families were glycoside hydrolases and those involved in carbohydrate metabolism. As predicted by metagenomics, we experimentally verified cellulase and chitinase activity for 29 and 74 fungi, respectively. We provide the first evidence of biomass recycling by fungi that are associated with plants. Culturing is essential to reveal the hidden microbial community and critical functions in plant-microbe interactions.
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Affiliation(s)
- C Li
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Y Wu
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - L Li
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - C Zhao
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - B Li
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Y Wu
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - H Wang
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Z Yan
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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19
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Li H, Lu Z, Hao MS, Kvammen A, Inman AR, Srivastava V, Bulone V, McKee LS. Family 92 carbohydrate-binding modules specific for β-1,6-glucans increase the thermostability of a bacterial chitinase. Biochimie 2023; 212:153-160. [PMID: 37121306 DOI: 10.1016/j.biochi.2023.04.019] [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: 02/15/2023] [Revised: 03/30/2023] [Accepted: 04/28/2023] [Indexed: 05/02/2023]
Abstract
In biomass-processing industries there is a need for enzymes that can withstand high temperatures. Extensive research efforts have been dedicated to finding new thermostable enzymes as well as developing new means of stabilising existing enzymes. The attachment of a stable non-catalytic domain to an enzyme can, in some instances, protect a biocatalyst from thermal denaturation. Carbohydrate-binding modules (CBMs) are non-catalytic domains typically found appended to biomass-degrading or modifying enzymes, such as glycoside hydrolases (GHs). Most often, CBMs interact with the same polysaccharide as their enzyme partners, leading to an enhanced reaction rate via the promotion of enzyme-substrate interactions. Contradictory to this general concept, we show an example of a chitin-degrading enzyme from GH family 18 that is appended to two CBM domains from family 92, both of which bind preferentially to the non-substrate polysaccharide β-1,6-glucan. During chitin hydrolysis, the CBMs do not contribute to enzyme-substrate interactions but instead confer a 10-15 °C increase in enzyme thermal stability. We propose that CBM92 domains may have a natural enzyme stabilisation role in some cases, which may be relevant to enzyme design for high-temperature applications in biorefinery.
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Affiliation(s)
- He Li
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Zijia Lu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Meng-Shu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Alma Kvammen
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden; College of Medicine & Public Health, Flinders University, Bedford Park Campus, Sturt Road, SA, 5042, Australia
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden; Wallenberg Wood Science Center, Teknikringen 56-58, 100 44, Stockholm, Sweden.
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20
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Cárdenas Pardo NJ, Rodriguez Robayo DE, Fernandez Lizarazo JC, Peña-Quemba DC, McGale E. Exploring the future of GM technology in sustainable local food systems in Colombia. Front Genome Ed 2023; 5:1181811. [PMID: 37457887 PMCID: PMC10349173 DOI: 10.3389/fgeed.2023.1181811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
The security of Earth's food systems is challenged by shifting regional climates. While agricultural processes are disrupted by climate change, they also play a large role in contributing to destabilizing greenhouse gases. Finding new strategies to increase yields while decreasing agricultural environmental impacts is essential. Tropical agriculture is particularly susceptible to climate change: local, smallholder farming, which provides a majority of the food supply, is high risk and has limited adaptation capacity. Rapid, inexpensive, intuitive solutions are needed, like the implementation of genetically modified (GM) crops. In the Latin American tropics, high awareness and acceptance of GM technologies, opportunities to test GM crops as part of local agricultural educations, and their known economic benefits, support their use. However, this is not all that is needed for the future of GM technologies in these areas: GM implementation must also consider environmental and social sustainability, which can be unique to a locality. Primarily from the perspective of its educators, the potential of a rural Colombian university in driving GM implementation is explored, including the role of this type of university in producing agricultural engineers who can innovate with GM to meet regionally-dependent environmental and cultural needs that could increase their sustainability.
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Affiliation(s)
| | | | | | - Diego Camilo Peña-Quemba
- Utopía, Universidad de La Salle, Yopal, Colombia
- Faculty of Natural Sciences and Engineering, Fundación Universitaria de San Gil, UNISANGIL, Yopal, Colombia
| | - Erica McGale
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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21
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Koehle AP, Brumwell SL, Seto EP, Lynch AM, Urbaniak C. Microbial applications for sustainable space exploration beyond low Earth orbit. NPJ Microgravity 2023; 9:47. [PMID: 37344487 DOI: 10.1038/s41526-023-00285-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Abstract
With the construction of the International Space Station, humans have been continuously living and working in space for 22 years. Microbial studies in space and other extreme environments on Earth have shown the ability for bacteria and fungi to adapt and change compared to "normal" conditions. Some of these changes, like biofilm formation, can impact astronaut health and spacecraft integrity in a negative way, while others, such as a propensity for plastic degradation, can promote self-sufficiency and sustainability in space. With the next era of space exploration upon us, which will see crewed missions to the Moon and Mars in the next 10 years, incorporating microbiology research into planning, decision-making, and mission design will be paramount to ensuring success of these long-duration missions. These can include astronaut microbiome studies to protect against infections, immune system dysfunction and bone deterioration, or biological in situ resource utilization (bISRU) studies that incorporate microbes to act as radiation shields, create electricity and establish robust plant habitats for fresh food and recycling of waste. In this review, information will be presented on the beneficial use of microbes in bioregenerative life support systems, their applicability to bISRU, and their capability to be genetically engineered for biotechnological space applications. In addition, we discuss the negative effect microbes and microbial communities may have on long-duration space travel and provide mitigation strategies to reduce their impact. Utilizing the benefits of microbes, while understanding their limitations, will help us explore deeper into space and develop sustainable human habitats on the Moon, Mars and beyond.
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Affiliation(s)
- Allison P Koehle
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
| | - Stephanie L Brumwell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada
| | | | - Anne M Lynch
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Camilla Urbaniak
- ZIN Technologies Inc, Middleburg Heights, OH, USA.
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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22
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He S, Maiti K, Ghaisas N, Upreti K, Rivera-Monroy VH. Potential methane production in oligohaline wetlands undergoing erosion and accretion in the Mississippi River Delta Plain, Louisiana, USA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162685. [PMID: 36894099 DOI: 10.1016/j.scitotenv.2023.162685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Methane (CH4) is steadily increasing in the atmosphere from different sources including wetlands. However, there is limited landscape level CH4 flux data in deltaic coastal systems where the availability of freshwater is impacted by the combined effect of climate change and anthropogenic impacts. Here we determine potential CH4 fluxes in oligohaline wetlands and benthic sediments in the Mississippi River Delta Plain (MRDP), which is undergoing the highest rate of wetland loss and most extensive hydrological wetland restoration in North America. We evaluate potential CH4 fluxes in two contrasting deltaic systems, one undergoing sediment accretion as result of a freshwater and sediment diversions (Wax Lake Delta, WLD), and one experiencing net land loss (Barataria-Lake Cataouatche, BLC). Short- (<4 days) and long-term (36 days) incubations using soil and sediment intact cores and slurries were performed at different temperatures representing seasonal differences (10, 20, 30 °C). Our study revealed that all habitats were net sources of atmospheric CH4 in all seasons, and CH4 fluxes were generally the highest for the 20 °C incubation. The CH4 flux was higher in the marsh habitat of the recently formed delta system (WLD) with total carbon content of 5-24 mg C cm-3 compared to the marsh habitat in BLC, which had high soil carbon content of 67-213 mg C cm-3. This suggests that the quantity of soil organic matter might not be a determining factor in CH4 flux. Overall, benthic habitats were found to have the lowest CH4 fluxes indicating that projected future conversions of marshes to open water in this region will impact the total wetland CH4 emission, although the overall contribution of such conversions to the regional and global carbon budgets is still unknown. Further research is needed to expand the CH4 flux studies by simultaneously using several methods across different wetland habitats.
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Affiliation(s)
- Songjie He
- Department of Oceanography and Coastal Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Kanchan Maiti
- Department of Oceanography and Coastal Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70808, USA.
| | - Neha Ghaisas
- Department of Oceanography and Coastal Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Kiran Upreti
- Department of Oceanography and Coastal Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Victor H Rivera-Monroy
- Department of Oceanography and Coastal Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70808, USA
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23
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Shah ST, Basit A, Mohamed HI, Ullah I, Sajid M, Sohrab A. Der Einsatz von Mulchen bei verschiedenen Bodenbearbeitungsbedingungen reduziert den Ausstoß von Treibhausgasen – ein Überblick. GESUNDE PFLANZEN 2023; 75:455-477. [DOI: 10.1007/s10343-022-00719-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/25/2022] [Indexed: 10/26/2023]
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24
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Mitra D, Panneerselvam P, Senapati A, Chidambaranathan P, Nayak AK, Mohapatra PKD. Arbuscular Mycorrhizal Fungi Response on Soil Phosphorus Utilization and Enzymes Activities in Aerobic Rice under Phosphorus-Deficient Conditions. Life (Basel) 2023; 13:life13051118. [PMID: 37240763 DOI: 10.3390/life13051118] [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: 04/03/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
The prominence of arbuscular mycorrhizal fungi (AMF) in sustainable rice production has long been recognized. However, there is little information about AMF response in aerobic rice cultivation under phosphorus (P)-deficient conditions. The aim of this experiment was to compare and determine the preeminent AMF effects on rice mycorrhizal colonization, responsiveness, P utilization, and different growth-promoting traits under P-deficient conditions. Different AMF genera viz. (Funneliformis sp., Rhizophagus sp., Glomus sp., Acaulospora sp., and Claroideoglomus sp.) in four different aerobic rice varieties developed by ICAR-NRRI, India (CR Dhan 201, CR Dhan 204, CR Dhan 205, and CR Dhan 207) were investigated using the check P-susceptible variety (IR 36) and the P-tolerant variety (Kasalath IC459373). Data analyzed through linear modeling approaches and bivariate associations found that AMF colonization was highly correlated with soil enzymes, particularly fluorescein diacetate (FDA) and plant P uptake. The microbial biomass carbon (MBC) and FDA content were significantly changed among rice varieties treated with AMF compared to uninoculated control. Out of four different rice varieties, CR Dhan 207 inoculated with AMF showed higher plant P uptake compared to other varieties. In all the rice varieties, AMF colonization had higher correlation coefficients with soil enzymes (FDA), MBC, and plant P uptake than uninoculated control. The present study indicates that AMF intervention in aerobic rice cultivation under P-deficient conditions significantly increased plant P uptake, soil enzymes activities and plant growth promotion. Thus, the information gathered from this study will help us to develop a viable AMF package for sustainable aerobic rice cultivation.
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Affiliation(s)
- Debasis Mitra
- Department of Microbiology, Raiganj University, Raiganj 733134, West Bengal, India
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | | | - Ansuman Senapati
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
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25
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Xiang D, Wang G, Tian J, Li W. Global patterns and edaphic-climatic controls of soil carbon decomposition kinetics predicted from incubation experiments. Nat Commun 2023; 14:2171. [PMID: 37061518 PMCID: PMC10105724 DOI: 10.1038/s41467-023-37900-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/03/2023] [Indexed: 04/17/2023] Open
Abstract
Knowledge about global patterns of the decomposition kinetics of distinct soil organic matter (SOM) pools is crucial to robust estimates of land-atmosphere carbon fluxes under climate change. However, the current Earth system models often adopt globally-consistent reference SOM decomposition rates (kref), ignoring effects from edaphic-climate heterogeneity. Here, we compile a comprehensive set of edaphic-climatic and SOM decomposition data from published incubation experiments and employ machine-learning techniques to develop models capable of predicting the expected sizes and kref of multiple SOM pools (fast, slow, and passive). We show that soil texture dominates the turnover of the fast pools, whereas pH predominantly regulates passive SOM decomposition. This suggests that pH-sensitive bacterial decomposers might have larger effects on stable SOM decomposition than previously believed. Using these predictive models, we provide a 1-km resolution global-scale dataset of the sizes and kref of these SOM pools, which may improve global biogeochemical model parameterization and predictions.
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Affiliation(s)
- Daifeng Xiang
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, 430072, China
- Institute for Water-Carbon Cycles and Carbon Neutrality, School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan, 430072, China
| | - Gangsheng Wang
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, 430072, China.
- Institute for Water-Carbon Cycles and Carbon Neutrality, School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan, 430072, China.
| | - Jing Tian
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, 430072, China
- Institute for Water-Carbon Cycles and Carbon Neutrality, School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan, 430072, China
| | - Wanyu Li
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, 430072, China
- Institute for Water-Carbon Cycles and Carbon Neutrality, School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan, 430072, China
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26
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Zhou R, Liu Y, Dungait JAJ, Kumar A, Wang J, Tiemann LK, Zhang F, Kuzyakov Y, Tian J. Microbial necromass in cropland soils: A global meta-analysis of management effects. GLOBAL CHANGE BIOLOGY 2023; 29:1998-2014. [PMID: 36751727 DOI: 10.1111/gcb.16613] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 05/28/2023]
Abstract
Microbial necromass is a large and persistent component of soil organic carbon (SOC), especially under croplands. The effects of cropland management on microbial necromass accumulation and its contribution to SOC have been measured in individual studies but have not yet been summarized on the global scale. We conducted a meta-analysis of 481-paired measurements from cropland soils to examine the management effects on microbial necromass and identify the optimal conditions for its accumulation. Nitrogen fertilization increased total microbial necromass C by 12%, cover crops by 14%, no or reduced tillage (NT/RT) by 20%, manure by 21%, and straw amendment by 21%. Microbial necromass accumulation was independent of biochar addition. NT/RT and straw amendment increased fungal necromass and its contribution to SOC more than bacterial necromass. Manure increased bacterial necromass higher than fungal, leading to decreased ratio of fungal-to-bacterial necromass. Greater microbial necromass increases after straw amendments were common under semi-arid and in cool climates in soils with pH <8, and were proportional to the amount of straw input. In contrast, NT/RT increased microbial necromass mainly under warm and humid climates. Manure application increased microbial necromass irrespective of soil properties and climate. Management effects were especially strong when applied during medium (3-10 years) to long (10+ years) periods to soils with larger initial SOC contents, but were absent in sandy soils. Close positive links between microbial biomass, necromass and SOC indicate the important role of stabilized microbial products for C accrual. Microbial necromass contribution to SOC increment (accumulation efficiency) under NT/RT, cover crops, manure and straw amendment ranged from 45% to 52%, which was 9%-16% larger than under N fertilization. In summary, long-term cropland management increases SOC by enhancing microbial necromass accumulation, and optimizing microbial necromass accumulation and its contribution to SOC sequestration requires site-specific management.
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Affiliation(s)
- Ranran Zhou
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, P.R. China
| | - Yuan Liu
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Jennifer A J Dungait
- Carbon Management Centre, SRUC-Scotland's Rural College, Edinburgh, UK
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Amit Kumar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, UAE
| | - Jinsong Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Lisa K Tiemann
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Fusuo Zhang
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, P.R. China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
| | - Jing Tian
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, P.R. China
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Terra MCNS, Nunes MH, Souza CR, Ferreira GWD, Prado-Junior JAD, Rezende VL, Maciel R, Mantovani V, Rodrigues A, Morais VA, Scolforo JRS, Mello JMD. The inverted forest: Aboveground and notably large belowground carbon stocks and their drivers in Brazilian savannas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161320. [PMID: 36603629 DOI: 10.1016/j.scitotenv.2022.161320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Savannas contribute to ca. 30 % of the total terrestrial net primary productivity and are responsible for significant carbon storage. Savannas in South America are mostly found within the Cerrado Domain, which is very threatened and presents remarkable carbon pools. Herein, we used a unique dataset of 21 Cerrado sites spanning 144 permanent field plots in Southeastern Brazil to assess the general patterns of above and belowground carbon stocks. We identified the main environmental and tree diversity drivers of aboveground wood carbon and productivity, belowground carbon stocks (roots and soil), carbon ratios (root:shoot and above:below) and total carbon stocks in the Cerrado through a combination of climatic estimates, fire frequency data, field measurements of vegetation, roots, soil carbon, nutrients and texture, and assessment of different components of diversity (species, functional and phylogenetic). Our findings reveal average aboveground, root, and soil carbon stocks of 20.4, 14.24, and 123.13 Mg.ha-1, respectively. Average Root:Shoot and Above:Below confirm the "inverted forest" concept with values of 1.58 and 0.21, respectively. Total carbon was 145.62 Mg.ha-1, reinforcing the great amount of carbon storage in the Cerrado and its role in the carbon cycle and dynamics. Tree diversity variables (mainly species diversity and functional composition variables) had more significant effects over aboveground variables, whereas environmental variables had more significant effects over belowground variables. Ratios and total carbon mixed up these effects. The impressive values of carbon storage, especially belowground, point out the need to better manage and protect the Cerrado. Moreover, our findings might be particularly relevant for discussions on restoration programs focused on the trees-for‑carbon idea that do not consider species diversity and belowground carbon stocks.
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Affiliation(s)
- Marcela C N S Terra
- Department of Forest Science, Federal University of Lavras, Campus Universitário, Campus Box 3037, 37200-900 Lavras, Minas Gerais, Brazil.
| | - Matheus Henrique Nunes
- Department of Geosciences and Geography, University of Helsinki, Helsinki 00014, Finland
| | - Cleber R Souza
- Department of Forest Science, Federal University of Lavras, Campus Universitário, Campus Box 3037, 37200-900 Lavras, Minas Gerais, Brazil
| | - Gabriel W D Ferreira
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80525, USA
| | - Jamir A do Prado-Junior
- Institute of Biology, Federal University of Uberlandia, 38400-902 Uberlândia, Minas Gerais, Brazil
| | - Vanessa L Rezende
- Programa de Pós-Graduação em Ecologia Aplicada, Departamento de Ecologia e Conservação, Instituto de Ciências Naturais, Universidade Federal de Lavras, Lavras, MG CEP 37200-900, Brazil
| | - Rafaella Maciel
- Instituto de Ciências Biológicas, Departamento de Zoologia, Universidade de Brasilia, 70910900 Brasília, Distrito Federal, Brazil
| | - Vanessa Mantovani
- Water Resources Department, Federal University of Lavras, Campus Universitário, Campus Box 3037, 37200-900 Lavras, Minas Gerais, Brazil
| | - André Rodrigues
- Water Resources Department, Federal University of Lavras, Campus Universitário, Campus Box 3037, 37200-900 Lavras, Minas Gerais, Brazil
| | - Vinícius Augusto Morais
- Mato Grosso State University, Av. Perimetral Deputado Rogério Silva, C.P. 324, Alta Floresta, MT 78580-000, Brazil
| | - José Roberto Soares Scolforo
- Department of Forest Science, Federal University of Lavras, Campus Universitário, Campus Box 3037, 37200-900 Lavras, Minas Gerais, Brazil
| | - José Marcio de Mello
- Department of Forest Science, Federal University of Lavras, Campus Universitário, Campus Box 3037, 37200-900 Lavras, Minas Gerais, Brazil
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Crescio S, Godeas AM, Silvani V. Detección de hongos micorrícicos arbusculares en la hojarasca de distintas especies arbóreas: evaluación de tres técnicas de clarificación. BOLETÍN DE LA SOCIEDAD ARGENTINA DE BOTÁNICA 2023. [DOI: 10.31055/1851.2372.v58.n2.37810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
Introducción y objetivos: Los hongos micorrícicos arbusculares (HMA) forman asociaciones simbióticas mutualistas con las raíces de las plantas y se desarrollan en el suelo y hojarasca. Hasta el momento, se ha empleado una única técnica de clarificación en hojarasca para el estudio de los HMA, pero dada la gran variabilidad anatómica y bioquímica de las hojas, es necesario analizar otras metodologías. En este trabajo se evaluaron y ajustaron tres técnicas de clarificación en hojarasca de distintas especies arbóreas para la detección de HMA.
M&M: Se recolectó hojarasca de Quercus robur, Tipuana tipu, Ulmus minor, Fraxinus pennsylvanica, Platanus acerifolia, Laurus nobilis, Populus alba and Melia azedarach de la superficie del suelo en dos parques de la ciudad de Buenos Aires. Además, se inoculó hojarasca de F. pennsylvanica con Rhizoglomus intraradices en un cultivo bajo condiciones semicontroladas. Fueron evaluadas tres técnicas de clarificación: “5 – 5 – 5” de Arambarri (2018), Phillips & Hayman (1970) y Peterson et al. (2008), y se ajustaron modificando la duración y condiciones de exposición a los reactivos.
Resultados: La técnica de clarificación propuesta por Peterson et al. (2008) fue la más apropiada para todas las hojarascas evaluadas, dado que se obtuvo una eficaz clarificación, conservación de la estructura foliar y la visualización de esporas e hifas de HMA.
Conclusión: La selección adecuada de la técnica depende de la calidad de la hojarasca. La optimización del método de Peterson et al. (2008) permitió detectar estructuras de HMA en la hojarasca delicada de F. pennsylvanica y T. tipu.
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29
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Do the Culturable Microbial Groups Present in Cutaway Bogs Change According to Temporal Variation? Pilot Study Based on the Midlands in the Republic of Ireland. Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Cutaway peatlands in the midlands of the Republic of Ireland are rarely the focus of scientific studies. The soil quality and related microenvironment have been severely impacted by peat extraction. Returning them to a ‘near-natural state’ would require greater insights into this ecological niche. The current research took the initiative to study the microbiology of vast cutaway sites in the midlands of Ireland. Peat was collected over two seasons in January, February and April. Homogenised peat was aseptically cultured on a range of specific and non-specific culture media. Microbial enumeration, Gram staining and other microscopic observations of morphologically distinct microorganisms were performed. The total viable bacterial and fungal numbers were highest in February (1.33 × 105 CFU ml−1 and 5.93 × 106 CFU ml−1, respectively) and were lowest in April (1.14 × 103 CFU ml−1 and 5.57 × 106 CFU ml−1). Penicillium spp. and Trichoderma spp. were common in all the sites. The highest values of phosphate solubilisation index were recorded in peat collected in April (SI = 3.167 & 3.000). Overall, there is a statistically significant difference (p ≤ 0.0001) among the microbial numbers across the three months. This variation could be due to the temperature and pH differences across peat soil.
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30
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Anand S, Hallsworth JE, Timmis J, Verstraete W, Casadevall A, Ramos JL, Sood U, Kumar R, Hira P, Dogra Rawat C, Kumar A, Lal S, Lal R, Timmis K. Weaponising microbes for peace. Microb Biotechnol 2023; 16:1091-1111. [PMID: 36880421 DOI: 10.1111/1751-7915.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 03/08/2023] Open
Abstract
There is much human disadvantage and unmet need in the world, including deficits in basic resources and services considered to be human rights, such as drinking water, sanitation and hygiene, healthy nutrition, access to basic healthcare, and a clean environment. Furthermore, there are substantive asymmetries in the distribution of key resources among peoples. These deficits and asymmetries can lead to local and regional crises among peoples competing for limited resources, which, in turn, can become sources of discontent and conflict. Such conflicts have the potential to escalate into regional wars and even lead to global instability. Ergo: in addition to moral and ethical imperatives to level up, to ensure that all peoples have basic resources and services essential for healthy living and to reduce inequalities, all nations have a self-interest to pursue with determination all available avenues to promote peace through reducing sources of conflicts in the world. Microorganisms and pertinent microbial technologies have unique and exceptional abilities to provide, or contribute to the provision of, basic resources and services that are lacking in many parts of the world, and thereby address key deficits that might constitute sources of conflict. However, the deployment of such technologies to this end is seriously underexploited. Here, we highlight some of the key available and emerging technologies that demand greater consideration and exploitation in endeavours to eliminate unnecessary deprivations, enable healthy lives of all and remove preventable grounds for competition over limited resources that can escalate into conflicts in the world. We exhort central actors: microbiologists, funding agencies and philanthropic organisations, politicians worldwide and international governmental and non-governmental organisations, to engage - in full partnership - with all relevant stakeholders, to 'weaponise' microbes and microbial technologies to fight resource deficits and asymmetries, in particular among the most vulnerable populations, and thereby create humanitarian conditions more conducive to harmony and peace.
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Affiliation(s)
- Shailly Anand
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, Delhi, India
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - James Timmis
- Athena Institute for Research on Innovation and Communication in Health and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, Maryland, USA
| | | | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi, India
| | - Roshan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, New Delhi, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | - Abhilash Kumar
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | - Sukanya Lal
- PhiXgen Pvt. Ltd, Gurugram, Gurgaon, Haryana, India
| | - Rup Lal
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, India
| | - Kenneth Timmis
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
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Idowu GA, Olalemi AO, Ileke KD. COVID-19 face masks attracted Cellulomonas and Acinetobacter bacteria and provided breeding haven for red cotton bug (Dysdercus suturellus) and house cricket (Acheta domesticus). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:23510-23526. [PMID: 36327070 PMCID: PMC9631651 DOI: 10.1007/s11356-022-23865-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
This study investigated the possibility of COVID-19 medical face masks to affect bacterial and macrofaunal communities in open soil environment. An estimated 1.24 trillion of face masks have been used and discarded as a result of the COVID-19 pandemic, with a significant part of this ending up in the soil environment, where they degrade gradually over time. Because bacteria and macrofauna are sensitive indicators of changes in soil ecosystem, we investigated possible impacts of face masks on population, distribution, and diversity of these soil species. Effect on soil bacterial community was studied by both culture-based and advanced molecular (metagenomics) approach, while impact on macrofauna was investigated by examining monoliths around heap of masks for soil insects. In both cases, control soil experiments without face masks were also set up and monitored over a period of 48 weeks. The study found that the presence of face masks led to a more diverse bacterial community, although no influence on overall bacterial population was evidenced. More importantly, bacteria belonging to the genera Cellulomonas and Acinetobacter were found prominently around face masks and are believed to be involved in biodegradation of the masks. The bacterial community around the masks was dominated by Proteobacteria (29.7-38.7%), but the diversity of species increased gradually with time. Tiny black ants (Monomorium invidium) were attracted to the face masks to take advantage of water retained by the masks during the period of little rainfall. The heaps of face masks also provided shelter and breeding "haven" for soil insects, notably the red cotton bug (Dysdercus suturellus) and house cricket (Acheta domesticus), thereby impacting positively on the population of insect species in the environment. This study provides insights into the actual impacts of face masks on soil organisms under normal outdoor environmental conditions.
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Affiliation(s)
- Gideon Aina Idowu
- Department of Chemistry, School of Physical Sciences, Federal University of Technology Akure, P. M. B. 704, Akure, Ondo State, Nigeria.
| | - Adewale Oluwasogo Olalemi
- Department of Microbiology, School of Life Sciences, Federal University of Technology Akure, Ondo State, Nigeria
| | - Kayode David Ileke
- Department of Biology, School of Life Sciences, Federal University of Technology Akure, Ondo State, Nigeria
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Das TK, Kabir A, Zhao W, Stenstrom MK, Dittrich TM, Mohanty SK. A review of compaction effect on subsurface processes in soil: Implications on stormwater treatment in roadside compacted soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:160121. [PMID: 36370790 DOI: 10.1016/j.scitotenv.2022.160121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/28/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Sustainable cities require spacious infrastructures such as roadways to serve multiple functions, including transportation and water treatment. This can be achieved by installing stormwater control measures (SCM) such as biofilters and swales on the roadside compacted soil, but compacted soil limits infiltration and other functions of SCM. Understanding the effect of compaction on subsurface processes could help design SCM that could alleviate the negative impacts of compaction. Therefore, we synthesize reported data on compaction effects on subsurface processes, including infiltration rate, plant health, root microbiome, and biochemical processes. The results show that compaction could reduce runoff infiltration rate, but adding sand to roadside soil could alleviate the negative impact of compaction. Compaction could decrease the oxygen diffusion rate in the root zone, thereby affecting plant root activities, vegetation establishment, and microbial functions in SCM. The impacts of compaction on carbon mineralization rate and root biomass vary widely based on soil type, aeration status, plant species, and inherent soil compaction level. As these processes are critical in maintaining the long-term functions of SCM, the analysis would help develop strategies to alleviate the negative impacts of compaction and turn road infrastructure into a water solution in sustainable cities.
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Affiliation(s)
- Tonoy K Das
- Department of Civil and Environmental Engineering, University of California at Los Angeles, CA, USA.
| | - Alija Kabir
- Department of Civil and Environmental Engineering, University of California at Los Angeles, CA, USA
| | - Weiyang Zhao
- Department of Civil and Environmental Engineering, University of California at Los Angeles, CA, USA
| | - Michael K Stenstrom
- Department of Civil and Environmental Engineering, University of California at Los Angeles, CA, USA
| | - Timothy M Dittrich
- Department of Civil and Environmental Engineering, Wayne State University, Detroit, USA
| | - Sanjay K Mohanty
- Department of Civil and Environmental Engineering, University of California at Los Angeles, CA, USA.
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Chen HM, Shi FX, Wang XW, Zhang XH, Mao R. Conversion of drylands to paddy fields on former wetlands restores soil organic carbon by accumulating labile carbon fractions in the Sanjiang Plain, northeast China. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:599-605. [PMID: 36468612 DOI: 10.1002/jsfa.12171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/30/2022] [Accepted: 08/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Since the 1990s, drylands have been extensively converted to rice paddy fields on the former wetlands in the Sanjiang Plain of northeast China. However, the influence of this successiveland-use change from native wetlands to drylands to rice paddy fields on soil organic carbon (C) dynamics remains unexplored. Here, we compared the difference in soil organic C stock among native wetlands, drylands, and paddy fields, and then used a two-step acid hydrolysis approach to examine the effect of this land-use change on labile C I (LPI-C), labile C II (LPII-C), and recalcitrant C (RP-C) fractions at depths of 0-15 cm, 15-30 cm, and 30-50 cm. RESULTS Soil organic C stock at a depth of 0-50 cm was reduced by 79% after the conversion of wetlands to drylands but increased by 24% when drylands were converted to paddy fields. Compared with wetlands, paddy fields had 74% lower soil organic C stock at a depth of 0-50 cm. The conversion of wetlands to drylands reduced the concentrations of LPI-C, LPII-C, and RP-C fractions at each soil depth. However, land-use change from drylands to paddy fields only increased the concentrations of LPI-C and LPII-C fractions at the 0-15 cm and 30-50 cm depths. CONCLUSION The conversion of drylands to paddy lands on former wetlands enhances the soil organic C stock by promoting labile C fraction accumulation, and labile C fractions are more sensitive to this successive land-use change than recalcitrant C fractions in the Sanjiang Plain of northeast China. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Hui-Min Chen
- Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, China
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Fu-Xi Shi
- Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Xian-Wei Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xin-Hou Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- School of Environment, Nanjing Normal University, Nanjing, China
| | - Rong Mao
- Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, China
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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McClure R, Garcia M, Couvillion S, Farris Y, Hofmockel KS. Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy. Front Microbiol 2023; 13:1046661. [PMID: 36762098 PMCID: PMC9902710 DOI: 10.3389/fmicb.2022.1046661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/21/2022] [Indexed: 01/25/2023] Open
Abstract
Introduction Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here, we used a model substrate, chitin, and a synthetic Model Soil Consortium (MSC-2) to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent. Methods To characterize specific roles within this synthetic community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members. Results Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed, as well as alterations in the metabolic profile, especially when Streptomyces was lacking. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration. Discussion Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.
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Affiliation(s)
- Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marci Garcia
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sneha Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kirsten S. Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
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Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome. Microorganisms 2023; 11:microorganisms11010224. [PMID: 36677516 PMCID: PMC9867489 DOI: 10.3390/microorganisms11010224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers' point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.
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Kuang B, Xiao R, Hu Y, Wang Y, Zhang L, Wei Z, Bai J, Zhang K, Acuña JJ, Jorquera MA, Pan W. Metagenomics reveals biogeochemical processes carried out by sediment microbial communities in a shallow eutrophic freshwater lake. Front Microbiol 2023; 13:1112669. [PMID: 36713194 PMCID: PMC9874162 DOI: 10.3389/fmicb.2022.1112669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction As the largest shallow freshwater lake in the North China Plain, Baiyangdian lake is essential for maintaining ecosystem functioning in this highly populated region. Sediments are considered to record the impacts of human activities. Methods The abundance, diversity and metabolic pathways of microbial communities in sediments were studied by metagenomic approach to reveal patterns and mechanism of C, N, P and S cycling under the threat of lake eutrophication. Results Many genera, with plural genes encoding key enzymes involved in genes, belonging to Proteobacteria and Actinobacteria which were the most main phylum in bacterial community of Baiyangdian sediment were involved in C, N, S, P cycling processes, such as Nocardioides (Actinobacteria), Thiobacillus, Nitrosomonas, Rhodoplanes and Sulfuricaulis (Proteobacteria).For instance, the abundance of Nocardioides were positively correlated to TN, EC, SOC and N/P ratio in pathways of phytase, regulation of phosphate starvation, dissimilatory sulfate reduction and oxidation, assimilatory sulfate reduction, assimilatory nitrate reduction and reductive tricarboxylic acid (rTCA) cycle. Many key genes in C, N, P, S cycling were closely related to the reductive citrate cycle. A complete while weaker sulfur cycle between SO4 2- and HS- might occur in Baiyangdian lake sediments compared to C fixation and N cycling. In addition, dissimilatory nitrate reduction to ammonia was determined to co-occur with denitrification. Methanogenesis was the main pathway of methane metabolism and the reductive citrate cycle was accounted for the highest proportion of C fixation processes. The abundance of pathways of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling in sediments with higher TN content was higher than those with lower TN content. Besides, Nocardioides with plural genes encoding key enzymes involved in nasAB and nirBD gene were involved in these pathways. Discussion Nocardioides involved in the processes of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling may have important effects on nitrogen transformation.
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Affiliation(s)
- Bo Kuang
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Rong Xiao
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China,*Correspondence: Rong Xiao, ✉
| | - Yanping Hu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Yaping Wang
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Ling Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Zhuoqun Wei
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Kegang Zhang
- Department of Environmental Science and Engineering, North China Electric Power University, Baoding, China
| | - Jacquelinne J. Acuña
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco, Chile
| | - Milko A. Jorquera
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco, Chile
| | - Wenbin Pan
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
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Lu Z, Rämgård C, Ergenlioğlu İ, Sandin L, Hammar H, Andersson H, King K, Inman AR, Hao M, Bulone V, McKee LS. Multiple enzymatic approaches to hydrolysis of fungal β-glucans by the soil bacterium Chitinophaga pinensis. FEBS J 2023. [PMID: 36610032 DOI: 10.1111/febs.16720] [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: 08/29/2022] [Revised: 10/26/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
The genome of the soil Bacteroidota Chitinophaga pinensis encodes a large number of glycoside hydrolases (GHs) with noteworthy features and potentially novel functions. Several are predicted to be active on polysaccharide components of fungal and oomycete cell walls, such as chitin, β-1,3-glucan and β-1,6-glucan. While several fungal β-1,6-glucanase enzymes are known, relatively few bacterial examples have been characterised to date. We have previously demonstrated that C. pinensis shows strong growth using β-1,6-glucan as the sole carbon source, with the efficient release of oligosaccharides from the polymer. We here characterise the capacity of the C. pinensis secretome to hydrolyse the β-1,6-glucan pustulan and describe three distinct enzymes encoded by its genome, all of which show different levels of β-1,6-glucanase activity and which are classified into different GH families. Our data show that C. pinensis has multiple tools to deconstruct pustulan, allowing the species' broad utility of this substrate, with potential implications for bacterial biocontrol of pathogens via cell wall disruption. Oligosaccharides derived from fungal β-1,6-glucans are valuable in biomedical research and drug synthesis, and these enzymes could be useful tools for releasing such molecules from microbial biomass, an underexploited source of complex carbohydrates.
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Affiliation(s)
- Zijia Lu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Carl Rämgård
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - İrem Ergenlioğlu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Lova Sandin
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Hugo Hammar
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Helena Andersson
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Katharine King
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Mengshu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,Wallenberg Wood Science Centre, Stockholm, Sweden
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Olabi AG, Shehata N, Sayed ET, Rodriguez C, Anyanwu RC, Russell C, Abdelkareem MA. Role of microalgae in achieving sustainable development goals and circular economy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158689. [PMID: 36108848 DOI: 10.1016/j.scitotenv.2022.158689] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
In 2015, the United Nations General Assembly (UNGA) set out 17 Sustainable Development Goals (SDGs) to be achieved by 2030. These goals highlight key objectives that must be addressed. Each target focuses on a unique perspective crucial to meeting these goals. Social, political, and economic issues are addressed to comprehensively review the main issues combating climate change and creating sustainable and environmentally friendly industries, jobs, and communities. Several mechanisms that involve judicious use of biological entities are among instruments that are being explored to achieve the targets of SDGs. Microalgae have an increasing interest in various sectors, including; renewable energy, food, environmental management, water purification, and the production of chemicals such as biofertilizers, cosmetics, and healthcare products. The significance of microalgae also arises from their tendency to consume CO2, which is the main greenhouse gas and the major contributor to the climate change. This work discusses the roles of microalgae in achieving the various SDGs. Moreover, this work elaborates on the contribution of microalgae to the circular economy. It was found that the microalgae contribute to all the 17th SDGs, where they directly contribute to 9th of the SDGs and indirectly contribute to the rest. The major contribution of the Microalgae is clear in SDG-6 "Clean water and sanitation", SDG-7 "Affordable and clean energy", and SDG-13 "Climate action". Furthermore, it was found that Microalgae have a significant contribution to the circular economy.
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Affiliation(s)
- A G Olabi
- Dept. of Sustainable and Renewable Energy Engineering, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates; Mechanical Engineering and Design, Aston University, School of Engineering and Applied Science, Aston Triangle, Birmingham B4 7ET, UK.
| | - Nabila Shehata
- Environmental Science and Industrial Development Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt.
| | - Enas Taha Sayed
- Center for Advanced Materials Research, University of Sharjah, PO Box 27272, Sharjah, United Arab Emirates; Faculty of Engineering, Minia University, Elminia, Egypt.
| | - Cristina Rodriguez
- School of Computing, Engineering, and Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK
| | - Ruth Chinyere Anyanwu
- School of Computing, Engineering, and Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK
| | - Callum Russell
- School of Computing, Engineering, and Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK
| | - Mohammad Ali Abdelkareem
- Dept. of Sustainable and Renewable Energy Engineering, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates; Faculty of Engineering, Minia University, Elminia, Egypt.
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Song H, Liu Z, Cui H, Chen J, Chen S, Gao H, Yang X, Wang Y, Wang J, Liu K, Xiao S, An L, Nielsen UN. Contrasting influences of two dominant plants, Dasiphora fruticosa and Ligularia virguarea, on aboveground and belowground communities in an alpine meadow. Front Microbiol 2023; 14:1118789. [PMID: 37125161 PMCID: PMC10140320 DOI: 10.3389/fmicb.2023.1118789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Soil organisms are abundant, phylogenetically and functionally diverse, and interact to catalyse and regulate critical soil processes. Understanding what structures belowground communities is therefore fundamental to gaining insight into ecosystem functioning. Dominant plants have been shown to influence belowground communities both directly and indirectly through changes in abiotic and biotic factors. In a field study, we used piecewise structural equation modelling to disentangle and compare the effects of a dominant allelopathic plant, Ligularia virgaurea, and a dominant facilitative plant, Dasiphora fruticosa, on understory plant, soil microbial and nematode community composition in an alpine meadow on the Tibetan plateau. Dasiphora fruticosa was associated with changes in edaphic variables (total nitrogen, soil organic carbon, pH and ammonium), understory plant and soil bacterial communities, whereas Ligularia virguarea was associated with increased soil ammonium content and soil fungal richness relative to dominant plant-free control plots. Moreover, nematode richness was significantly greater under D. fruticosa, with no change in nematode community composition. By contrast, nematode richness under Ligularia virgaurea was similar to that of dominant plant-free control plots, but nematode community composition differed from the control. The effects of both plants were predominantly direct rather than mediated by indirect pathways despite the observed effects on understory plant communities, soil properties and microbial assemblages. Our results highlight the importance of plants in determining soil communities and provide new insight to disentangle the complex above- and belowground linkages.
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Affiliation(s)
- Hongxian Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Ziyang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Hanwen Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Jingwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Shuyan Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Shuyan Chen,
| | - Haining Gao
- College of Life Sciences and Engineering, Hexi University, Zhangye, Gansu, China
| | - Xiaoli Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Yajun Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Jiajia Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Kun Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Sa Xiao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Uffe N. Nielsen
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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Ahn YJ, Lee JA, Choi KR, Bang J, Lee SY. Can microbes be harnessed to reduce atmospheric loads of greenhouse gases? Environ Microbiol 2023; 25:17-25. [PMID: 36655716 DOI: 10.1111/1462-2920.16161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 01/21/2023]
Abstract
Reducing atmospheric loads of greenhouse gases (GHGs), especially CO2 and CH4 , has been considered the key to alleviating global crises we are facing, such as climate change, sea level elevation and ocean acidification. To this end, development of strategies and technologies for carbon capture, sequestration and utilization (CCSU) is urgently needed. Although physicochemical methods have been the most actively studied in the early stages of developing CCSU technologies, there have recently been growing interests in developing microbe-based CCSU processes. In this article, we discuss advantages of microbe-based CCSU technologies over physicochemical approaches and even plant-based approaches. Next, various parts of the global carbon cycle where microorganisms can contribute, such as sequestering atmospheric GHGs, facilitating the carbon cycle, and slowing down the depletion of carbon reservoirs are described, emphasizing the impacts of microbes on the carbon cycle. Strategies to upgrade microbes and increase their performance in assimilating GHGs or converting GHGs to value-added chemicals are also provided. Moreover, several examples of exploiting microbes to address environmental crises are discussed. Finally, we discuss things to overcome in microbe-based CCSU technologies and provide future perspectives.
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Affiliation(s)
- Yeah-Ji Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jong An Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Junho Bang
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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41
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Rani N, Kaur G, Kaur S, Mutreja V, Upadhyay SK, Tripathi M. Comparison of diversity and zinc solubilizing efficiency of rhizobacteria obtained from solanaceous crops under polyhouse and open field conditions. Biotechnol Genet Eng Rev 2022:1-22. [PMID: 36544391 DOI: 10.1080/02648725.2022.2157949] [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: 10/07/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]
Abstract
Zinc-solubilizing bacteria (Zn-SB) play a crucial role in regulating soil fertility and plant health by maintaining Zn availability in the rhizosphere. It is uncertain how the Zn-SB population fluctuates across various cultivation systems since varied land-use patterns for agricultural aims may affect microbial activity and plant development effectiveness. The current study aims to examine the Zn-SB potential of various farming systems using Solanum lycopersicum, Solanum melongena, and Capsicum annuum grown in polyhouse soil (PS) and open fields (OF). Only twenty rhizobacterial isolates from PS and two isolates from OF out of 80 showed a strong ability to solubilize Zn, which was evaluated using Atomic Absorption Spectroscopy. Bacterial strain-PS4 solubilized 253.06 ppm of ZnO and produced a high quantity of lactic acid (168.62 g/ml) and acetic acid (470.5 g/ml), whereas bacterial strain OF1 solubilized 16.02 ppm of ZnO by releasing glycolic acid (42.89 g/ml), lactic acid (22.30 g/ml), formic acid (106.03 g/ml), and acetic acid (48.5 µg/ml). Further, in vitro studies demonstrated higher production of auxin, gibberellic acid and siderophore by PS1 as compared to OF1 strain. A large diversity of Zn-SB in the soil was indicated by biochemical analysis, which revealed that isolates belonged to the families Enterobacteriaceae, Bacillaceae, Burkholderiaceae, Streptococcaceae, Paenibacillaceae, Micrococcaceae, Morganellaceae, and Dietziaceae. The isolates PS4 and OF1 were identified as Bacillus cereus and Enterobacter hormaechei, respectively, using 16S rRNA sequencing. The findings show that soil from polyhouses has a greater diversity of Zn-solubilization rhizobacteria than soil from open areas. The findings suggested a potential land-use method for enhancing crop yields by employing microorganisms and polyhouse technology, which could be useful in the future study.
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Affiliation(s)
- Nitu Rani
- Department of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Gurparteek Kaur
- Department of Agricultural Sciences, Chandigarh University, Mohali, Punjab, India
| | - Sukhminderjit Kaur
- Department of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Vishal Mutreja
- Department of Chemistry, University Institute of Science, Chandigarh University, Mohali, Punjab, India
| | - Sudhir K Upadhyay
- Department of Environmental Science, Veer Bahadur Singh Purvanchal University, Jaunpur, Uttar Pradesh, India
| | - Manikant Tripathi
- Biotechnology Program, Dr. Rammanohar Lohia Avadh University, Ayodhya, Uttar Pradesh, India
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Fang Z, Zhou S, Zhang S, Xing W, Feng X, Yang Q, Zhao F, Liu K, Wang J. Spatial distribution and influencing factors of urban soil organic carbon stocks in Xi'an City, China. Urban Ecosyst 2022. [DOI: 10.1007/s11252-022-01316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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43
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Gill SP, Learman DR, Annis ML, Woolnough DA. Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure. J Appl Microbiol 2022; 133:3645-3658. [PMID: 36056619 PMCID: PMC9825887 DOI: 10.1111/jam.15801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 01/11/2023]
Abstract
AIMS We examined the effects of a mixture of contaminants found in agricultural watersheds on the gut microbiota and physiology of both the freshwater mussel Lampsilis cardium, and L. cardium host fish Micropterus salmoides. METHODS AND RESULTS Lampsilis cardium and M. salmoides were exposed to three concentrations of agricultural contaminants for 60 days (observing behaviour daily) before being sampled for gut microbiota analyses. DNA was extracted from the gut samples, amplified via PCR, and sequenced using the Illumina Mi-Seq platform. Only L. cardium guts had differing microbiota across treatments, with an increase in potentially pathogenic Aeromonas. We also provide novel evidence of a core microbiota within L. cardium and M. salmoides. In terms of physiology, female L. cardium exhibited a decrease in movement and marsupial gill display in contaminant exposures. CONCLUSIONS Exposure to contaminants from agricultural watersheds may affect population recruitment within freshwater mussel communities over time. Specifically, increased pathogenic micro-organisms and altered behaviour can reduce the likelihood of glochidia dispersal. SIGNIFICANCE AND IMPACT OF THE STUDY This study supports emerging research that contaminants found in agricultural watersheds may be a factor in freshwater mussel population declines. It also provides novel evidence that unionids have a core gut microbiota.
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Affiliation(s)
- Stephanie P. Gill
- Biology Department and Institute for Great Lakes ResearchCentral Michigan UniversityMount PleasantMichiganUSA
| | - Deric R. Learman
- Biology Department and Institute for Great Lakes ResearchCentral Michigan UniversityMount PleasantMichiganUSA
| | - Mandy L. Annis
- US Fish & Wildlife Service, Michigan Ecological Services Field OfficeEast LansingMichiganUSA
| | - Daelyn A. Woolnough
- Biology Department and Institute for Great Lakes ResearchCentral Michigan UniversityMount PleasantMichiganUSA
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Feng H, Gonzalez Viejo C, Vaghefi N, Taylor PWJ, Tongson E, Fuentes S. Early Detection of Fusarium oxysporum Infection in Processing Tomatoes ( Solanum lycopersicum) and Pathogen-Soil Interactions Using a Low-Cost Portable Electronic Nose and Machine Learning Modeling. SENSORS (BASEL, SWITZERLAND) 2022; 22:8645. [PMID: 36433241 PMCID: PMC9693623 DOI: 10.3390/s22228645] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
The early detection of pathogen infections in plants has become an important aspect of integrated disease management. Although previous research demonstrated the idea of applying digital technologies to monitor and predict plant health status, there is no effective system for detecting pathogen infection before symptomatology appears. This paper presents the use of a low-cost and portable electronic nose coupled with machine learning (ML) models for early disease detection. Several artificial neural network models were developed to predict plant physiological data and classify processing tomato plants and soil samples according to different levels of pathogen inoculum by using e-nose outputs as inputs, plant physiological data, and the level of infection as targets. Results showed that the pattern recognition models based on different infection levels had an overall accuracy of 94.4-96.8% for tomato plants and between 94.81% and 96.22% for soil samples. For the prediction of plant physiological parameters (photosynthesis, stomatal conductance, and transpiration) using regression models or tomato plants, the overall correlation coefficient was 0.97-0.99, with very significant slope values in the range 0.97-1. The performance of all models shows no signs of under or overfitting. It is hence proven accurate and valid to use the electronic nose coupled with ML modeling for effective early disease detection of processing tomatoes and could also be further implemented to monitor other abiotic and biotic stressors.
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Affiliation(s)
- Hanyue Feng
- Digital Agriculture Food and Wine Group, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Claudia Gonzalez Viejo
- Digital Agriculture Food and Wine Group, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul W. J. Taylor
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Eden Tongson
- Digital Agriculture Food and Wine Group, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Sigfredo Fuentes
- Digital Agriculture Food and Wine Group, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
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45
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Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands. Proc Natl Acad Sci U S A 2022; 119:e2209132119. [PMID: 36322723 PMCID: PMC9659419 DOI: 10.1073/pnas.2209132119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Viruses shape microbial communities, food web dynamics, and carbon and nutrient cycling in diverse ecosystems. However, little is known about the patterns and drivers of viral community composition, particularly in soil, precluding a predictive understanding of viral impacts on terrestrial habitats. To investigate soil viral community assembly processes, here we analyzed 43 soil viromes from a rainfall manipulation experiment in a Mediterranean grassland in California. We identified 5,315 viral populations (viral operational taxonomic units [vOTUs] with a representative sequence ≥10 kbp) and found that viral community composition exhibited a highly significant distance-decay relationship within the 200-m<sup>2</sup> field site. This pattern was recapitulated by the intrapopulation microheterogeneity trends of prevalent vOTUs (detected in ≥90% of the viromes), which tended to exhibit negative correlations between spatial distance and the genomic similarity of their predominant allelic variants. Although significant spatial structuring was also observed in the bacterial and archaeal communities, the signal was dampened relative to the viromes, suggesting differences in local assembly drivers for viruses and prokaryotes and/or differences in the temporal scales captured by viromes and total DNA. Despite the overwhelming spatial signal, evidence for environmental filtering was revealed in a protein-sharing network analysis, wherein a group of related vOTUs predicted to infect actinobacteria was shown to be significantly enriched in low-moisture samples distributed throughout the field. Overall, our results indicate a highly diverse, dynamic, active, and spatially structured soil virosphere capable of rapid responses to changing environmental conditions.
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Ngashangva N, Mukherjee PK, Sharma C, Kalita MC, Sarangthem I. Integrated genomics and proteomics analysis of Paenibacillus peoriae IBSD35 and insights into its antimicrobial characteristics. Sci Rep 2022; 12:18861. [PMID: 36344671 PMCID: PMC9640621 DOI: 10.1038/s41598-022-23613-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: 07/04/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance has been developing fast and incurring a loss of human life, and there is a need for new antimicrobial agents. Naturally occurring antimicrobial peptides offer the characteristics to counter AMR because the resistance development is low or no resistance. Antimicrobial peptides from Paenibacillus peoriae IBSD35 cell-free supernatant were salted out and purified using chromatography and characterized with liquid chromatography-tandem-mass spectrometry. The extract has shown a high and broad spectrum of antimicrobial activity. Combining the strain IBSD35 genome sequence with its proteomic data enabled the prediction of biosynthetic gene clusters by connecting the peptide from LC-MS/MS data to the gene that encode. Antimicrobial peptide databases offered a platform for the effective search, prediction, and design of AMPs and expanded the studies on their isolation, structure elucidation, biological evaluation, and pathway engineering. The genome-based taxonomy and comparisons have shown that P. peoriae IBSD35 is closely related to Paenibacillus peoriae FSL J3-0120. P. peoriae IBSD35 harbored endophytic trait genes and nonribosomal peptide synthases biosynthetic gene clusters. The comparative genomics revealed evolutionary insights and facilitated the discovery of novel SMs using proteomics from the extract of P. peoriae IBSD35. It will increase the potential to find novel bio-molecules to counter AMR.
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Affiliation(s)
- Ng Ngashangva
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Pulok K. Mukherjee
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Chandradev Sharma
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Mohan C. Kalita
- grid.411779.d0000 0001 2109 4622Department of Biotechnology, Gauhati University, Jalukbari, Guwahati, Assam 781014 India
| | - Indira Sarangthem
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
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Zhao F, He L, Bond-Lamberty B, Janssens IA, Wang J, Pang G, Wu Y, Xu X. Latitudinal shifts of soil microbial biomass seasonality. PNAS NEXUS 2022; 1:pgac254. [PMID: 36712352 PMCID: PMC9802431 DOI: 10.1093/pnasnexus/pgac254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/26/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Soil microbes ultimately drive the mineralization of soil organic carbon and thus ecosystem functions. We compiled a dataset of the seasonality of microbial biomass carbon (MBC) and developed a semi-mechanistic model to map monthly MBC across the globe. MBC exhibits an equatorially symmetric seasonality between the Northern and Southern Hemispheres. In the Northern Hemisphere, MBC peaks in autumn and is minimal in spring at low latitudes (<25°N), peaks in the spring and is minimal in autumn at mid-latitudes (25°N to 50°N), while peaks in autumn and is minimal in spring at high latitudes (>50°N). This latitudinal shift of MBC seasonality is attributed to an interaction of soil temperature, soil moisture, and substrate availability. The MBC seasonality is inconsistent with patterns of heterotrophic respiration, indicating that MBC as a proxy for microbial activity is inappropriate at this resolution. This study highlights the need to explicitly represent microbial physiology in microbial models. The interactive controls of environments and substrate on microbial seasonality provide insights for better representing microbial mechanisms in simulating ecosystem functions at the seasonal scale.
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Affiliation(s)
| | - Liyuan He
- To whom correspondence should be addressed:
| | - Ben Bond-Lamberty
- Pacific Northwest National Laboratory, Joint Global Change Research Institute at the University of Maryland–College Park, College Park, MD 20740, USA
| | - Ivan A Janssens
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Jieying Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an 710127, China
| | - Guowei Pang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an 710127, China
| | - Yuwei Wu
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an 710127, China
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Sim JXF, Drigo B, Doolette CL, Vasileiadis S, Karpouzas DG, Lombi E. Impact of twenty pesticides on soil carbon microbial functions and community composition. CHEMOSPHERE 2022; 307:135820. [PMID: 35944675 DOI: 10.1016/j.chemosphere.2022.135820] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 05/20/2023]
Abstract
Pesticides are known to affect non-targeted soil microorganisms. Still, studies comparing the effect of multiple pesticides on a wide range of microbial endpoints associated with carbon cycling are scarce. Here, we employed fluorescence enzymatic assay and real-time PCR to evaluate the effect of 20 commercial pesticides, applied at their recommended dose and five times their recommended dose, on soil carbon cycling related enzymatic activities (α-1,4-glucosidase, β-1,4-glucosidase, β-d-cellobiohydrolase and β-xylosidase), and on the absolute abundance of functional genes (cbhl and chiA), in three different South Australian agricultural soils. The effects on cellulolytic and chitinolytic microorganisms, and the total microbial community composition were determined using shotgun metagenomic sequencing in selected pesticide-treated and untreated samples. The application of insecticides significantly increased the cbhl and chiA genes absolute abundance in the acidic soil. At the community level, insecticide fipronil had the greatest stimulating effect on cellulolytic and chitinolytic microorganisms, followed by fungicide metalaxyl-M and insecticide imidacloprid. A shift towards a fungal dominated microbial community was observed in metalaxyl-M treated soil. Overall, our results suggest that the application of pesticides might affect the soil carbon cycle and may disrupt the formation of soil organic matter and structure stabilisation.
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Affiliation(s)
- Jowenna X F Sim
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia.
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Casey L Doolette
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis, 41500, Greece
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis, 41500, Greece
| | - Enzo Lombi
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia; University of South Australia, UniSA STEM, Mawson Lakes, South Australia, 5095, Australia
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49
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Yang D, Kato H, Kawatsu K, Osada Y, Azuma T, Nagata Y, Kondoh M. Reconstruction of a Soil Microbial Network Induced by Stress Temperature. Microbiol Spectr 2022; 10:e0274822. [PMID: 35972265 PMCID: PMC9602341 DOI: 10.1128/spectrum.02748-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 01/04/2023] Open
Abstract
The microbial community is viewed as a network of diverse microorganisms connected by various interspecific interactions. While the stress gradient hypothesis (SGH) predicts that positive interactions are favored in more stressful environments, the prediction has been less explored in complex microbial communities due to the challenges of identifying interactions. Here, by applying a nonlinear time series analysis to the amplicon-based diversity time series data of the soil microbiota cultured under less stressful (30°C) or more stressful (37°C) temperature conditions, we show how the microbial network responds to temperature stress. While the genera that persisted only under the less stressful condition showed fewer positive effects, the genera that appeared only under the more stressful condition received more positive effects, in agreement with SGH. However, temperature difference also induced reconstruction of the community network, leading to an increased proportion of negative interactions at the whole-community level. The anti-SGH pattern can be explained by the stronger competition caused by increased metabolic rate and population densities. IMPORTANCE By combining amplicon-based diversity survey with recently developed nonlinear analytical tools, we successfully determined the interaction networks of more than 150 natural soil microbial genera under less or more temperature stress and explored the applicability of the stress gradient hypothesis to soil microbiota, shedding new light on the well-known hypothesis.
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Affiliation(s)
- Dailin Yang
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Kazutaka Kawatsu
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yutaka Osada
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | - Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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50
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Chen J, Xing Y, Wang Y, Zhang W, Guo Z, Su W. Application of iron and steel slags in mitigating greenhouse gas emissions: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157041. [PMID: 35803422 DOI: 10.1016/j.scitotenv.2022.157041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
The comprehensive consideration of climate warming and by-product management in the iron and steel industry, has a significant impact on the realization of environmental protection and green production. Blast furnace slag (BFS) and steel slag (SS), collectively called iron and steel slags, are the main by-products of steelmaking. The economical and efficient use of iron and steel slags to reduce greenhouse gas (GHG) emissions is an urgent problem to be solved. This paper reviewed the carbonization and waste heat recovery of iron and steel slags, and the utilization of iron and steel slags as soil amendments, discussed their application status and limitations in GHG reduction. Iron and steel slags are rich in CaO, which can be used as CO2 adsorbents to achieve a maximum concentration of 0.4-0.5 kg CO2/kg SS. Blast furnace molten slag contains a considerable amount of waste heat, and thermal methods can recover more than 60 % of the heat energy. Chemical methods can use waste heat in the reaction to generate gas fuel, and iron in slags can be used as a catalytic component to promote chemical reaction. Waste heat recovery saves fuel and reduces the CO2 emissions caused by combustion. When iron and steel slags are used as soil amendments, the iron oxides, alkaline substances, and SiO2 in iron and steel slags can affect the emission of CH4, N2O, and CO2 from soil, microorganisms, and crops, and achieve a maximum reduction of more than 60 % of the overall GHG of paddy fields. Finally, This paper provided valuable suggestions for future GHG reduction studies of iron and steel slags in energy, industry, and agriculture.
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Affiliation(s)
- Jing Chen
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Yan Wang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Wenbo Zhang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Zefeng Guo
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Wei Su
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, PR China; Guangdong Province Engineering Laboratory for Air Pollution Control, Guangzhou, 510530, PR China.
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